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_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5.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_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_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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| oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5) |
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; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; sssccvGCCCCGCCCCvGggCsss
; Alignment reference
a 101 91 46 48 64 205 39 44 46 29 40 40 34 20 22 35 240 35 49 49 33 143 74 96
c 259 251 165 424 440 198 107 499 457 487 472 43 489 506 494 485 168 110 146 147 514 218 261 255
g 195 204 376 135 119 177 461 84 110 94 82 528 103 97 91 106 187 482 429 421 71 203 236 214
t 98 107 66 46 30 73 46 26 40 43 59 42 27 30 46 27 58 26 29 36 35 89 82 88
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| MA0079.3_shift6 (SP1) |
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0.887 |
0.406 |
3.477 |
0.405 |
0.935 |
1.033 |
0.953 |
1 |
2 |
1 |
2 |
1 |
1 |
1 |
1.286 |
1 |
; oligos_6nt_test_vs_ctrl_m5 versus MA0079.3 (SP1); m=1/2; ncol2=11; w=11; offset=6; strand=D; shift=6; score= 1.2857; ------gCCCCkCCCCy-------
; cor=0.887; Ncor=0.406; logoDP=3.477; NIcor=0.405; NsEucl=0.935; SSD=1.033; NSW=0.953; rcor=1; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a 0 0 0 0 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 0 0 0
c 0 0 0 0 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 0 0 0
g 0 0 0 0 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 0 0 0
t 0 0 0 0 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0 0 0 0
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| MA0516.1_shift6 (SP2) |
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0.781 |
0.488 |
3.445 |
0.477 |
0.932 |
2.107 |
0.930 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
1.714 |
2 |
; oligos_6nt_test_vs_ctrl_m5 versus MA0516.1 (SP2); m=2/2; ncol2=15; w=15; offset=6; strand=D; shift=6; score= 1.7143; ------gyCCCGCCyCyyccs---
; cor=0.781; Ncor=0.488; logoDP=3.445; NIcor=0.477; NsEucl=0.932; SSD=2.107; NSW=0.930; rcor=2; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.714; match_rank=2
a 0 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 0 0 0
c 0 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 0 0 0
g 0 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 0 0 0
t 0 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316 0 0 0
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