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_m5/peak-motifs_oligos_7nt_mkv4_m5.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_m5/peak-motifs_oligos_7nt_mkv4_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_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_m5_shift0 (oligos_7nt_mkv4_m5) |
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; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; yrTTGCGyAAtm
; Alignment reference
a 42 81 1 1 15 0 4 23 151 164 16 51
c 45 32 2 2 2 165 3 50 13 2 42 45
g 38 43 0 0 150 1 162 2 4 2 28 33
t 46 15 168 168 4 5 2 96 3 3 85 42
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| MA0043.1_rc_shift0 (HLF_rc) |
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0.876 |
0.876 |
5.172 |
0.789 |
0.937 |
1.131 |
0.953 |
1 |
1 |
3 |
1 |
1 |
1 |
1 |
1.286 |
1 |
; oligos_7nt_mkv4_m5 versus MA0043.1_rc (HLF_rc); m=1/3; ncol2=12; w=12; offset=0; strand=R; shift=0; score= 1.2857; daTTryGTAAym
; cor=0.876; Ncor=0.876; logoDP=5.172; NIcor=0.789; NsEucl=0.937; SSD=1.131; NSW=0.953; rcor=1; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a 5 12 2 0 9 0 2 2 15 17 0 5
c 3 1 1 1 0 12 1 2 3 0 12 8
g 5 3 0 4 9 0 15 1 0 0 0 4
t 5 2 15 13 0 6 0 13 0 1 6 1
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| MA0102.3_shift1 (CEBPA) |
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0.828 |
0.759 |
7.867 |
0.756 |
0.917 |
1.652 |
0.925 |
2 |
2 |
1 |
2 |
2 |
2 |
2 |
1.857 |
2 |
; oligos_7nt_mkv4_m5 versus MA0102.3 (CEBPA); m=2/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 1.8571; -aTTGCAyAAym
; cor=0.828; Ncor=0.759; logoDP=7.867; NIcor=0.756; NsEucl=0.917; SSD=1.652; NSW=0.925; rcor=2; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.857; match_rank=2
a 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804
c 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963
g 0 3635 0 0 11304 0 1066 0 0 0 1804 890
t 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
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| MA0466.1_shift0 (CEBPB) |
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0.813 |
0.745 |
7.739 |
0.732 |
0.913 |
1.814 |
0.918 |
3 |
3 |
2 |
3 |
3 |
3 |
3 |
2.857 |
3 |
; oligos_7nt_mkv4_m5 versus MA0466.1 (CEBPB); m=3/3; ncol2=11; w=11; offset=0; strand=D; shift=0; score= 2.8571; kATTGCAymAy-
; cor=0.813; Ncor=0.745; logoDP=7.739; NIcor=0.732; NsEucl=0.913; SSD=1.814; NSW=0.918; rcor=3; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.857; match_rank=3
a 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0
c 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0
g 33617 18428 0 0 75531 0 10015 0 0 0 2043 0
t 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0
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