; 2012_03_11.082549
peak-motifs  -v 1 -title _Kr_D.mel_1-3h_Markov_m=k-2_ -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifspeak_seq.masked -max_seq_len 2000 -min_markov -2 -max_markov -2 -disco oligos,positions -nmotifs 3 -minol 6 -maxol 7 -2str -motif_db jaspar_core_insects tf $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -motif_db FlyFactorSurvey tf $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -motif_db DMMPMM_drosophila tf $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -motif_db IDMMPMM_drosophila tf $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -ref_motifs $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifs_ref_motifs.tf -source galaxy -task purge,seqlen,composition,disco,merge_words,collect_motifs,motifs_vs_motifs,timelog,archive,synthesis,motifs_vs_db,ref_motifs,motifs_vs_ref,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424



; 2012_03_11.082549
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/images_html


; 2012_03_11.082549
$RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifspeak_seq.masked -from fasta -to fasta -mask non-dna| $RSAT/perl-scripts/sub-sequence -origin center -from -1000 -to 999 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta


; 2012_03_11.082550
$RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -ml 30 -mis 0 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta


; 2012_03_11.082556
$RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqlen_distrib.tab


; 2012_03_11.082556
$RSAT/perl-scripts/XYgraph -lines -pointsize 0 -legend -format png -title 'Sequence lengths; _Kr_D.mel_1-3h_Markov_m=k-2_' -ysize 200 -ycol 4 -yleg1 'Number of peaks' -xsize 800 -xcol 3 -xleg1 'Peak length' -xmin 0 -ymin 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqlen_distrib.tab -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqlen_distrib.png


; 2012_03_11.082556
$RSAT/perl-scripts/convert-features -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifspeak_seq.masked -from galaxy_seq -to bed  | sed '1s/^.*/track name="test_peaks" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_ test: peaks" visibility=2 use_score=1 color=13,115,67/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed


; 2012_03_11.082558
time ($RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta -l 1 -1str > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab_time.txt


; 2012_03_11.082558
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1  -out_format png -col_width 50 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png


; 2012_03_11.082558
time ($RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta -l 2 -1str > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab_time.txt


; 2012_03_11.082559
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1  -out_format png -col_width 50 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png


; 2012_03_11.082559
time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta -format fasta -sort  -return chi,sig,distrib,graphs,rank -max_graphs 20 -1str -ovlp -seqtype dna -l 1 -ci 20 -img_format png -title '_Kr_D.mel_1-3h_Markov_m=k-2_' -origin center  -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab_time.txt


; 2012_03_11.082734
grep -v ";" $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-5 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/1nt-1str_colors.tab -title 'Nucleotide composition profiles : ; test sequence; _Kr_D.mel_1-3h_Markov_m=k-2_' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300  -ymin 0 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png


; 2012_03_11.082734
time ($RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta -format fasta -sort  -return chi,sig,distrib,graphs,rank -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title '_Kr_D.mel_1-3h_Markov_m=k-2_' -origin center  -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab_time.txt


; 2012_03_11.082930
grep -v ";" $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-17 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/2nt-1str_colors.tab -title 'Dinucleotide composition profiles : ; test sequence; _Kr_D.mel_1-3h_Markov_m=k-2_' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300  -ymin 0 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png


; 2012_03_11.082930
rsync -ruptL  $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifs_ref_motifs.tf $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.transfac >& /dev/null


; 2012_03_11.082930
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifs_ref_motifs.tf -from transfac -to transfac -decimals 1  -bg_format motifsampler -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -return counts,consensus,parameters -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf


; 2012_03_11.082930
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifs_ref_motifs.tf -from transfac -to tab -return counts,logo  -bg_format motifsampler -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -logo_file $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs_logo -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs_tab.tab


; 2012_03_11.082931
time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 50 -return occ,proba,rank -2str -noov -seqtype dna -l 6 -markov 4 -pseudo 0.01 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab_time.txt


; 2012_03_11.082938
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -pl $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 50 -max_asmb_nb 3 -subst 1 -prefix oligos_6nt_mkv4 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_time.txt


; 2012_03_11.083002
time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 50 -return occ,proba,rank -2str -noov -seqtype dna -l 7 -markov 5 -pseudo 0.01 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab_time.txt


; 2012_03_11.083012
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -pl $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 50 -max_asmb_nb 3 -subst 1 -prefix oligos_7nt_mkv5 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5_pssm) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5_pssm_time.txt


; 2012_03_11.083039
time ($RSAT/perl-scripts/position-analysis -v 2 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta -format fasta -sort  -return chi,sig,distrib,graphs,rank -max_graphs 50 -2str -noov -seqtype dna -l 6 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 50 -img_format png -title '_Kr_D.mel_1-3h_Markov_m=k-2_' -origin center  -max_graphs 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab_time.txt


; 2012_03_11.083335
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -pl $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 50 -max_asmb_nb 3 -subst 1 -prefix positions_6nt -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_time.txt


; 2012_03_11.083407
time ($RSAT/perl-scripts/position-analysis -v 2 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta -format fasta -sort  -return chi,sig,distrib,graphs,rank -max_graphs 50 -2str -noov -seqtype dna -l 7 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 50 -img_format png -title '_Kr_D.mel_1-3h_Markov_m=k-2_' -origin center  -max_graphs 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab_time.txt


; 2012_03_11.083733
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -seq $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -pl $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 50 -max_asmb_nb 3 -subst 1 -prefix positions_7nt -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_time.txt


; 2012_03_11.083808
time ($RSAT/perl-scripts/compare-scores -v 1  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab -sc1 8 -suppress $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/ -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab -sc2 9 -suppress $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_6nt/ -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5.tab -sc3 8 -suppress $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_7nt_mkv5/ -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -sc4 9 -suppress $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/ -ic 1 -lc -null . -suppress peak-motifs_ -suppress '.tab' | $RSAT/perl-scripts/row-stats -after 1 -sort  -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/merged_words/peak-motifs_merged_words.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/merged_words/peak-motifs_merged_words.tab_time.txt


; 2012_03_11.083808
$RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/merged_words/peak-motifs_merged_words.tab -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/merged_words/peak-motifs_merged_words.html


; 2012_03_11.083808
$RSAT/perl-scripts/draw-heatmap -min 0 -max 10  -out_format png -col_width 40 -rownames -gradient fire -row_height 16 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/merged_words/peak-motifs_merged_words.tab -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/merged_words/peak-motifs_merged_words_heatmap.png


; 2012_03_11.083808
rm -f $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_count_matrices.tf >> $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_7nt_mkv5/peak-motifs_oligos-2str-noov_7nt_mkv5_pssm_count_matrices.tf >> $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf


; 2012_03_11.083808
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tab


; 2012_03_11.083808
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tab


; 2012_03_11.083808
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tab


; 2012_03_11.083809
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tab


; 2012_03_11.083809
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tab


; 2012_03_11.083809
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tab


; 2012_03_11.083809
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tab


; 2012_03_11.083809
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tab


; 2012_03_11.083809
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tab


; 2012_03_11.083810
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tab


; 2012_03_11.083810
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tab


; 2012_03_11.083810
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tab


; 2012_03_11.083810
$RSAT/perl-scripts/compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab; $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_disco_compa.html


; 2012_03_11.083812
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml


; 2012_03_11.083812
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_ref


; 2012_03_11.083812
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_ref


; 2012_03_11.083813
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_ref


; 2012_03_11.083813
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_ref


; 2012_03_11.083814
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_ref


; 2012_03_11.083814
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_ref


; 2012_03_11.083815
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_ref


; 2012_03_11.083815
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_ref


; 2012_03_11.083816
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_ref


; 2012_03_11.083816
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_ref


; 2012_03_11.083817
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_ref


; 2012_03_11.083817
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_ref


; 2012_03_11.083818
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -format2 transfac -file2 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_ref/peak-motifs_motifs_vs_ref


; 2012_03_11.083819
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_ref/peak-motifs_motifs_vs_ref.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_ref/peak-motifs_motifs_vs_ref.gml


; 2012_03_11.083820
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_jaspar_core_insects


; 2012_03_11.083821
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_db_jaspar_core_insects


; 2012_03_11.083823
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_jaspar_core_insects


; 2012_03_11.083824
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_jaspar_core_insects


; 2012_03_11.083826
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_jaspar_core_insects


; 2012_03_11.083827
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_jaspar_core_insects


; 2012_03_11.083828
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_jaspar_core_insects


; 2012_03_11.083830
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_jaspar_core_insects


; 2012_03_11.083832
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_jaspar_core_insects


; 2012_03_11.083833
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_insects


; 2012_03_11.083835
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_jaspar_core_insects


; 2012_03_11.083836
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_insects


; 2012_03_11.083838
time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_insects.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_insects.tab_time.txt


; 2012_03_11.083850
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_insects.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_insects.gml


; 2012_03_11.083851
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_FlyFactorSurvey


; 2012_03_11.083856
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_db_FlyFactorSurvey


; 2012_03_11.083900
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_FlyFactorSurvey


; 2012_03_11.083904
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_FlyFactorSurvey


; 2012_03_11.083909
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_FlyFactorSurvey


; 2012_03_11.083915
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_FlyFactorSurvey


; 2012_03_11.083920
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_FlyFactorSurvey


; 2012_03_11.083925
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_FlyFactorSurvey


; 2012_03_11.083930
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_FlyFactorSurvey


; 2012_03_11.083936
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_FlyFactorSurvey


; 2012_03_11.083941
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_FlyFactorSurvey


; 2012_03_11.083947
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_FlyFactorSurvey


; 2012_03_11.083951
time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey.tab_time.txt


; 2012_03_11.084039
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey.gml


; 2012_03_11.084043
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_DMMPMM_drosophila


; 2012_03_11.084044
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_db_DMMPMM_drosophila


; 2012_03_11.084044
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_DMMPMM_drosophila


; 2012_03_11.084045
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_DMMPMM_drosophila


; 2012_03_11.084046
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_DMMPMM_drosophila


; 2012_03_11.084047
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_DMMPMM_drosophila


; 2012_03_11.084048
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_DMMPMM_drosophila


; 2012_03_11.084049
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_DMMPMM_drosophila


; 2012_03_11.084049
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_DMMPMM_drosophila


; 2012_03_11.084050
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_DMMPMM_drosophila


; 2012_03_11.084051
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_DMMPMM_drosophila


; 2012_03_11.084052
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_DMMPMM_drosophila


; 2012_03_11.084053
time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab_time.txt


; 2012_03_11.084058
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.gml


; 2012_03_11.084058
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_IDMMPMM_drosophila


; 2012_03_11.084059
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_db_IDMMPMM_drosophila


; 2012_03_11.084100
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_IDMMPMM_drosophila


; 2012_03_11.084100
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_IDMMPMM_drosophila


; 2012_03_11.084101
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_IDMMPMM_drosophila


; 2012_03_11.084102
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_IDMMPMM_drosophila


; 2012_03_11.084103
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_IDMMPMM_drosophila


; 2012_03_11.084104
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_IDMMPMM_drosophila


; 2012_03_11.084105
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_IDMMPMM_drosophila


; 2012_03_11.084105
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_IDMMPMM_drosophila


; 2012_03_11.084106
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_IDMMPMM_drosophila


; 2012_03_11.084108
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_IDMMPMM_drosophila


; 2012_03_11.084108
time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_IDMMPMM_drosophila.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_IDMMPMM_drosophila.tab_time.txt


; 2012_03_11.084113
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_IDMMPMM_drosophila.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_IDMMPMM_drosophila.gml


; 2012_03_11.084114
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab_time.txt


; 2012_03_11.084120
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="oligos_6nt_mkv4_m1" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: oligos_6nt_mkv4_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_genomic.bed


; 2012_03_11.084121
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.tab


; 2012_03_11.084121
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv4_m1' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.png


; 2012_03_11.084121
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.tab


; 2012_03_11.084121
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv4_m1' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.png


; 2012_03_11.084121
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084130
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv2_enrichment.png


; 2012_03_11.084130
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab_time.txt


; 2012_03_11.084136
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="oligos_6nt_mkv4_m2" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: oligos_6nt_mkv4_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_genomic.bed


; 2012_03_11.084137
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.tab


; 2012_03_11.084138
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv4_m2' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.png


; 2012_03_11.084138
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.tab


; 2012_03_11.084138
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv4_m2' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.png


; 2012_03_11.084138
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084146
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_scan_mkv2_enrichment.png


; 2012_03_11.084146
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab_time.txt


; 2012_03_11.084153
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="oligos_6nt_mkv4_m3" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: oligos_6nt_mkv4_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_genomic.bed


; 2012_03_11.084154
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_site_distrib.tab


; 2012_03_11.084154
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv4_m3' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_site_distrib.png


; 2012_03_11.084155
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_per_peak.tab


; 2012_03_11.084155
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv4_m3' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_per_peak.png


; 2012_03_11.084155
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084204
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_scan_mkv2_enrichment.png


; 2012_03_11.084204
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab_time.txt


; 2012_03_11.084212
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="positions_6nt_m1" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: positions_6nt_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_genomic.bed


; 2012_03_11.084213
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.tab


; 2012_03_11.084213
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m1' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.png


; 2012_03_11.084213
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.tab


; 2012_03_11.084213
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m1' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.png


; 2012_03_11.084213
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084232
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_scan_mkv2_enrichment.png


; 2012_03_11.084232
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab_time.txt


; 2012_03_11.084243
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="positions_6nt_m2" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: positions_6nt_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_genomic.bed


; 2012_03_11.084245
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.tab


; 2012_03_11.084245
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m2' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.png


; 2012_03_11.084245
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.tab


; 2012_03_11.084246
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m2' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.png


; 2012_03_11.084246
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084334
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_scan_mkv2_enrichment.png


; 2012_03_11.084334
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab_time.txt


; 2012_03_11.084340
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="positions_6nt_m3" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: positions_6nt_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_genomic.bed


; 2012_03_11.084341
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.tab


; 2012_03_11.084341
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_6nt_m3' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_site_distrib.png


; 2012_03_11.084341
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.tab


; 2012_03_11.084342
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_6nt_m3' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_per_peak.png


; 2012_03_11.084342
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084350
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_scan_mkv2_enrichment.png


; 2012_03_11.084350
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab_time.txt


; 2012_03_11.084357
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="oligos_7nt_mkv5_m1" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: oligos_7nt_mkv5_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_genomic.bed


; 2012_03_11.084358
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_site_distrib.tab


; 2012_03_11.084358
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv5_m1' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_site_distrib.png


; 2012_03_11.084358
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_per_peak.tab


; 2012_03_11.084358
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv5_m1' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_per_peak.png


; 2012_03_11.084359
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084410
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_scan_mkv2_enrichment.png


; 2012_03_11.084410
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab_time.txt


; 2012_03_11.084417
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="oligos_7nt_mkv5_m2" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: oligos_7nt_mkv5_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_genomic.bed


; 2012_03_11.084418
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_site_distrib.tab


; 2012_03_11.084418
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv5_m2' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_site_distrib.png


; 2012_03_11.084418
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_per_peak.tab


; 2012_03_11.084419
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv5_m2' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_per_peak.png


; 2012_03_11.084419
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084430
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_scan_mkv2_enrichment.png


; 2012_03_11.084430
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab_time.txt


; 2012_03_11.084437
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="oligos_7nt_mkv5_m3" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: oligos_7nt_mkv5_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_genomic.bed


; 2012_03_11.084438
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_site_distrib.tab


; 2012_03_11.084438
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv5_m3' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_site_distrib.png


; 2012_03_11.084438
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_per_peak.tab


; 2012_03_11.084438
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv5_m3' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_per_peak.png


; 2012_03_11.084438
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084449
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_scan_mkv2_enrichment.png


; 2012_03_11.084449
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab_time.txt


; 2012_03_11.084457
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="positions_7nt_m1" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: positions_7nt_m1" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_genomic.bed


; 2012_03_11.084458
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.tab


; 2012_03_11.084458
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m1' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.png


; 2012_03_11.084458
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.tab


; 2012_03_11.084458
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m1' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.png


; 2012_03_11.084458
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084518
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_scan_mkv2_enrichment.png


; 2012_03_11.084518
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab_time.txt


; 2012_03_11.084528
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="positions_7nt_m2" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: positions_7nt_m2" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_genomic.bed


; 2012_03_11.084529
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.tab


; 2012_03_11.084529
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m2' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.png


; 2012_03_11.084529
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.tab


; 2012_03_11.084530
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m2' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.png


; 2012_03_11.084530
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084618
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_scan_mkv2_enrichment.png


; 2012_03_11.084618
time ($RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -return sites -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab_time.txt


; 2012_03_11.084625
$RSAT/perl-scripts/convert-features -from ft -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab -coord $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed -origin center  -to bed  | sed '1s/^.*/track name="positions_7nt_m3" description="RSAT peak-motifs _Kr_D.mel_1-3h_Markov_m=k-2_: positions_7nt_m3" visibility=2 itemRgb="On" use_score=1 color=247,73,2/'  > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_genomic.bed


; 2012_03_11.084626
grep -v '^;' $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.tab


; 2012_03_11.084627
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : positions_7nt_m3' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.png


; 2012_03_11.084627
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.tab


; 2012_03_11.084627
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : positions_7nt_m3' -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.png


; 2012_03_11.084627
time ($RSAT/perl-scripts/matrix-scan -v 3 -quick -seq_format fasta -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score -5 -bginput -markov 2 -return distrib -return occ_proba -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv2_enrichment.tab) >& $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv2_enrichment.tab_time.txt


; 2012_03_11.084641
$RSAT/perl-scripts/XYgraph  -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv2_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_scan_mkv2_enrichment.png


; 2012_03_11.084642
cat $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/sites/peak-motifs_all_motifs_seqcoord.tab


; 2012_03_11.084642
cat $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_genomic.bed $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_genomic.bed > $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/results/sites/peak-motifs_all_motifs_seqcoord.bed


; 2012_03_11.084650
$RSAT/perl-scripts/text-to-html -font variable -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/reports/peak-motifs_timelog.txt -o $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/reports/peak-motifs_timelog.html

; peak-motifs  -v 1 -title _Kr_D.mel_1-3h_Markov_m=k-2_ -i $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifspeak_seq.masked -max_seq_len 2000 -min_markov -2 -max_markov -2 -disco oligos,positions -nmotifs 3 -minol 6 -maxol 7 -2str -motif_db jaspar_core_insects tf $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -motif_db FlyFactorSurvey tf $RSAT/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -motif_db DMMPMM_drosophila tf $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -motif_db IDMMPMM_drosophila tf $RSAT/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf -ref_motifs $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifs_ref_motifs.tf -source galaxy -task purge,seqlen,composition,disco,merge_words,collect_motifs,motifs_vs_motifs,timelog,archive,synthesis,motifs_vs_db,ref_motifs,motifs_vs_ref,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/peak-motifs.2012_03_11.082424
; Program version       	1.231
; Parameter values
;	seq_format            	fasta
;	img_format            	png
;	ref_motifs_format     	transfac
;	purge_match_length    	30
;	purge_mismatches      	0
;	profiles_ci           	20
;	profiles_max_graphs   	20
;	profiles_strand       	-1str
;	profiles_oligo_lengths	1,2
;	profiles_noov         	-ovlp
;	strand                	-2str
;	disco_noov            	-noov
;	oligo_min_len         	6
;	oligo_max_len         	7
;	patterns_max_rank     	50
;	min_ratio             	1
;	min_zscore            	6
;	min_sig               	0
;	oligo_min_mkv         	-2
;	oligo_max_mkv         	-2
;	positions_max_graphs  	20
;	asmb_toppat           	50
;	matrix_nmotifs        	3
; Input files
;	motif_db_DMMPMM_drosophila	/home/rsat/rsa-tools/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf
;	motif_db_FlyFactorSurvey	/home/rsat/rsa-tools/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf
;	motif_db_IDMMPMM_drosophila	/home/rsat/rsa-tools/public_html/data/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.tf
;	motif_db_jaspar_core_insects	/home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf
;	ref_motifs            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifs_ref_motifs.tf
;	test_seq              	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifspeak_seq.masked
; Directories
;	output                        	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/
;	oligos_6nt_mkv4_m1            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/
;	oligos_6nt_mkv4_m2            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/
;	oligos_6nt_mkv4_m3            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/
;	positions_6nt_m1              	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/
;	positions_6nt_m2              	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m2/
;	positions_6nt_m3              	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m3/
;	oligos_7nt_mkv5_m1            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/
;	oligos_7nt_mkv5_m2            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m2/
;	oligos_7nt_mkv5_m3            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/
;	positions_7nt_m1              	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m1/
;	positions_7nt_m2              	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m2/
;	positions_7nt_m3              	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/
; Output files
;	1nt_test_freq                 	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab
;	2nt_test_freq                 	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_test_transitions          	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab
;	archive                       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifs_archive.zip
;	links                         	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/reports/peak-motifs_links.html
;	log                           	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/reports/peak-motifs_log.txt
;	merged_sites                  	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/sites/peak-motifs_all_motifs_seqcoord.tab
;	merged_sites_bed              	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/sites/peak-motifs_all_motifs_seqcoord.bed
;	merged_words                  	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/merged_words/peak-motifs_merged_words.tab
;	merged_words_heatmap          	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/merged_words/peak-motifs_merged_words_heatmap.png
;	merged_words_html             	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/merged_words/peak-motifs_merged_words.html
;	motifs_disco_compa            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
;	motifs_disco_compa_alignments_1ton	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.tab
;	motifs_disco_compa_alignments_1ton_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.html
;	motifs_disco_compa_gml        	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml
;	motifs_disco_compa_html       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_disco_compa.html
;	motifs_discovered             	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf
;	motifs_discovered_table       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered_table.tab
;	motifs_vs_db_DMMPMM_drosophila	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab
;	motifs_vs_db_DMMPMM_drosophila_alignments_1ton	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila_alignments_1ton.tab
;	motifs_vs_db_DMMPMM_drosophila_alignments_1ton_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila_alignments_1ton.html
;	motifs_vs_db_DMMPMM_drosophila_gml	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.gml
;	motifs_vs_db_DMMPMM_drosophila_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.html
;	motifs_vs_db_FlyFactorSurvey  	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey.tab
;	motifs_vs_db_FlyFactorSurvey_alignments_1ton	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey_alignments_1ton.tab
;	motifs_vs_db_FlyFactorSurvey_alignments_1ton_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey_alignments_1ton.html
;	motifs_vs_db_FlyFactorSurvey_gml	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey.gml
;	motifs_vs_db_FlyFactorSurvey_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey.html
;	motifs_vs_db_IDMMPMM_drosophila	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_IDMMPMM_drosophila.tab
;	motifs_vs_db_IDMMPMM_drosophila_alignments_1ton	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_IDMMPMM_drosophila_alignments_1ton.tab
;	motifs_vs_db_IDMMPMM_drosophila_alignments_1ton_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_IDMMPMM_drosophila_alignments_1ton.html
;	motifs_vs_db_IDMMPMM_drosophila_gml	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_IDMMPMM_drosophila.gml
;	motifs_vs_db_IDMMPMM_drosophila_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_IDMMPMM_drosophila.html
;	motifs_vs_db_jaspar_core_insects	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_insects.tab
;	motifs_vs_db_jaspar_core_insects_alignments_1ton	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_insects_alignments_1ton.tab
;	motifs_vs_db_jaspar_core_insects_alignments_1ton_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_insects_alignments_1ton.html
;	motifs_vs_db_jaspar_core_insects_gml	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_insects.gml
;	motifs_vs_db_jaspar_core_insects_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_insects.html
;	motifs_vs_ref                 	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_ref/peak-motifs_motifs_vs_ref.tab
;	motifs_vs_ref_alignments_1ton 	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_ref/peak-motifs_motifs_vs_ref_alignments_1ton.tab
;	motifs_vs_ref_alignments_1ton_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_ref/peak-motifs_motifs_vs_ref_alignments_1ton.html
;	motifs_vs_ref_gml             	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_ref/peak-motifs_motifs_vs_ref.gml
;	motifs_vs_ref_html            	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_ref/peak-motifs_motifs_vs_ref.html
;	oligos_6nt_mkv4               	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4.tab
;	oligos_6nt_mkv4_2pssm         	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm_log.txt
;	oligos_6nt_mkv4_asmb          	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/oligos_6nt_mkv4/peak-motifs_oligos-2str-noov_6nt_mkv4_pssm.asmb
;	oligos_6nt_mkv4_m1_logo       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_logo.png
;	oligos_6nt_mkv4_m1_logo_rc    	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_logo_rc.png
;	oligos_6nt_mkv4_m1_pssm_enrichment	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv2_enrichment.tab
;	oligos_6nt_mkv4_m1_pssm_enrichment_png	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_scan_mkv2_enrichment.png
;	oligos_6nt_mkv4_m1_pssm_site_distrib	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.tab
;	oligos_6nt_mkv4_m1_pssm_site_distrib_graph	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_site_distrib.png
;	oligos_6nt_mkv4_m1_pssm_sites 	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites.tab
;	oligos_6nt_mkv4_m1_pssm_sites_genomic	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_genomic.bed
;	oligos_6nt_mkv4_m1_pssm_sites_per_peak	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.tab
;	oligos_6nt_mkv4_m1_pssm_sites_per_peak_graph	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_sites_per_peak.png
;	oligos_6nt_mkv4_m1_tab        	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tab
;	oligos_6nt_mkv4_m1_tf         	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf
;	oligos_6nt_mkv4_m1_vs_db_DMMPMM_drosophila	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_DMMPMM_drosophila.tab
;	oligos_6nt_mkv4_m1_vs_db_DMMPMM_drosophila_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_DMMPMM_drosophila.html
;	oligos_6nt_mkv4_m1_vs_db_FlyFactorSurvey	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_FlyFactorSurvey.tab
;	oligos_6nt_mkv4_m1_vs_db_FlyFactorSurvey_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_FlyFactorSurvey.html
;	oligos_6nt_mkv4_m1_vs_db_IDMMPMM_drosophila	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_IDMMPMM_drosophila.tab
;	oligos_6nt_mkv4_m1_vs_db_IDMMPMM_drosophila_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_IDMMPMM_drosophila.html
;	oligos_6nt_mkv4_m1_vs_db_jaspar_core_insects	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_jaspar_core_insects.tab
;	oligos_6nt_mkv4_m1_vs_db_jaspar_core_insects_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_jaspar_core_insects.html
;	oligos_6nt_mkv4_m1_vs_ref     	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_ref.tab
;	oligos_6nt_mkv4_m1_vs_ref_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_ref.html
;	oligos_6nt_mkv4_m2_logo       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_logo.png
;	oligos_6nt_mkv4_m2_logo_rc    	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_logo_rc.png
;	oligos_6nt_mkv4_m2_pssm_enrichment	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_scan_mkv2_enrichment.tab
;	oligos_6nt_mkv4_m2_pssm_enrichment_png	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_scan_mkv2_enrichment.png
;	oligos_6nt_mkv4_m2_pssm_site_distrib	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.tab
;	oligos_6nt_mkv4_m2_pssm_site_distrib_graph	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_site_distrib.png
;	oligos_6nt_mkv4_m2_pssm_sites 	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites.tab
;	oligos_6nt_mkv4_m2_pssm_sites_genomic	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_genomic.bed
;	oligos_6nt_mkv4_m2_pssm_sites_per_peak	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.tab
;	oligos_6nt_mkv4_m2_pssm_sites_per_peak_graph	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_sites_per_peak.png
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;	positions_7nt_m3_pssm_site_distrib	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.tab
;	positions_7nt_m3_pssm_site_distrib_graph	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_site_distrib.png
;	positions_7nt_m3_pssm_sites   	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites.tab
;	positions_7nt_m3_pssm_sites_genomic	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_genomic.bed
;	positions_7nt_m3_pssm_sites_per_peak	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.tab
;	positions_7nt_m3_pssm_sites_per_peak_graph	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_sites_per_peak.png
;	positions_7nt_m3_tab          	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tab
;	positions_7nt_m3_tf           	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf
;	positions_7nt_m3_vs_db_DMMPMM_drosophila	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_DMMPMM_drosophila.tab
;	positions_7nt_m3_vs_db_DMMPMM_drosophila_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_DMMPMM_drosophila.html
;	positions_7nt_m3_vs_db_FlyFactorSurvey	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_FlyFactorSurvey.tab
;	positions_7nt_m3_vs_db_FlyFactorSurvey_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_FlyFactorSurvey.html
;	positions_7nt_m3_vs_db_IDMMPMM_drosophila	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_IDMMPMM_drosophila.tab
;	positions_7nt_m3_vs_db_IDMMPMM_drosophila_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_IDMMPMM_drosophila.html
;	positions_7nt_m3_vs_db_jaspar_core_insects	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_insects.tab
;	positions_7nt_m3_vs_db_jaspar_core_insects_html	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_insects.html
;	positions_7nt_m3_vs_ref       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_ref.tab
;	positions_7nt_m3_vs_ref_html  	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_ref.html
;	positions_7nt_pssm_counts     	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.txt
;	positions_7nt_pssm_logo1      	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m1.png
;	positions_7nt_pssm_logo2      	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m2.png
;	positions_7nt_pssm_logo3      	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m3.png
;	positions_7nt_pssm_logo_rc1   	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m1_rc.png
;	positions_7nt_pssm_logo_rc2   	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m2_rc.png
;	positions_7nt_pssm_logo_rc3   	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m3_rc.png
;	positions_7nt_pssm_sig        	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices.tf
;	positions_7nt_pssm_tf         	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf
;	ref_motifs                    	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.transfac
;	ref_motifs_tab                	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs_tab.tab
;	ref_motifs_transfac           	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf
;	synthesis                     	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/peak-motifs_synthesis.html
;	test_converted                	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000.fasta
;	test_purged                   	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_maxlen2000_purged_ml30_mis0.fasta
;	test_seq_coord                	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqcoord.bed
;	test_seqlen                   	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqlen.tab
;	test_seqlen_distrib           	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/sequences/peak-motifs_test_seqlen_distrib.png
;	timelog                       	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/reports/peak-motifs_timelog.txt
;	timelog_html                  	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/reports/peak-motifs_timelog.html
;	timetable                     	/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/reports/peak-motifs_timetable.txt

; 2012_03_11.084650
(cd $RSAT/public_html/tmp ;  zip -ryq peak-motifs.2012_03_11.082424/peak-motifs_archive.zip peak-motifs.2012_03_11.082424 -x peak-motifs_archive.zip)

