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_8nt_m1/peak-motifs_positions_8nt_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_8nt_m1/peak-motifs_positions_8nt_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_8nt_m1_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_8nt_m1_shift0 (positions_8nt_m1) |
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; positions_8nt_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; amAGATTGCAAAACww
; Alignment reference
a 172 182 482 52 497 2 2 12 3 517 451 522 535 8 215 163
c 112 161 5 27 15 3 0 2 539 6 70 25 3 479 124 119
g 134 132 23 439 22 2 2 518 5 15 2 2 7 22 43 128
t 131 74 39 31 15 542 545 17 2 11 26 0 4 40 167 139
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| MA0102.3_shift4 (CEBPA) |
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0.888 |
0.610 |
9.440 |
0.600 |
0.925 |
1.358 |
0.938 |
1 |
2 |
1 |
1 |
1 |
1 |
1 |
1.143 |
1 |
; positions_8nt_m1 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 1.1429; ----aTTGCAyAAym-
; cor=0.888; Ncor=0.610; logoDP=9.440; NIcor=0.600; NsEucl=0.925; SSD=1.358; NSW=0.938; rcor=1; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.143; match_rank=1
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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| MA0102.2_rc_shift4 (CEBPA_rc) |
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0.861 |
0.484 |
3.266 |
0.135 |
0.901 |
1.596 |
0.911 |
2 |
4 |
3 |
3 |
4 |
2 |
2 |
2.857 |
2 |
; positions_8nt_m1 versus MA0102.2_rc (CEBPA_rc); m=2/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score= 2.8571; ----rTTGcrmaA---
; cor=0.861; Ncor=0.484; logoDP=3.266; NIcor=0.135; NsEucl=0.901; SSD=1.596; NSW=0.911; rcor=2; rNcor=4; rlogoDP=3; rNIcor=3; rNsEucl=4; rSSD=2; rNSW=2; rank_mean=2.857; match_rank=2
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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0.833 |
0.625 |
0.301 |
-0.199 |
0.913 |
2.200 |
0.908 |
3 |
1 |
4 |
4 |
2 |
4 |
3 |
3.000 |
3 |
; positions_8nt_m1 versus MA0102.1_rc (Cebpa_rc); m=3/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 3; -vrbrTTGcrmaA---
; cor=0.833; Ncor=0.625; logoDP=0.301; NIcor=-0.199; NsEucl=0.913; SSD=2.200; NSW=0.908; rcor=3; rNcor=1; rlogoDP=4; rNIcor=4; rNsEucl=2; rSSD=4; rNSW=3; rank_mean=3.000; match_rank=3
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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| MA0466.1_shift3 (CEBPB) |
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0.828 |
0.569 |
9.326 |
0.559 |
0.906 |
2.128 |
0.903 |
4 |
3 |
2 |
2 |
3 |
3 |
4 |
3.000 |
4 |
; positions_8nt_m1 versus MA0466.1 (CEBPB); m=4/4; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 3; ---kATTGCAymAy--
; cor=0.828; Ncor=0.569; logoDP=9.326; NIcor=0.559; NsEucl=0.906; SSD=2.128; NSW=0.903; rcor=4; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=3; rNSW=4; rank_mean=3.000; match_rank=4
a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0
c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0
g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0
t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
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