One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.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/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_jaspar_core_vertebrates
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=17; shift=0; ncol=17; ccGCCCCCCAGCCCCss
; Alignment reference
a 2 6 3 5 0 2 0 0 0 18 1 0 0 2 1 4 5
c 13 11 0 19 22 23 24 25 24 3 3 24 21 22 25 8 8
g 6 5 23 0 2 1 2 1 2 3 22 1 2 1 0 10 9
t 5 4 0 2 2 0 0 0 0 2 0 1 3 1 0 4 4
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| MA0079.2_shift6 (SP1) |
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0.822 |
0.483 |
5.411 |
0.472 |
0.910 |
1.631 |
0.918 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; dyads_m1 versus MA0079.2 (SP1); m=1/1; ncol2=10; w=10; offset=6; strand=D; shift=6; score= 1; ------CCCCkCCCCC-
; cor=0.822; Ncor=0.483; logoDP=5.411; NIcor=0.472; NsEucl=0.910; SSD=1.631; NSW=0.918; 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 0 0 0 0 0 0 4 2 0 1 0 6 3 0
c 0 0 0 0 0 0 32 30 35 27 5 28 31 24 25 26 0
g 0 0 0 0 0 0 1 1 0 0 15 1 0 3 0 3 0
t 0 0 0 0 0 0 2 4 0 4 13 6 3 8 4 3 0
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