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/positions_7nt_m2/peak-motifs_positions_7nt_m2.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/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m2_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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| positions_7nt_m2_shift0 (positions_7nt_m2) |
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; positions_7nt_m2; m=0 (reference); ncol1=21; shift=0; ncol=21; dsTsatTTCCcrGAAATsAsr
; Alignment reference
a 66 48 25 10 127 13 2 1 10 7 49 122 1 210 255 230 20 7 187 63 71
c 57 72 23 129 41 56 3 0 200 226 143 4 1 4 1 12 24 102 22 72 57
g 68 77 23 105 47 15 1 2 3 2 7 132 241 46 4 8 17 137 29 73 68
t 69 63 189 16 45 176 254 257 47 25 61 2 17 0 0 10 199 14 22 52 64
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| MA0137.2_shift3 (STAT1) |
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0.916 |
0.654 |
7.464 |
0.646 |
0.953 |
0.973 |
0.968 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
1.143 |
1 |
; positions_7nt_m2 versus MA0137.2 (STAT1); m=1/2; ncol2=15; w=15; offset=3; strand=D; shift=3; score= 1.1429; ---cayTTCChrGAAryc---
; cor=0.916; Ncor=0.654; logoDP=7.464; NIcor=0.646; NsEucl=0.953; SSD=0.973; NSW=0.968; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.143; 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_rc_shift5 (Stat3_rc) |
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0.906 |
0.432 |
2.935 |
0.118 |
0.931 |
0.939 |
0.953 |
2 |
2 |
2 |
2 |
2 |
1 |
2 |
1.857 |
2 |
; positions_7nt_m2 versus MA0144.1_rc (Stat3_rc); m=2/2; ncol2=10; w=10; offset=5; strand=R; shift=5; score= 1.8571; -----yTTCCtGGAA------
; cor=0.906; Ncor=0.432; logoDP=2.935; NIcor=0.118; NsEucl=0.931; SSD=0.939; NSW=0.953; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=2; rank_mean=1.857; match_rank=2
a 0 0 0 0 0 14 1 0 13 0 123 65 14 461 549 0 0 0 0 0 0
c 0 0 0 0 0 393 5 7 592 605 148 1 9 129 25 0 0 0 0 0 0
g 0 0 0 0 0 15 1 21 2 0 21 541 552 10 19 0 0 0 0 0 0
t 0 0 0 0 0 191 606 585 6 8 321 6 38 13 20 0 0 0 0 0 0
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