One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.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/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 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_mkv4_m1_shift0 (oligos_7nt_mkv4_m1) |
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; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; ytATTGCACAATmcy
; Alignment reference
a 71 70 210 0 2 11 0 253 6 283 282 4 86 69 60
c 78 69 25 0 0 0 282 5 271 3 1 43 76 81 78
g 56 70 36 0 0 260 0 18 0 0 2 22 65 65 62
t 81 77 15 286 284 15 4 10 9 0 1 217 59 71 86
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| MA0102.3_shift2 (CEBPA) |
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0.949 |
0.696 |
9.638 |
0.689 |
0.949 |
0.627 |
0.971 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_7nt_mkv4_m1 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 1; --aTTGCAyAAym--
; cor=0.949; Ncor=0.696; logoDP=9.638; NIcor=0.689; NsEucl=0.949; SSD=0.627; NSW=0.971; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0
c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0
g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0
t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
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| MA0466.1_shift1 (CEBPB) |
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0.931 |
0.683 |
9.474 |
0.676 |
0.942 |
0.822 |
0.963 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; oligos_7nt_mkv4_m1 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 2; -kATTGCAymAy---
; cor=0.931; Ncor=0.683; logoDP=9.474; NIcor=0.676; NsEucl=0.942; SSD=0.822; NSW=0.963; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0
c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0
g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0
t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
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| MA0078.1_rc_shift6 (Sox17_rc) |
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0.856 |
0.514 |
2.520 |
0.171 |
0.918 |
1.099 |
0.939 |
3 |
3 |
3 |
3 |
3 |
3 |
3 |
3.000 |
3 |
; oligos_7nt_mkv4_m1 versus MA0078.1_rc (Sox17_rc); m=3/3; ncol2=9; w=9; offset=6; strand=R; shift=6; score= 3; ------sACAATrdr
; cor=0.856; Ncor=0.514; logoDP=2.520; NIcor=0.171; NsEucl=0.918; SSD=1.099; NSW=0.939; rcor=3; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.000; match_rank=3
a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9
c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6
g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9
t 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7
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