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/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.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/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_regulonDB.tab
One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 2 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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| ECK120011229_shift3 (FNR) |
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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 ECK120011229 (FNR); m=1/1; 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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One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 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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| ECK120011229_rc_shift3 (FNR_rc) |
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0.915 |
0.641 |
6.428 |
0.637 |
0.948 |
1.060 |
0.962 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; dyads_m2 versus ECK120011229_rc (FNR_rc); m=1/1; ncol2=14; w=14; offset=3; strand=R; shift=3; score= 2; ---TTGATrtwrAtCAa---
; cor=0.915; Ncor=0.641; logoDP=6.428; NIcor=0.637; NsEucl=0.948; SSD=1.060; NSW=0.962; 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 2 2 6 79 6 29 12 29 35 57 14 2 64 48 0 0 0
c 0 0 0 0 0 5 0 11 11 11 16 3 13 8 58 6 10 0 0 0
g 0 0 0 8 1 72 0 0 23 12 10 28 3 14 10 8 8 0 0 0
t 0 0 0 73 80 0 4 66 20 48 28 17 10 47 13 5 17 0 0 0
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One-to-n matrix alignment; reference matrix: dyads_m3_shift6 ; 2 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_m3_shift6 (dyads_m3) |
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; dyads_m3; m=0 (reference); ncol1=11; shift=6; ncol=17; ------ymGATCAAAtw
; Alignment reference
a 0 0 0 0 0 0 2 6 0 11 0 0 11 11 11 2 4
c 0 0 0 0 0 0 3 3 0 0 0 11 0 0 0 2 1
g 0 0 0 0 0 0 2 0 11 0 0 0 0 0 0 0 0
t 0 0 0 0 0 0 4 2 0 0 11 0 0 0 0 7 6
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| ECK120011229_shift0 (FNR) |
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0.863 |
0.406 |
6.313 |
0.409 |
0.903 |
1.216 |
0.924 |
4 |
6 |
3 |
4 |
3 |
3 |
3 |
3.714 |
3 |
; dyads_m3 versus ECK120011229 (FNR); m=1/1; ncol2=14; w=8; offset=-6; strand=D; shift=0; score= 3.7143; tTGaTywayATCAA---
; cor=0.863; Ncor=0.406; logoDP=6.313; NIcor=0.409; NsEucl=0.903; SSD=1.216; NSW=0.924; rcor=4; rNcor=6; rlogoDP=3; rNIcor=4; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.714; match_rank=3
a 17 5 13 47 10 17 28 48 20 66 4 0 80 73 0 0 0
c 8 8 10 14 3 28 10 12 23 0 0 72 1 8 0 0 0
g 10 6 58 8 13 3 16 11 11 11 0 5 0 0 0 0 0
t 48 64 2 14 57 35 29 12 29 6 79 6 2 2 0 0 0
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One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_shift6 ; 2 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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| oligos_6nt_mkv2_shift6 (oligos_6nt_mkv2) |
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; oligos_6nt_mkv2; m=0 (reference); ncol1=11; shift=6; ncol=17; ------taGATCAATrw
; Alignment reference
a 0 0 0 0 0 0 1 2 0 5 0 0 5 5 0 3 2
c 0 0 0 0 0 0 1 1 0 0 0 5 0 0 0 0 0
g 0 0 0 0 0 0 1 1 5 0 0 0 0 0 0 2 1
t 0 0 0 0 0 0 2 1 0 0 5 0 0 0 5 0 2
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| ECK120011229_rc_shift0 (FNR_rc) |
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0.863 |
0.406 |
6.281 |
0.405 |
0.889 |
1.568 |
0.902 |
3 |
5 |
4 |
5 |
4 |
4 |
4 |
4.143 |
4 |
; oligos_6nt_mkv2 versus ECK120011229_rc (FNR_rc); m=1/1; ncol2=14; w=8; offset=-6; strand=R; shift=0; score= 4.1429; TTGATrtwrAtCAa---
; cor=0.863; Ncor=0.406; logoDP=6.281; NIcor=0.405; NsEucl=0.889; SSD=1.568; NSW=0.902; rcor=3; rNcor=5; rlogoDP=4; rNIcor=5; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.143; match_rank=4
a 2 2 6 79 6 29 12 29 35 57 14 2 64 48 0 0 0
c 0 0 5 0 11 11 11 16 3 13 8 58 6 10 0 0 0
g 8 1 72 0 0 23 12 10 28 3 14 10 8 8 0 0 0
t 73 80 0 4 66 20 48 28 17 10 47 13 5 17 0 0 0
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One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_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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| oligos_7nt_mkv2_shift0 (oligos_7nt_mkv2) |
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; oligos_7nt_mkv2; m=0 (reference); ncol1=11; shift=0; ncol=11; TsAGGAGTAhw
; Alignment reference
a 1 1 7 0 0 7 0 0 7 2 3
c 0 2 0 0 0 0 0 0 0 2 0
g 0 3 0 7 7 0 7 0 0 0 1
t 6 1 0 0 0 0 0 7 0 3 3
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| ECK120011508_rc_shift2 (NarP_rc) |
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0.789 |
0.574 |
0.939 |
-0.161 |
0.874 |
2.044 |
0.872 |
5 |
3 |
6 |
6 |
5 |
5 |
5 |
5.000 |
5 |
; oligos_7nt_mkv2 versus ECK120011508_rc (NarP_rc); m=1/2; ncol2=8; w=8; offset=2; strand=R; shift=2; score= 5; --AgrrGTAk-
; cor=0.789; Ncor=0.574; logoDP=0.939; NIcor=-0.161; NsEucl=0.874; SSD=2.044; NSW=0.872; rcor=5; rNcor=3; rlogoDP=6; rNIcor=6; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=5.000; match_rank=5
a 0 0 14 4 5 6 0 0 20 2 0
c 0 0 3 0 2 1 0 2 0 0 0
g 0 0 2 12 10 13 16 0 0 9 0
t 0 0 1 4 3 0 4 18 0 9 0
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| ECK120011502_shift1 (NarL) |
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0.764 |
0.555 |
4.299 |
0.537 |
0.866 |
2.289 |
0.857 |
6 |
4 |
5 |
3 |
6 |
6 |
6 |
5.143 |
6 |
; oligos_7nt_mkv2 versus ECK120011502 (NarL); m=2/2; ncol2=8; w=8; offset=1; strand=D; shift=1; score= 5.1429; -wakrrkTA--
; cor=0.764; Ncor=0.555; logoDP=4.299; NIcor=0.537; NsEucl=0.866; SSD=2.289; NSW=0.857; rcor=6; rNcor=4; rlogoDP=5; rNIcor=3; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=5.143; match_rank=6
a 0 38 54 8 25 41 9 0 86 0 0
c 0 4 9 0 12 5 0 4 0 0 0
g 0 17 15 36 45 45 54 2 0 0 0
t 0 32 13 47 9 0 28 85 5 0 0
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