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/positions_6nt_m2/peak-motifs_positions_6nt_m2.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/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_6nt_m2_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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| positions_6nt_m2_shift0 (positions_6nt_m2) |
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; positions_6nt_m2; m=0 (reference); ncol1=18; shift=0; ncol=18; mwgTGTTGCACAATcacw
; Alignment reference
a 12 13 6 4 5 0 0 2 0 37 1 41 41 0 5 26 9 15
c 14 1 7 2 4 0 0 0 42 1 40 0 0 1 24 6 16 8
g 7 8 27 5 31 0 0 39 0 3 0 0 1 3 9 3 9 7
t 9 20 2 31 2 42 42 1 0 1 1 1 0 38 4 7 8 12
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| MA0102.3_shift4 (CEBPA) |
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0.878 |
0.536 |
9.783 |
0.527 |
0.921 |
1.497 |
0.932 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
1.143 |
1 |
; positions_6nt_m2 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 1.1429; ----aTTGCAyAAym---
; cor=0.878; Ncor=0.536; logoDP=9.783; NIcor=0.527; NsEucl=0.921; SSD=1.497; NSW=0.932; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.143; match_rank=1
a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 0
c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 0
g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 0
t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0 0
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| MA0466.1_shift3 (CEBPB) |
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0.858 |
0.524 |
9.688 |
0.511 |
0.915 |
1.763 |
0.920 |
2 |
2 |
2 |
2 |
2 |
3 |
3 |
2.286 |
2 |
; positions_6nt_m2 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 2.2857; ---kATTGCAymAy----
; cor=0.858; Ncor=0.524; logoDP=9.688; NIcor=0.511; NsEucl=0.915; SSD=1.763; NSW=0.920; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.286; match_rank=2
a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 0
c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 0
g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 0
t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0 0
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| MA0078.1_rc_shift8 (Sox17_rc) |
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0.827 |
0.414 |
3.180 |
0.149 |
0.906 |
1.417 |
0.921 |
3 |
3 |
3 |
3 |
3 |
1 |
2 |
2.571 |
3 |
; positions_6nt_m2 versus MA0078.1_rc (Sox17_rc); m=3/3; ncol2=9; w=9; offset=8; strand=R; shift=8; score= 2.5714; --------sACAATrdr-
; cor=0.827; Ncor=0.414; logoDP=3.180; NIcor=0.149; NsEucl=0.906; SSD=1.417; NSW=0.921; rcor=3; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=2.571; match_rank=3
a 0 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 0
c 0 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 0
g 0 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 0
t 0 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7 0
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