One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/oligos_6nt_mkv3/peak-motifs_oligos_6nt_mkv3.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/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/oligos_6nt_mkv3/peak-motifs_oligos_6nt_mkv3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_shift2 ; 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_6nt_mkv3_shift2 (oligos_6nt_mkv3) |
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; oligos_6nt_mkv3; m=0 (reference); ncol1=12; shift=2; ncol=14; --hkGAAGAGATcd
; Alignment reference
a 0 0 3 2 0 12 12 0 12 0 12 0 2 4
c 0 0 4 2 0 0 0 0 0 0 0 0 8 1
g 0 0 2 4 12 0 0 12 0 12 0 1 2 4
t 0 0 3 4 0 0 0 0 0 0 0 11 0 3
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| MA0080.1_shift2 (SPI1) |
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0.878 |
0.439 |
5.219 |
0.428 |
0.901 |
0.712 |
0.941 |
1 |
2 |
2 |
1 |
1 |
1 |
1 |
1.286 |
1 |
; oligos_6nt_mkv3 versus MA0080.1 (SPI1); m=1/2; ncol2=6; w=6; offset=0; strand=D; shift=2; score= 1.2857; --sGGAAs------
; cor=0.878; Ncor=0.439; logoDP=5.219; NIcor=0.428; NsEucl=0.901; SSD=0.712; NSW=0.941; rcor=1; rNcor=2; rlogoDP=2; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a 0 0 14 4 3 56 56 3 0 0 0 0 0 0
c 0 0 21 2 0 1 0 18 0 0 0 0 0 0
g 0 0 19 48 52 0 0 34 0 0 0 0 0 0
t 0 0 3 3 2 0 1 2 0 0 0 0 0 0
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| MA0062.1_shift0 (GABPA) |
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0.809 |
0.462 |
8.128 |
0.420 |
0.884 |
1.722 |
0.892 |
2 |
1 |
1 |
2 |
2 |
2 |
2 |
1.714 |
2 |
; oligos_6nt_mkv3 versus MA0062.1 (GABPA); m=2/2; ncol2=10; w=8; offset=-2; strand=D; shift=0; score= 1.7143; ACCGGAAGws----
; cor=0.809; Ncor=0.462; logoDP=8.128; NIcor=0.420; NsEucl=0.884; SSD=1.722; NSW=0.892; rcor=2; rNcor=1; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.714; match_rank=2
a 5 1 1 0 0 7 7 0 3 0 0 0 0 0
c 1 5 6 0 0 0 0 0 1 2 0 0 0 0
g 1 1 0 7 7 0 0 7 1 4 0 0 0 0
t 0 0 0 0 0 0 0 0 2 1 0 0 0 0
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