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_m3/peak-motifs_oligos_6nt_mkv3_m3.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_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_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_m3_shift0 (oligos_6nt_mkv3_m3) |
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; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=0; ncol=14; dhGATTGCGhm---
; Alignment reference
a 20 21 2 60 0 5 6 0 0 21 38 0 0 0
c 8 17 1 2 1 2 1 65 2 18 18 0 0 0
g 20 12 54 4 1 0 59 0 62 3 5 0 0 0
t 19 17 10 1 65 60 1 2 3 25 6 0 0 0
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| MA0043.1_rc_shift2 (HLF_rc) |
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0.824 |
0.530 |
3.854 |
0.414 |
0.908 |
1.376 |
0.924 |
1 |
2 |
3 |
3 |
1 |
1 |
1 |
1.714 |
1 |
; oligos_6nt_mkv3_m3 versus MA0043.1_rc (HLF_rc); m=1/3; ncol2=12; w=9; offset=2; strand=R; shift=2; score= 1.7143; --daTTryGTAAym
; cor=0.824; Ncor=0.530; logoDP=3.854; NIcor=0.414; NsEucl=0.908; SSD=1.376; NSW=0.924; rcor=1; rNcor=2; rlogoDP=3; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.714; match_rank=1
a 0 0 5 12 2 0 9 0 2 2 15 17 0 5
c 0 0 3 1 1 1 0 12 1 2 3 0 12 8
g 0 0 5 3 0 4 9 0 15 1 0 0 0 4
t 0 0 5 2 15 13 0 6 0 13 0 1 6 1
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| MA0466.1_shift2 (CEBPB) |
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0.777 |
0.538 |
5.698 |
0.529 |
0.894 |
1.818 |
0.899 |
3 |
1 |
1 |
1 |
2 |
3 |
2 |
1.857 |
2 |
; oligos_6nt_mkv3_m3 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=9; offset=2; strand=D; shift=2; score= 1.8571; --kATTGCAymAy-
; cor=0.777; Ncor=0.538; logoDP=5.698; NIcor=0.529; NsEucl=0.894; SSD=1.818; NSW=0.899; rcor=3; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=1.857; match_rank=2
a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0
c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0
g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0
t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0
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| MA0102.3_shift3 (CEBPA) |
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0.783 |
0.448 |
5.527 |
0.444 |
0.886 |
1.660 |
0.896 |
2 |
3 |
2 |
2 |
3 |
2 |
3 |
2.429 |
3 |
; oligos_6nt_mkv3_m3 versus MA0102.3 (CEBPA); m=3/3; ncol2=11; w=8; offset=3; strand=D; shift=3; score= 2.4286; ---aTTGCAyAAym
; cor=0.783; Ncor=0.448; logoDP=5.527; NIcor=0.444; NsEucl=0.886; SSD=1.660; NSW=0.896; rcor=2; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=2.429; match_rank=3
a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804
c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963
g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890
t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
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