One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/peak-motifs_motifs_disco_compa.tab
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=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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| dyads_m2_rc_shift0 (dyads_m2_rc) |
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0.958 |
0.958 |
11.514 |
0.947 |
0.972 |
0.615 |
0.985 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; dyads_m1 versus dyads_m2_rc; m=1/3; ncol2=20; w=20; offset=0; strand=R; shift=0; score= 1; wwaTTGATctasrTCAAwww
; cor=0.958; Ncor=0.958; logoDP=11.514; NIcor=0.947; NsEucl=0.972; SSD=0.615; NSW=0.985; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 13 15 19 0 0 2 26 0 4 5 15 6 13 1 0 27 26 9 12 9
c 5 0 5 0 0 0 0 1 14 5 3 7 3 0 25 0 1 4 3 3
g 1 2 0 2 0 26 0 1 5 3 4 9 12 0 0 1 0 4 5 4
t 9 11 4 26 28 0 2 26 5 15 6 6 0 27 3 0 1 11 8 12
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| oligos_6nt_mkv2_rc_shift0 (oligos_6nt_mkv2_rc) |
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0.866 |
0.477 |
3.597 |
0.103 |
0.923 |
1.422 |
0.935 |
3 |
3 |
5 |
5 |
3 |
3 |
3 |
3.571 |
3 |
; dyads_m1 versus oligos_6nt_mkv2_rc; m=2/3; ncol2=11; w=11; offset=0; strand=R; shift=0; score= 3.5714; wyATTGATCta---------
; cor=0.866; Ncor=0.477; logoDP=3.597; NIcor=0.103; NsEucl=0.923; SSD=1.422; NSW=0.935; rcor=3; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=3
a 2 0 5 0 0 0 5 0 0 1 2 0 0 0 0 0 0 0 0 0
c 1 2 0 0 0 0 0 0 5 1 1 0 0 0 0 0 0 0 0 0
g 0 0 0 0 0 5 0 0 0 1 1 0 0 0 0 0 0 0 0 0
t 2 3 0 5 5 0 0 5 0 2 1 0 0 0 0 0 0 0 0 0
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| dyads_m3_rc_shift0 (dyads_m3_rc) |
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0.855 |
0.470 |
3.697 |
0.126 |
0.919 |
1.575 |
0.928 |
4 |
4 |
4 |
4 |
4 |
4 |
4 |
4.000 |
4 |
; dyads_m1 versus dyads_m3_rc; m=3/3; ncol2=11; w=11; offset=0; strand=R; shift=0; score= 4; waTTTGATCkr---------
; cor=0.855; Ncor=0.470; logoDP=3.697; NIcor=0.126; NsEucl=0.919; SSD=1.575; NSW=0.928; rcor=4; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.000; match_rank=4
a 6 7 0 0 0 0 11 0 0 2 4 0 0 0 0 0 0 0 0 0
c 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
g 1 2 0 0 0 11 0 0 0 3 3 0 0 0 0 0 0 0 0 0
t 4 2 11 11 11 0 0 11 0 6 2 0 0 0 0 0 0 0 0 0
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One-to-n matrix alignment; reference matrix: dyads_m2_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_m2_shift0 (dyads_m2) |
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; dyads_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; wwwTTGAystagATCAAtww
; Alignment reference
a 12 8 11 1 0 3 27 0 6 6 15 5 26 2 0 28 26 4 11 9
c 4 5 4 0 1 0 0 12 9 4 3 5 1 0 26 0 2 0 2 1
g 3 3 4 1 0 25 0 3 7 3 5 14 1 0 0 0 0 5 0 5
t 9 12 9 26 27 0 1 13 6 15 5 4 0 26 2 0 0 19 15 13
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| oligos_6nt_mkv2_shift9 (oligos_6nt_mkv2) |
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0.900 |
0.495 |
8.396 |
0.501 |
0.933 |
1.094 |
0.950 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; dyads_m2 versus oligos_6nt_mkv2; m=1/2; ncol2=11; w=11; offset=9; strand=D; shift=9; score= 2; ---------taGATCAATrw
; cor=0.900; Ncor=0.495; logoDP=8.396; NIcor=0.501; NsEucl=0.933; SSD=1.094; NSW=0.950; 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 0 0 1 2 0 5 0 0 5 5 0 3 2
c 0 0 0 0 0 0 0 0 0 1 1 0 0 0 5 0 0 0 0 0
g 0 0 0 0 0 0 0 0 0 1 1 5 0 0 0 0 0 0 2 1
t 0 0 0 0 0 0 0 0 0 2 1 0 0 5 0 0 0 5 0 2
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| dyads_m3_shift9 (dyads_m3) |
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0.829 |
0.456 |
8.052 |
0.449 |
0.913 |
1.822 |
0.917 |
5 |
5 |
3 |
3 |
5 |
5 |
5 |
4.429 |
5 |
; dyads_m2 versus dyads_m3; m=2/2; ncol2=11; w=11; offset=9; strand=D; shift=9; score= 4.4286; ---------ymGATCAAAtw
; cor=0.829; Ncor=0.456; logoDP=8.052; NIcor=0.449; NsEucl=0.913; SSD=1.822; NSW=0.917; rcor=5; rNcor=5; rlogoDP=3; rNIcor=3; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=4.429; match_rank=5
a 0 0 0 0 0 0 0 0 0 2 6 0 11 0 0 11 11 11 2 4
c 0 0 0 0 0 0 0 0 0 3 3 0 0 0 11 0 0 0 2 1
g 0 0 0 0 0 0 0 0 0 2 0 11 0 0 0 0 0 0 0 0
t 0 0 0 0 0 0 0 0 0 4 2 0 0 11 0 0 0 0 7 6
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