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_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.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_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_jaspar_core_insects
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift4 ; 5 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_m2_shift4 (oligos_7nt_mkv5_m2) |
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; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----waAACAyAAww
; Alignment reference
a | 0 0 0 0 2194 2297 6636 6636 0 6636 0 6636 6636 2283 2203
c | 0 0 0 0 1355 1342 0 0 5129 0 3468 0 0 1367 1387
g | 0 0 0 0 1234 1358 0 0 0 0 1211 0 0 1096 1135
t | 0 0 0 0 1853 1639 0 0 1507 0 1957 0 0 1890 1911
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| MA0233.1_shift5 (mirr) |
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0.930 |
0.423 |
5.396 |
0.419 |
0.913 |
0.382 |
0.962 |
1 |
1 |
3 |
1 |
1 |
1 |
1 |
1.286 |
1 |
; oligos_7nt_mkv5_m2 versus MA0233.1 (mirr); m=1/4; ncol2=5; w=5; offset=1; strand=D; shift=5; score= 1.2857; -----wAACA-----
; cor=0.930; Ncor=0.423; logoDP=5.396; NIcor=0.419; NsEucl=0.913; SSD=0.382; NSW=0.962; rcor=1; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a | 0 0 0 0 0 20 29 41 0 41 0 0 0 0 0
c | 0 0 0 0 0 1 0 0 41 0 0 0 0 0 0
g | 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0
t | 0 0 0 0 0 19 10 0 0 0 0 0 0 0 0
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| MA0210.1_shift5 (ara) |
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0.926 |
0.421 |
5.467 |
0.417 |
0.911 |
0.399 |
0.960 |
2 |
2 |
1 |
2 |
2 |
2 |
2 |
1.857 |
2 |
; oligos_7nt_mkv5_m2 versus MA0210.1 (ara); m=2/4; ncol2=5; w=5; offset=1; strand=D; shift=5; score= 1.8571; -----wwACA-----
; cor=0.926; Ncor=0.421; logoDP=5.467; NIcor=0.417; NsEucl=0.911; SSD=0.399; NSW=0.960; rcor=2; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.857; match_rank=2
a | 0 0 0 0 0 14 23 34 0 34 0 0 0 0 0
c | 0 0 0 0 0 0 0 0 34 0 0 0 0 0 0
g | 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0
t | 0 0 0 0 0 15 11 0 0 0 0 0 0 0 0
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| MA0217.1_shift5 (caup) |
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0.926 |
0.421 |
5.404 |
0.412 |
0.910 |
0.407 |
0.959 |
3 |
3 |
2 |
3 |
3 |
3 |
3 |
2.857 |
3 |
; oligos_7nt_mkv5_m2 versus MA0217.1 (caup); m=3/4; ncol2=5; w=5; offset=1; strand=D; shift=5; score= 2.8571; -----tAACA-----
; cor=0.926; Ncor=0.421; logoDP=5.404; NIcor=0.412; NsEucl=0.910; SSD=0.407; NSW=0.959; rcor=3; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.857; match_rank=3
a | 0 0 0 0 0 4 14 19 0 19 0 0 0 0 0
c | 0 0 0 0 0 1 0 0 19 0 0 0 0 0 0
g | 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0
t | 0 0 0 0 0 12 3 0 0 0 0 0 0 0 0
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| MA0458.1_rc_shift0 (slp1_rc) |
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0.866 |
0.404 |
0.606 |
-0.012 |
0.902 |
0.945 |
0.932 |
4 |
4 |
4 |
4 |
4 |
4 |
4 |
4.000 |
4 |
; oligos_7nt_mkv5_m2 versus MA0458.1_rc (slp1_rc); m=4/4; ncol2=11; w=7; offset=-4; strand=R; shift=0; score= 4; wryrtAAACAm----
; cor=0.866; Ncor=0.404; logoDP=0.606; NIcor=-0.012; NsEucl=0.902; SSD=0.945; NSW=0.932; rcor=4; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.000; match_rank=4
a | 19 21 1 11 10 39 40 41 0 41 16 0 0 0 0
c | 4 3 15 7 4 2 1 0 38 0 14 0 0 0 0
g | 3 13 8 22 0 0 0 0 0 0 3 0 0 0 0
t | 15 4 17 1 27 0 0 0 3 0 8 0 0 0 0
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