One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.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/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 5 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_7nt_m3_shift0 (positions_7nt_m3) |
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; positions_7nt_m3; m=0 (reference); ncol1=16; shift=0; ncol=16; arAGATTGCGAAATrw
; Alignment reference
a 162 113 401 15 413 0 0 7 36 40 396 423 432 2 126 150
c 77 108 4 27 6 0 0 0 303 14 17 10 0 15 102 90
g 98 128 9 350 11 0 1 422 24 365 2 0 1 7 112 76
t 96 84 19 41 3 433 432 4 70 14 18 0 0 409 93 117
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| MA0102.2_rc_shift4 (CEBPA_rc) |
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0.914 |
0.514 |
3.780 |
0.178 |
0.918 |
1.082 |
0.940 |
1 |
4 |
2 |
2 |
2 |
1 |
1 |
1.857 |
1 |
; positions_7nt_m3 versus MA0102.2_rc (CEBPA_rc); m=1/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score= 1.8571; ----rTTGcrmaA---
; cor=0.914; Ncor=0.514; logoDP=3.780; NIcor=0.178; NsEucl=0.918; SSD=1.082; NSW=0.940; rcor=1; rNcor=4; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.857; match_rank=1
a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0
c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0
g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0
t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
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| MA0102.1_rc_shift1 (Cebpa_rc) |
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0.876 |
0.657 |
0.379 |
-0.211 |
0.922 |
1.748 |
0.927 |
2 |
1 |
4 |
4 |
1 |
2 |
2 |
2.286 |
2 |
; positions_7nt_m3 versus MA0102.1_rc (Cebpa_rc); m=2/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 2.2857; -vrbrTTGcrmaA---
; cor=0.876; Ncor=0.657; logoDP=0.379; NIcor=-0.211; NsEucl=0.922; SSD=1.748; NSW=0.927; rcor=2; rNcor=1; rlogoDP=4; rNIcor=4; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=2.286; match_rank=2
a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0
c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0
g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0
t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0
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| MA0102.3_shift4 (CEBPA) |
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0.763 |
0.524 |
8.483 |
0.503 |
0.894 |
2.703 |
0.877 |
3 |
2 |
1 |
1 |
3 |
3 |
3 |
2.286 |
3 |
; positions_7nt_m3 versus MA0102.3 (CEBPA); m=3/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 2.2857; ----aTTGCAyAAym-
; cor=0.763; Ncor=0.524; logoDP=8.483; NIcor=0.503; NsEucl=0.894; SSD=2.703; NSW=0.877; rcor=3; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.286; match_rank=3
a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0
c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0
g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0
t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
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| MA0466.1_rc_shift4 (CEBPB_rc) |
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0.756 |
0.520 |
3.051 |
0.047 |
0.893 |
2.788 |
0.873 |
4 |
3 |
3 |
3 |
4 |
4 |
4 |
3.571 |
4 |
; positions_7nt_m3 versus MA0466.1_rc (CEBPB_rc); m=4/4; ncol2=11; w=11; offset=4; strand=R; shift=4; score= 3.5714; ----rTkrTGCAATm-
; cor=0.756; Ncor=0.520; logoDP=3.051; NIcor=0.047; NsEucl=0.893; SSD=2.788; NSW=0.873; rcor=4; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=3.571; match_rank=4
a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0
c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0
g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0
t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0
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