One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.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/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_footprintDB
One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 3 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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| dyads_m1_shift0 (dyads_m1) |
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; dyads_m1; m=0 (reference); ncol1=20; shift=0; ncol=20; wwwTTGATctadATCAAwww
; Alignment reference
a 13 17 18 2 0 2 26 0 6 5 16 7 25 1 0 28 26 9 9 7
c 3 2 2 0 0 0 0 3 13 3 2 5 1 0 25 0 0 0 2 5
g 5 1 0 0 0 26 0 1 3 3 4 9 2 0 0 0 0 3 2 5
t 7 8 8 26 28 0 2 24 6 17 6 7 0 27 3 0 2 16 15 11
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| 3061_FNR_RegulonDB_7.5__shift3 (3061_FNR_RegulonDB_7.5_) |
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0.948 |
0.663 |
6.730 |
0.655 |
0.954 |
0.822 |
0.971 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; dyads_m1 versus 3061_FNR_RegulonDB_7.5_; m=1/2; ncol2=14; w=14; offset=3; strand=D; shift=3; score= 1; ---tTGaTywayATCAA---
; cor=0.948; Ncor=0.663; logoDP=6.730; NIcor=0.655; NsEucl=0.954; SSD=0.822; NSW=0.971; 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 17 5 13 47 10 17 28 48 20 66 4 0 80 73 0 0 0
c 0 0 0 8 8 10 14 3 28 10 12 23 0 0 72 1 8 0 0 0
g 0 0 0 10 6 58 8 13 3 16 11 11 11 0 5 0 0 0 0 0
t 0 0 0 48 64 2 14 57 35 29 12 29 6 79 6 2 2 0 0 0
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| 7440_HNF6_f1_HOCOMOCO_v9__rc_shift7 (7440_HNF6_f1_HOCOMOCO_v9__rc) |
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0.780 |
0.507 |
1.034 |
-0.102 |
0.922 |
2.080 |
0.920 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; dyads_m1 versus 7440_HNF6_f1_HOCOMOCO_v9__rc; m=2/2; ncol2=13; w=13; offset=7; strand=R; shift=7; score= 2; -------whwaARTCAATAw
; cor=0.780; Ncor=0.507; logoDP=1.034; NIcor=-0.102; NsEucl=0.922; SSD=2.080; NSW=0.920; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 0 0 0 0 0 0 9 9 11 16 19 17 0 0 20 24 0 17 13
c 0 0 0 0 0 0 0 3 7 2 0 2 0 1 24 3 0 0 1 0
g 0 0 0 0 0 0 0 5 2 3 3 1 7 0 0 1 0 0 4 4
t 0 0 0 0 0 0 0 7 6 8 5 2 0 23 0 0 0 24 2 7
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