One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/local_words_7nt_m1/peak-motifs_local_words_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_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/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/local_words_7nt_m1/peak-motifs_local_words_7nt_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: local_words_7nt_m1_shift0 ; 3 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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local_words_7nt_m1_shift0 (local_words_7nt_m1) |
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; local_words_7nt_m1; m=0 (reference); ncol1=21; shift=0; ncol=21; wbwCATTTcchgkAAATGtat
; Alignment reference
a 53 36 70 5 143 5 3 14 23 15 40 20 22 116 154 129 8 6 39 46 38
c 28 40 24 139 4 1 1 11 97 108 41 10 8 9 1 1 4 10 24 39 39
g 35 40 22 8 8 2 1 11 7 0 29 100 84 20 1 25 4 137 24 36 33
t 43 43 43 7 4 151 154 123 32 36 49 29 45 14 3 4 143 6 72 38 49
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MA0137.2_shift3 (STAT1) |
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0.778 |
0.556 |
4.892 |
0.505 |
0.925 |
2.501 |
0.917 |
2 |
1 |
1 |
1 |
1 |
2 |
2 |
1.429 |
1 |
; local_words_7nt_m1 versus MA0137.2 (STAT1); m=1/2; ncol2=15; w=15; offset=3; strand=D; shift=3; score= 1.4286; ---cayTTCChrGAAryc---
; cor=0.778; Ncor=0.556; logoDP=4.892; NIcor=0.505; NsEucl=0.925; SSD=2.501; NSW=0.917; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.429; match_rank=1
a 0 0 0 208 859 251 10 8 106 23 528 696 53 1900 2030 954 336 417 0 0 0
c 0 0 0 1076 496 574 22 14 1921 1900 762 31 30 124 17 263 760 804 0 0 0
g 0 0 0 415 279 144 11 38 14 7 115 1292 1700 29 23 552 270 425 0 0 0
t 0 0 0 378 446 1112 2038 2023 44 155 680 66 302 32 15 315 714 431 0 0 0
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MA0144.1_shift6 (Stat3) |
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0.860 |
0.410 |
4.350 |
0.385 |
0.917 |
1.374 |
0.931 |
1 |
2 |
2 |
2 |
2 |
1 |
1 |
1.571 |
2 |
; local_words_7nt_m1 versus MA0144.1 (Stat3); m=2/2; ncol2=10; w=10; offset=6; strand=D; shift=6; score= 1.5714; ------TTCCaGGAAr-----
; cor=0.860; Ncor=0.410; logoDP=4.350; NIcor=0.385; NsEucl=0.917; SSD=1.374; NSW=0.931; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.571; match_rank=2
a 0 0 0 0 0 0 20 13 38 6 321 8 6 585 606 191 0 0 0 0 0
c 0 0 0 0 0 0 19 10 552 541 21 0 2 21 1 15 0 0 0 0 0
g 0 0 0 0 0 0 25 129 9 1 148 605 592 7 5 393 0 0 0 0 0
t 0 0 0 0 0 0 549 461 14 65 123 0 13 0 1 14 0 0 0 0 0
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