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_m3/peak-motifs_local_words_7nt_m3.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_m3/peak-motifs_local_words_7nt_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: local_words_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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| local_words_7nt_m3_shift0 (local_words_7nt_m3) |
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; local_words_7nt_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; kdaCATTTyCmrgaAATGtmw
; Alignment reference
a 38 43 81 8 142 9 3 13 24 22 40 68 25 103 157 154 13 10 36 48 40
c 26 35 15 136 4 5 3 5 85 112 75 13 7 11 0 3 9 11 17 40 36
g 43 41 27 6 6 8 0 10 8 0 10 65 96 34 2 1 9 127 21 37 32
t 53 41 37 10 8 138 154 132 43 26 35 14 32 12 1 2 129 12 86 35 52
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| MA0137.2_shift3 (STAT1) |
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0.783 |
0.559 |
4.929 |
0.508 |
0.927 |
2.382 |
0.921 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; local_words_7nt_m3 versus MA0137.2 (STAT1); m=1/1; ncol2=15; w=15; offset=3; strand=D; shift=3; score= 1; ---cayTTCChrGAAryc---
; cor=0.783; Ncor=0.559; logoDP=4.929; NIcor=0.508; NsEucl=0.927; SSD=2.382; NSW=0.921; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; 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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