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/positions_7nt_m2/peak-motifs_positions_7nt_m2.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/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift1 ; 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 |
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| positions_7nt_m2_shift1 (positions_7nt_m2) |
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; positions_7nt_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -wwATATAAGkb
; Alignment reference
a 0 2 3 7 0 7 0 7 7 0 0 1
c 0 1 1 0 0 0 0 0 0 0 1 2
g 0 1 1 0 0 0 0 0 0 7 3 2
t 0 3 2 0 7 0 7 0 0 0 3 2
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| MA0033.1_shift0 (FOXL1) |
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0.854 |
0.498 |
4.621 |
0.481 |
0.895 |
1.090 |
0.922 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m2 versus MA0033.1 (FOXL1); m=1/2; ncol2=8; w=7; offset=-1; strand=D; shift=0; score= 1; wwdayATA----
; cor=0.854; Ncor=0.498; logoDP=4.621; NIcor=0.481; NsEucl=0.895; SSD=1.090; NSW=0.922; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 7 10 6 13 4 21 0 22 0 0 0 0
c 1 4 3 4 10 0 2 1 0 0 0 0
g 4 2 6 4 2 2 0 0 0 0 0 0
t 11 7 8 2 7 0 21 0 0 0 0 0
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| MA0124.1_rc_shift6 (NKX3-1_rc) |
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0.808 |
0.404 |
2.199 |
0.041 |
0.860 |
1.421 |
0.882 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; positions_7nt_m2 versus MA0124.1_rc (NKX3-1_rc); m=2/2; ncol2=7; w=6; offset=5; strand=R; shift=6; score= 2; ------TAAGTA
; cor=0.808; Ncor=0.404; logoDP=2.199; NIcor=0.041; NsEucl=0.860; SSD=1.421; NSW=0.882; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 0 0 0 0 0 0 19 19 1 0 19
c 0 0 0 0 0 0 1 0 0 0 0 0
g 0 0 0 0 0 0 0 0 0 19 0 1
t 0 0 0 0 0 0 19 1 1 0 20 0
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