One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.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/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift2 ; 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_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4) |
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; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --aaACAAAAACaa
; Alignment reference
a 0 0 596 606 1117 0 1138 1144 1145 1145 1145 0 621 489
c 0 0 148 179 6 1145 0 0 0 0 0 1145 225 198
g 0 0 165 156 9 0 7 0 0 0 0 0 78 212
t 0 0 236 204 13 0 0 1 0 0 0 0 221 246
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| MA0084.1_shift0 (SRY) |
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0.847 |
0.424 |
6.343 |
0.414 |
0.893 |
1.115 |
0.920 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_7nt_mkv5_m4 versus MA0084.1 (SRY); m=1/1; ncol2=9; w=7; offset=-2; strand=D; shift=0; score= 1; kwwaACAAw-----
; cor=0.847; Ncor=0.424; logoDP=6.343; NIcor=0.414; NsEucl=0.893; SSD=1.115; NSW=0.920; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 5 8 15 18 25 0 28 27 7 0 0 0 0 0
c 5 3 0 3 0 26 0 0 0 0 0 0 0 0
g 10 4 3 3 0 0 0 1 2 0 0 0 0 0
t 8 13 10 4 3 2 0 0 19 0 0 0 0 0
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