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_m4/peak-motifs_positions_8nt_m4.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_m4/peak-motifs_positions_8nt_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_8nt_m4_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 |
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| positions_8nt_m4_shift0 (positions_8nt_m4) |
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; positions_8nt_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; raTGGTTGCACAAyAwt
; Alignment reference
a 176 350 19 19 55 1 1 11 1 634 4 646 645 6 548 174 92
c 61 81 8 2 8 0 0 2 643 3 635 1 0 239 29 149 112
g 352 112 19 612 578 0 0 628 0 5 1 0 0 12 34 147 50
t 58 104 601 14 6 646 646 6 3 5 7 0 2 390 36 177 393
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| MA0102.3_shift4 (CEBPA) |
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0.872 |
0.564 |
10.262 |
0.542 |
0.916 |
1.725 |
0.922 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_8nt_m4 versus MA0102.3 (CEBPA); m=1/5; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 1; ----aTTGCAyAAym--
; cor=0.872; Ncor=0.564; logoDP=10.262; NIcor=0.542; NsEucl=0.916; SSD=1.725; NSW=0.922; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0
c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0
g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0
t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
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| MA0466.1_shift3 (CEBPB) |
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0.825 |
0.534 |
10.032 |
0.501 |
0.902 |
2.334 |
0.894 |
2 |
3 |
2 |
3 |
3 |
4 |
3 |
2.857 |
2 |
; positions_8nt_m4 versus MA0466.1 (CEBPB); m=2/5; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 2.8571; ---kATTGCAymAy---
; cor=0.825; Ncor=0.534; logoDP=10.032; NIcor=0.501; NsEucl=0.902; SSD=2.334; NSW=0.894; rcor=2; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=4; rNSW=3; rank_mean=2.857; match_rank=2
a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0
c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0
g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0
t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
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| MA0102.1_shift5 (Cebpa) |
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0.771 |
0.544 |
6.562 |
0.521 |
0.902 |
2.771 |
0.885 |
5 |
2 |
3 |
2 |
2 |
5 |
4 |
3.286 |
3 |
; positions_8nt_m4 versus MA0102.1 (Cebpa); m=3/5; ncol2=12; w=12; offset=5; strand=D; shift=5; score= 3.2857; -----TtkygCAAyvyb
; cor=0.771; Ncor=0.544; logoDP=6.562; NIcor=0.521; NsEucl=0.902; SSD=2.771; NSW=0.885; rcor=5; rNcor=2; rlogoDP=3; rNIcor=2; rNsEucl=2; rSSD=5; rNSW=4; rank_mean=3.286; match_rank=3
a 0 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1
c 0 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6
g 0 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5
t 0 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
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| MA0078.1_rc_shift8 (Sox17_rc) |
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0.781 |
0.414 |
2.538 |
0.089 |
0.893 |
1.869 |
0.896 |
4 |
5 |
5 |
5 |
4 |
2 |
2 |
3.857 |
4 |
; positions_8nt_m4 versus MA0078.1_rc (Sox17_rc); m=4/5; ncol2=9; w=9; offset=8; strand=R; shift=8; score= 3.8571; --------sACAATrdr
; cor=0.781; Ncor=0.414; logoDP=2.538; NIcor=0.089; NsEucl=0.893; SSD=1.869; NSW=0.896; rcor=4; rNcor=5; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=2; rNSW=2; rank_mean=3.857; match_rank=4
a 0 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9
c 0 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6
g 0 0 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 0 0 30 3 8 7
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| MA0102.2_shift5 (CEBPA) |
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0.815 |
0.431 |
6.536 |
0.408 |
0.886 |
2.101 |
0.883 |
3 |
4 |
4 |
4 |
5 |
3 |
5 |
4.000 |
5 |
; positions_8nt_m4 versus MA0102.2 (CEBPA); m=5/5; ncol2=9; w=9; offset=5; strand=D; shift=5; score= 4; -----TtkygCAAy---
; cor=0.815; Ncor=0.431; logoDP=6.536; NIcor=0.408; NsEucl=0.886; SSD=2.101; NSW=0.883; rcor=3; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=5; rSSD=3; rNSW=5; rank_mean=4.000; match_rank=5
a 0 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0
c 0 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0
g 0 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0
t 0 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
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