One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.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/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_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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| oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3) |
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; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wsAGACCAgm
; Alignment reference
a 164 115 526 0 527 0 0 527 123 194
c 79 143 1 0 0 527 524 0 99 134
g 116 145 0 527 0 0 3 0 181 79
t 168 124 0 0 0 0 0 0 124 120
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| MA0095.1_shift4 (YY1) |
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0.751 |
0.451 |
5.399 |
0.419 |
0.855 |
1.509 |
0.874 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_6nt_mkv4_m3 versus MA0095.1 (YY1); m=1/1; ncol2=6; w=6; offset=4; strand=D; shift=4; score= 1; ----rCCATc
; cor=0.751; Ncor=0.451; logoDP=5.399; NIcor=0.419; NsEucl=0.855; SSD=1.509; NSW=0.874; 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 6 0 0 17 0 3
c 0 0 0 0 1 16 17 0 0 8
g 0 0 0 0 7 0 0 0 0 3
t 0 0 0 0 3 1 0 0 17 3
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