One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/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/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_footprintDB
One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 4 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=15; shift=0; ncol=15; wyATCGCCAGCGygg
; Alignment reference
a 10 6 28 2 0 1 1 0 32 0 1 2 7 6 5
c 8 12 2 3 29 0 31 34 1 0 32 0 9 8 8
g 5 4 3 5 2 33 1 0 0 33 1 29 2 14 16
t 11 12 1 24 3 0 1 0 1 1 0 3 16 6 5
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| 4955_brk_DrosophilaTF_1.1__rc_shift2 (4955_brk_DrosophilaTF_1.1__rc) |
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0.889 |
0.415 |
0.836 |
-0.106 |
0.904 |
0.910 |
0.935 |
1 |
2 |
3 |
3 |
1 |
1 |
1 |
1.714 |
1 |
; dyads_m1 versus 4955_brk_DrosophilaTF_1.1__rc; m=1/3; ncol2=7; w=7; offset=2; strand=R; shift=2; score= 1.7143; --RrCGCCA------
; cor=0.889; Ncor=0.415; logoDP=0.836; NIcor=-0.106; NsEucl=0.904; SSD=0.910; NSW=0.935; rcor=1; rNcor=2; rlogoDP=3; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.714; match_rank=1
a 0 0 0.75 0.4167 0 0 0 0 0.9167 0 0 0 0 0 0
c 0 0 0 0 1 0 1 1 0.0833 0 0 0 0 0 0
g 0 0 0.25 0.5833 0 1 0 0 0 0 0 0 0 0 0
t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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| 1772_MA0213.1_JASPAR_CORE_2009__rc_shift2 (1772_MA0213.1_JASPAR_CORE_2009__rc) |
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0.784 |
0.418 |
3.376 |
0.093 |
0.880 |
1.837 |
0.885 |
2 |
1 |
2 |
2 |
2 |
2 |
2 |
1.857 |
2 |
; dyads_m1 versus 1772_MA0213.1_JASPAR_CORE_2009__rc; m=2/3; ncol2=8; w=8; offset=2; strand=R; shift=2; score= 1.8571; --rGCGCCrs-----
; cor=0.784; Ncor=0.418; logoDP=3.376; NIcor=0.093; NsEucl=0.880; SSD=1.837; NSW=0.885; rcor=2; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.857; match_rank=2
a 0 0 4 1 0 0 0 0 6 0 0 0 0 0 0
c 0 0 1 0 9 0 10 10 0 4 0 0 0 0 0
g 0 0 5 8 0 10 0 0 4 5 0 0 0 0 0
t 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0
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| 6287_1qqa_A_3D-footprint_20130124__rc_shift4 (6287_1qqa_A_3D-footprint_20130124__rc) |
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0.759 |
0.405 |
4.470 |
0.370 |
0.872 |
2.109 |
0.868 |
3 |
3 |
1 |
1 |
3 |
3 |
3 |
2.429 |
3 |
; dyads_m1 versus 6287_1qqa_A_3D-footprint_20130124__rc; m=3/3; ncol2=8; w=8; offset=4; strand=R; shift=4; score= 2.4286; ----cGcntGCG---
; cor=0.759; Ncor=0.405; logoDP=4.470; NIcor=0.370; NsEucl=0.872; SSD=2.109; NSW=0.868; rcor=3; rNcor=3; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.429; match_rank=3
a 0 0 0 0 12 4 21 24 19 7 0 0 0 0 0
c 0 0 0 0 60 2 31 24 20 4 96 0 0 0 0
g 0 0 0 0 12 88 23 24 19 81 0 96 0 0 0
t 0 0 0 0 12 2 21 24 38 4 0 0 0 0 0
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