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_m2/peak-motifs_oligos_7nt_mkv4_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/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_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 |
|---|
| oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2) |
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; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; wrATTGCACAAcwy
; Alignment reference
a 72 59 190 1 0 11 1 209 3 233 233 4 90 46
c 55 56 14 0 0 2 234 8 223 2 0 153 53 71
g 39 63 26 0 1 213 0 9 2 0 0 22 28 54
t 69 57 5 234 234 9 0 9 7 0 2 56 64 64
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| MA0102.3_shift2 (CEBPA) |
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0.946 |
0.744 |
9.783 |
0.734 |
0.947 |
0.670 |
0.970 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_7nt_mkv4_m2 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 1; --aTTGCAyAAym-
; cor=0.946; Ncor=0.744; logoDP=9.783; NIcor=0.734; NsEucl=0.947; SSD=0.670; NSW=0.970; 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
c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0
g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0
t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
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| MA0466.1_shift1 (CEBPB) |
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0.915 |
0.719 |
9.589 |
0.707 |
0.936 |
1.006 |
0.954 |
2 |
2 |
2 |
2 |
2 |
3 |
2 |
2.143 |
2 |
; oligos_7nt_mkv4_m2 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 2.1429; -kATTGCAymAy--
; cor=0.915; Ncor=0.719; logoDP=9.589; NIcor=0.707; NsEucl=0.936; SSD=1.006; NSW=0.954; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.143; match_rank=2
a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0
c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0
g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0
t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
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| MA0133.1_shift7 (BRCA1) |
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0.874 |
0.437 |
3.092 |
0.443 |
0.916 |
0.700 |
0.950 |
3 |
3 |
3 |
3 |
3 |
2 |
3 |
2.857 |
3 |
; oligos_7nt_mkv4_m2 versus MA0133.1 (BRCA1); m=3/3; ncol2=7; w=7; offset=7; strand=D; shift=7; score= 2.8571; -------mCAAcms
; cor=0.874; Ncor=0.437; logoDP=3.092; NIcor=0.443; NsEucl=0.916; SSD=0.700; NSW=0.950; rcor=3; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=2.857; match_rank=3
a 0 0 0 0 0 0 0 15 4 41 36 7 19 3
c 0 0 0 0 0 0 0 11 35 1 2 29 14 22
g 0 0 0 0 0 0 0 10 2 1 4 6 7 15
t 0 0 0 0 0 0 0 7 2 0 1 1 3 3
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