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_m1/peak-motifs_positions_7nt_m1.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_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 6 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 |
|---|
| positions_7nt_m1_shift0 (positions_7nt_m1) |
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; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; wtATTTCACAATCwy
; Alignment reference
a 394 218 1344 6 10 132 6 1281 17 1366 1387 18 237 486 348
c 277 242 17 9 7 9 1392 26 1335 33 4 63 1048 300 369
g 313 341 33 4 46 166 3 48 5 1 6 13 43 155 231
t 419 602 9 1384 1340 1096 2 48 46 3 6 1309 75 462 455
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| MA0466.1_shift1 (CEBPB) |
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0.862 |
0.632 |
9.285 |
0.609 |
0.917 |
1.673 |
0.924 |
1 |
2 |
2 |
2 |
1 |
1 |
1 |
1.429 |
1 |
; positions_7nt_m1 versus MA0466.1 (CEBPB); m=1/5; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 1.4286; -kATTGCAymAy---
; cor=0.862; Ncor=0.632; logoDP=9.285; NIcor=0.609; NsEucl=0.917; SSD=1.673; NSW=0.924; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.429; match_rank=1
a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0
c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0
g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0
t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
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| MA0102.3_shift2 (CEBPA) |
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0.858 |
0.629 |
9.288 |
0.601 |
0.914 |
1.799 |
0.918 |
2 |
3 |
1 |
3 |
3 |
4 |
2 |
2.571 |
2 |
; positions_7nt_m1 versus MA0102.3 (CEBPA); m=2/5; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 2.5714; --aTTGCAyAAym--
; cor=0.858; Ncor=0.629; logoDP=9.288; NIcor=0.601; NsEucl=0.914; SSD=1.799; NSW=0.918; rcor=2; rNcor=3; rlogoDP=1; rNIcor=3; rNsEucl=3; rSSD=4; rNSW=2; rank_mean=2.571; match_rank=2
a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0
c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0
g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0
t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
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| MA0102.1_shift3 (Cebpa) |
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0.813 |
0.650 |
6.099 |
0.632 |
0.914 |
2.138 |
0.911 |
4 |
1 |
3 |
1 |
2 |
5 |
3 |
2.714 |
3 |
; positions_7nt_m1 versus MA0102.1 (Cebpa); m=3/5; ncol2=12; w=12; offset=3; strand=D; shift=3; score= 2.7143; ---TtkygCAAyvyb
; cor=0.813; Ncor=0.650; logoDP=6.099; NIcor=0.632; NsEucl=0.914; SSD=2.138; NSW=0.911; rcor=4; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=2; rSSD=5; rNSW=3; rank_mean=2.714; match_rank=3
a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1
c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6
g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5
t 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
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| MA0102.2_shift3 (CEBPA) |
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0.841 |
0.504 |
6.083 |
0.482 |
0.896 |
1.760 |
0.902 |
3 |
4 |
4 |
4 |
5 |
3 |
5 |
4.000 |
4 |
; positions_7nt_m1 versus MA0102.2 (CEBPA); m=4/5; ncol2=9; w=9; offset=3; strand=D; shift=3; score= 4; ---TtkygCAAy---
; cor=0.841; Ncor=0.504; logoDP=6.083; NIcor=0.482; NsEucl=0.896; SSD=1.760; NSW=0.902; rcor=3; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=5; rSSD=3; rNSW=5; rank_mean=4.000; match_rank=4
a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0
c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0
g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0
t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
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| MA0078.1_rc_shift6 (Sox17_rc) |
 |
0.800 |
0.480 |
3.198 |
0.181 |
0.898 |
1.673 |
0.907 |
5 |
5 |
5 |
5 |
4 |
2 |
4 |
4.286 |
5 |
; positions_7nt_m1 versus MA0078.1_rc (Sox17_rc); m=5/5; ncol2=9; w=9; offset=6; strand=R; shift=6; score= 4.2857; ------sACAATrdr
; cor=0.800; Ncor=0.480; logoDP=3.198; NIcor=0.181; NsEucl=0.898; SSD=1.673; NSW=0.907; rcor=5; rNcor=5; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=2; rNSW=4; rank_mean=4.286; match_rank=5
a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9
c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6
g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9
t 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7
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