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/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.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_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_regulonDB
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 |
|---|
| 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 |
1 |
1 |
2 |
2 |
1 |
1 |
1 |
1.286 |
1 |
; oligos_7nt_mkv2 versus ECK120011508_rc (NarP_rc); m=1/2; ncol2=8; w=8; offset=2; strand=R; shift=2; score= 1.2857; --AgrrGTAk-
; cor=0.789; Ncor=0.574; logoDP=0.939; NIcor=-0.161; NsEucl=0.874; SSD=2.044; NSW=0.872; rcor=1; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
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 |
2 |
2 |
1 |
1 |
2 |
2 |
2 |
1.714 |
2 |
; oligos_7nt_mkv2 versus ECK120011502 (NarL); m=2/2; ncol2=8; w=8; offset=1; strand=D; shift=1; score= 1.7143; -wakrrkTA--
; cor=0.764; Ncor=0.555; logoDP=4.299; NIcor=0.537; NsEucl=0.866; SSD=2.289; NSW=0.857; rcor=2; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.714; match_rank=2
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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