; matrix-from-patterns  -v 1 -sites -seq Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -pl Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 50 -max_asmb_width 20 -subst 0 -prefix dyads -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm
; Input files
;	patterns	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab
;	sequence	Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta
; Output files
;	sig_matrices_split	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_matrix_list.tab
;	sig_matrices	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf
;	count_matrices	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.txt
;	logo_basename	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo
;	count_matrices_tf	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf
;	gibbs_matrices	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_gibbs_matrices.txt
;	sig_sites	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft
;	err	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_err.txt
;	output	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm
;	log	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt
;	links	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_links.txt
;	assembly	Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
; Number of patterns	87
; patterns -> assemblies
/data/rsat/perl-scripts/pattern-assembly -v 1 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -2str -maxfl 1 -subst 0 -max_asmb_width 20 -toppat 100 -max_asmb_size 50 -max_asmb_width 20 -max_asmb_nb 50 -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb


/data/rsat/perl-scripts/pattern-assembly -v 1 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -2str -maxfl 1 -subst 0 -max_asmb_width 20 -toppat 100 -max_asmb_size 50 -max_asmb_width 20 -max_asmb_nb 50 -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
; Number of assemblies	40
; Number of assembled patterns	196
; assemblies -> significance matrices
/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 50 -prefix dyads -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf


/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 50 -prefix dyads -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf
; Rescaling significance matrices
/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 100 -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_rescaled.tf


/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 100 -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_rescaled.tf


/data/rsat/perl-scripts/convert-matrix -from tf -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_rescaled.tf -to tab -split  -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split; rm -f Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.txt

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m1.tab -name dyads_m1 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m1.tab -name dyads_m1 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m2.tab -name dyads_m2 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m2.tab -name dyads_m2 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m3.tab -name dyads_m3 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m3.tab -name dyads_m3 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m4.tab -name dyads_m4 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m4.tab -name dyads_m4 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m5.tab -name dyads_m5 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m5.tab -name dyads_m5 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m6.tab -name dyads_m6 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m6.tab -name dyads_m6 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m7.tab -name dyads_m7 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m7.tab -name dyads_m7 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m8.tab -name dyads_m8 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m8.tab -name dyads_m8 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m9.tab -name dyads_m9 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m9.tab -name dyads_m9 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m10.tab -name dyads_m10 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m10.tab -name dyads_m10 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m11.tab -name dyads_m11 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m11.tab -name dyads_m11 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m12.tab -name dyads_m12 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m12.tab -name dyads_m12 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m13.tab -name dyads_m13 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m13.tab -name dyads_m13 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m14.tab -name dyads_m14 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m14.tab -name dyads_m14 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m15.tab -name dyads_m15 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m15.tab -name dyads_m15 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m16.tab -name dyads_m16 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m16.tab -name dyads_m16 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m17.tab -name dyads_m17 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m17.tab -name dyads_m17 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m18.tab -name dyads_m18 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m18.tab -name dyads_m18 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m19.tab -name dyads_m19 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m19.tab -name dyads_m19 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m20.tab -name dyads_m20 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m20.tab -name dyads_m20 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m21.tab -name dyads_m21 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m21.tab -name dyads_m21 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m22.tab -name dyads_m22 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m22.tab -name dyads_m22 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m23.tab -name dyads_m23 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m23.tab -name dyads_m23 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m24.tab -name dyads_m24 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m24.tab -name dyads_m24 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m25.tab -name dyads_m25 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m25.tab -name dyads_m25 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m26.tab -name dyads_m26 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m26.tab -name dyads_m26 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m27.tab -name dyads_m27 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m27.tab -name dyads_m27 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m28.tab -name dyads_m28 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m28.tab -name dyads_m28 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m29.tab -name dyads_m29 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m29.tab -name dyads_m29 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m30.tab -name dyads_m30 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m30.tab -name dyads_m30 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m31.tab -name dyads_m31 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m31.tab -name dyads_m31 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m32.tab -name dyads_m32 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m32.tab -name dyads_m32 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m33.tab -name dyads_m33 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m33.tab -name dyads_m33 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m34.tab -name dyads_m34 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m34.tab -name dyads_m34 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m35.tab -name dyads_m35 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m35.tab -name dyads_m35 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m36.tab -name dyads_m36 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m36.tab -name dyads_m36 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m37.tab -name dyads_m37 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m37.tab -name dyads_m37 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m38.tab -name dyads_m38 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m38.tab -name dyads_m38 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m39.tab -name dyads_m39 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m39.tab -name dyads_m39 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m40.tab -name dyads_m40 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep3_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices_split_dyads_m40.tab -name dyads_m40 -2str -t 5 -return sites -bgfile Myogenin_Rep3_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft
; sites -> transfac matrices
/data/rsat/perl-scripts/convert-matrix -v 0 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft -from feature -to transfac -prefix dyads -return counts -return sites -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf


/data/rsat/perl-scripts/convert-matrix -v 0 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_sites.ft -from feature -to transfac -prefix dyads -return counts -return sites -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf
; transfac-formatted -> tab-formatted matrices
/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf -from transfac -to tab -return counts -return sites -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.txt


/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf -from transfac -to tab -return counts -return sites -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.txt
; sites -> count matrices
/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf -from tf -to tab -return counts -return sites -return logo -logo_format png -logo_file Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_links.txt


/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf -from tf -to tab -return counts -return sites -return logo -logo_format png -logo_file Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo -o Myogenin_Rep3_motifs50/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_links.txt
; Host name	pedagogix
; Job started	2020-04-13.202357
; Job done	2020-04-13.202511
; Seconds	0.43
;	user	0.43
;	system	0.05
;	cuser	70.87
;	csystem	3.08
