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_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_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_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_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_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1) |
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; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=15; shift=0; ncol=16; rtgATTGCACAATmy-
; Alignment reference
a 41 31 23 122 1 1 5 0 129 4 148 147 5 40 31 0
c 30 35 21 8 0 0 0 150 2 143 1 1 18 42 45 0
g 46 29 89 13 0 0 137 0 15 0 0 1 9 36 36 0
t 33 55 17 7 149 149 8 0 4 3 1 1 118 32 38 0
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| MA0102.3_shift3 (CEBPA) |
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0.944 |
0.692 |
9.686 |
0.687 |
0.946 |
0.704 |
0.968 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_6nt_mkv3_m1 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 1; ---aTTGCAyAAym--
; cor=0.944; Ncor=0.692; logoDP=9.686; NIcor=0.687; NsEucl=0.946; SSD=0.704; NSW=0.968; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0
c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0
g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0
t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
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| MA0466.1_shift2 (CEBPB) |
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0.923 |
0.677 |
9.579 |
0.671 |
0.937 |
0.960 |
0.956 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; oligos_6nt_mkv3_m1 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 2; --kATTGCAymAy---
; cor=0.923; Ncor=0.677; logoDP=9.579; NIcor=0.671; NsEucl=0.937; SSD=0.960; NSW=0.956; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0
c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0
g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0
t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
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| MA0078.1_rc_shift7 (Sox17_rc) |
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0.857 |
0.428 |
2.551 |
0.146 |
0.908 |
1.094 |
0.932 |
3 |
3 |
3 |
3 |
3 |
3 |
3 |
3.000 |
3 |
; oligos_6nt_mkv3_m1 versus MA0078.1_rc (Sox17_rc); m=3/3; ncol2=9; w=8; offset=7; strand=R; shift=7; score= 3; -------sACAATrdr
; cor=0.857; Ncor=0.428; logoDP=2.551; NIcor=0.146; NsEucl=0.908; SSD=1.094; NSW=0.932; 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 0 4 29 0 31 30 1 9 11 9
c 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6
g 0 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 0 30 3 8 7
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