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_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.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_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift4 ; 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_6nt_mkv4_m2_shift4 (oligos_6nt_mkv4_m2) |
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; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=4; ncol=14; ----ssCGCCCGss
; Alignment reference
a 0 0 0 0 86 94 4 2 17 25 0 3 75 91
c 0 0 0 0 348 238 731 1 644 536 700 15 338 254
g 0 0 0 0 217 359 11 742 66 168 47 726 253 319
t 0 0 0 0 97 57 2 3 21 19 1 4 82 84
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| MA0024.2_rc_shift1 (E2F1_rc) |
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0.840 |
0.517 |
1.305 |
-0.042 |
0.905 |
1.143 |
0.929 |
1 |
1 |
2 |
2 |
1 |
1 |
1 |
1.286 |
1 |
; oligos_6nt_mkv4_m2 versus MA0024.2_rc (E2F1_rc); m=1/3; ncol2=11; w=8; offset=-3; strand=R; shift=1; score= 1.2857; -byTSSCGCscs--
; cor=0.840; Ncor=0.517; logoDP=1.305; NIcor=-0.042; NsEucl=0.905; SSD=1.143; NSW=0.929; rcor=1; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a 0 0 0 0 0 0 0 0 0 0 213 203 0 0
c 0 485 551 0 773 722 1059 0 1059 641 628 280 0 0
g 0 269 0 0 286 337 0 1059 0 274 0 317 0 0
t 0 305 508 1059 0 0 0 0 0 144 218 259 0 0
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| MA0003.1_shift7 (TFAP2A) |
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0.769 |
0.448 |
3.531 |
0.410 |
0.885 |
1.295 |
0.908 |
3 |
2 |
1 |
1 |
3 |
3 |
3 |
2.286 |
2 |
; oligos_6nt_mkv4_m2 versus MA0003.1 (TFAP2A); m=2/3; ncol2=9; w=7; offset=3; strand=D; shift=7; score= 2.2857; -------GCCcbrr
; cor=0.769; Ncor=0.448; logoDP=3.531; NIcor=0.410; NsEucl=0.885; SSD=1.295; NSW=0.908; rcor=3; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.286; match_rank=2
a 0 0 0 0 0 0 0 0 0 0 22 19 55 53
c 0 0 0 0 0 0 0 0 185 185 71 57 44 30
g 0 0 0 0 0 0 0 185 0 0 46 61 67 91
t 0 0 0 0 0 0 0 0 0 0 46 48 19 11
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| MA0470.1_rc_shift0 (E2F4_rc) |
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0.833 |
0.417 |
0.340 |
-0.096 |
0.891 |
1.165 |
0.917 |
2 |
3 |
3 |
3 |
2 |
2 |
2 |
2.429 |
3 |
; oligos_6nt_mkv4_m2 versus MA0470.1_rc (E2F4_rc); m=3/3; ncol2=11; w=7; offset=-4; strand=R; shift=0; score= 2.4286; yyyTCCCGCsc---
; cor=0.833; Ncor=0.417; logoDP=0.340; NIcor=-0.096; NsEucl=0.891; SSD=1.165; NSW=0.917; rcor=2; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.429; match_rank=3
a 366 97 0 0 0 0 0 0 0 0 388 0 0 0
c 616 720 625 75 1822 1633 1878 0 1867 1213 848 0 0 0
g 393 349 0 0 41 218 0 1878 11 510 370 0 0 0
t 503 712 1253 1803 15 27 0 0 0 155 272 0 0 0
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