One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1.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.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift2 ; 4 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_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1) |
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; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=2; ncol=16; --csGCCCCaGGgcss
; Alignment reference
a 0 0 195 244 54 37 19 21 11 808 21 17 123 132 281 174
c 0 0 548 431 70 1140 1083 1093 1108 179 89 101 283 849 359 410
g 0 0 314 350 1071 58 138 117 132 248 1147 1134 747 185 425 448
t 0 0 210 242 72 32 27 36 16 32 10 15 114 101 202 235
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| MA0524.1_shift0 (TFAP2C) |
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0.883 |
0.717 |
5.323 |
0.719 |
0.944 |
1.048 |
0.960 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_7nt_test_vs_ctrl_m1 versus MA0524.1 (TFAP2C); m=1/3; ncol2=15; w=13; offset=-2; strand=D; shift=0; score= 1; hmydsCCyCAGGsca-
; cor=0.883; Ncor=0.717; logoDP=5.323; NIcor=0.719; NsEucl=0.944; SSD=1.048; NSW=0.960; 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 0
c 6752 4693 4943 2009 6040 18426 14817 9317 14790 0 0 0 7908 9235 3259 0
g 2123 3347 2643 6098 11033 0 0 1237 1768 1195 18235 18426 10222 1788 2536 0
t 4750 3909 8290 5401 932 0 3609 7872 786 789 0 0 11 3060 3726 0
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| MA0003.2_shift0 (TFAP2A) |
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0.841 |
0.684 |
5.056 |
0.681 |
0.935 |
1.441 |
0.945 |
2 |
2 |
2 |
2 |
2 |
3 |
2 |
2.143 |
2 |
; oligos_7nt_test_vs_ctrl_m1 versus MA0003.2 (TFAP2A); m=2/3; ncol2=15; w=13; offset=-2; strand=D; shift=0; score= 2.1429; maywGCCysAGGsCa-
; cor=0.841; Ncor=0.684; logoDP=5.056; NIcor=0.681; NsEucl=0.935; SSD=1.441; NSW=0.945; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.143; match_rank=2
a 1387 2141 727 1517 56 0 0 62 346 3738 460 0 116 451 3146 0
c 1630 1060 1506 519 1199 5098 4762 1736 2729 236 0 0 1443 3672 690 0
g 851 792 884 985 3712 0 0 85 1715 920 4638 5098 3455 465 168 0
t 1230 1105 1981 2077 131 0 336 3215 308 204 0 0 84 510 1094 0
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| MA0003.1_shift4 (TFAP2A) |
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0.818 |
0.526 |
3.671 |
0.485 |
0.909 |
1.351 |
0.925 |
3 |
3 |
3 |
3 |
3 |
2 |
3 |
2.857 |
3 |
; oligos_7nt_test_vs_ctrl_m1 versus MA0003.1 (TFAP2A); m=3/3; ncol2=9; w=9; offset=2; strand=D; shift=4; score= 2.8571; ----GCCcbrrGs---
; cor=0.818; Ncor=0.526; logoDP=3.671; NIcor=0.485; NsEucl=0.909; SSD=1.351; NSW=0.925; rcor=3; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=2.857; match_rank=3
a 0 0 0 0 0 0 0 22 19 55 53 19 9 0 0 0
c 0 0 0 0 0 185 185 71 57 44 30 16 78 0 0 0
g 0 0 0 0 185 0 0 46 61 67 91 137 79 0 0 0
t 0 0 0 0 0 0 0 46 48 19 11 13 19 0 0 0
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