One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 /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 -format2 tf -file2 /home/rsat/rsa-tools/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 /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
One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| positions_7nt_m3_shift0 (positions_7nt_m3) |
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; positions_7nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; yckCTCkCKCtc
; Alignment reference
a | 576 599 23 0 0 0 0 0 0 0 798 520
c | 1281 2822 4 5043 0 5043 0 5043 0 5043 816 2766
g | 950 581 1788 0 0 0 1653 0 1290 0 972 752
t | 2236 1041 3228 0 5043 0 3390 0 3753 0 2457 1005
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| MA0205.1_shift0 (Trl) |
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0.893 |
0.744 |
4.967 |
0.731 |
0.927 |
1.071 |
0.946 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m3 versus MA0205.1 (Trl); m=1/1; ncol2=10; w=10; offset=0; strand=D; shift=0; score= 1; yykCTCTCty--
; cor=0.893; Ncor=0.744; logoDP=4.967; NIcor=0.731; NsEucl=0.927; SSD=1.071; NSW=0.946; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a | 4 6 12 0 3 1 13 5 7 9 0 0
c | 22 23 6 64 0 70 0 54 13 33 0 0
g | 9 11 30 3 14 0 2 7 11 10 0 0
t | 36 31 23 4 54 0 56 5 40 19 0 0
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