One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.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 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_jaspar_core_insects
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift0 ; 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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| 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=11; yaTACATAta-
; Alignment reference
a | 1566 3368 0 7443 0 7443 0 7443 1588 3283 0
c | 1981 835 0 0 7443 0 0 0 1762 858 0
g | 900 1799 0 0 0 0 0 0 757 1698 0
t | 2996 1441 7443 0 0 0 7443 0 3336 1604 0
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| MA0015.1_rc_shift1 (Cf2_II_rc) |
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0.825 |
0.675 |
6.525 |
0.570 |
0.902 |
1.544 |
0.914 |
2 |
1 |
1 |
1 |
1 |
2 |
1 |
1.286 |
1 |
; oligos_6nt_mkv4_m3 versus MA0015.1_rc (Cf2_II_rc); m=1/2; ncol2=10; w=9; offset=1; strand=R; shift=1; score= 1.2857; -ryAyATATAy
; cor=0.825; Ncor=0.675; logoDP=6.525; NIcor=0.570; NsEucl=0.902; SSD=1.544; NSW=0.914; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.286; match_rank=1
a | 0 24 4 68 1 74 0 67 0 76 2
c | 0 15 20 1 36 1 0 4 4 1 40
g | 0 29 3 9 2 4 2 9 2 2 13
t | 0 12 53 2 41 1 78 0 74 1 25
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| MA0210.1_shift1 (ara) |
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0.828 |
0.414 |
6.119 |
0.401 |
0.859 |
1.000 |
0.900 |
1 |
2 |
2 |
2 |
2 |
1 |
2 |
1.714 |
2 |
; oligos_6nt_mkv4_m3 versus MA0210.1 (ara); m=2/2; ncol2=5; w=5; offset=1; strand=D; shift=1; score= 1.7143; -wwACA-----
; cor=0.828; Ncor=0.414; logoDP=6.119; NIcor=0.401; NsEucl=0.859; SSD=1.000; NSW=0.900; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=2; rank_mean=1.714; match_rank=2
a | 0 14 23 34 0 34 0 0 0 0 0
c | 0 0 0 0 34 0 0 0 0 0 0
g | 0 5 0 0 0 0 0 0 0 0 0
t | 0 15 11 0 0 0 0 0 0 0 0
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