One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.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/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift3 ; 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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| oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4) |
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; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=3; ncol=15; ---rsCCTCAGGsm-
; Alignment reference
a 0 0 0 195 115 1 0 1 0 700 0 0 114 214 0
c 0 0 0 160 206 746 744 1 748 20 10 2 274 219 0
g 0 0 0 237 283 1 5 20 1 29 739 746 239 151 0
t 0 0 0 157 145 1 0 727 0 0 0 1 122 165 0
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| MA0524.1_shift0 (TFAP2C) |
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0.902 |
0.661 |
8.344 |
0.658 |
0.937 |
0.955 |
0.957 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_7nt_mkv5_m4 versus MA0524.1 (TFAP2C); m=1/2; ncol2=15; w=11; offset=-3; strand=D; shift=0; score= 1; hmydsCCyCAGGsca
; cor=0.902; Ncor=0.661; logoDP=8.344; NIcor=0.658; NsEucl=0.937; SSD=0.955; NSW=0.957; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 4801 6477 2550 4918 421 0 0 0 1082 16442 191 0 285 4343 8905
c 6752 4693 4943 2009 6040 18426 14817 9317 14790 0 0 0 7908 9235 3259
g 2123 3347 2643 6098 11033 0 0 1237 1768 1195 18235 18426 10222 1788 2536
t 4750 3909 8290 5401 932 0 3609 7872 786 789 0 0 11 3060 3726
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| MA0003.2_shift0 (TFAP2A) |
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0.864 |
0.634 |
7.633 |
0.617 |
0.926 |
1.314 |
0.940 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; oligos_7nt_mkv5_m4 versus MA0003.2 (TFAP2A); m=2/2; ncol2=15; w=11; offset=-3; strand=D; shift=0; score= 2; maywGCCysAGGsCa
; cor=0.864; Ncor=0.634; logoDP=7.633; NIcor=0.617; NsEucl=0.926; SSD=1.314; NSW=0.940; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 1387 2141 727 1517 56 0 0 62 346 3738 460 0 116 451 3146
c 1630 1060 1506 519 1199 5098 4762 1736 2729 236 0 0 1443 3672 690
g 851 792 884 985 3712 0 0 85 1715 920 4638 5098 3455 465 168
t 1230 1105 1981 2077 131 0 336 3215 308 204 0 0 84 510 1094
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