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_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.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_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_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_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1) |
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; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; wwTATYTkKAww
; Alignment reference
a | 1274 1387 0 4484 0 0 0 0 0 4484 1227 1330
c | 685 584 0 0 0 1204 0 0 0 0 707 1019
g | 685 1071 0 0 0 0 0 1682 1241 0 715 758
t | 1840 1442 4484 0 4484 3280 4484 2802 3243 0 1835 1377
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| Antp_rc_shift0 (Antp_rc) |
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0.858 |
0.429 |
3.592 |
0.239 |
0.890 |
0.875 |
0.927 |
1 |
2 |
1 |
1 |
2 |
1 |
1 |
1.286 |
1 |
; oligos_7nt_mkv5_m1 versus Antp_rc; m=1/2; ncol2=6; w=6; offset=0; strand=R; shift=0; score= 1.2857; wTTATk------
; cor=0.858; Ncor=0.429; logoDP=3.592; NIcor=0.239; NsEucl=0.890; SSD=0.875; NSW=0.927; rcor=1; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a | 10.5 0 0 18 0 0 0 0 0 0 0 0
c | 0 0 1.5 0 0 3 0 0 0 0 0 0
g | 0 0 0 0 0 4.5 0 0 0 0 0 0
t | 7.5 18 16.5 0 18 10.5 0 0 0 0 0 0
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| br-Z1_rc_shift4 (br-Z1_rc) |
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0.802 |
0.535 |
1.425 |
0.089 |
0.901 |
1.244 |
0.922 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1.714 |
2 |
; oligos_7nt_mkv5_m1 versus br-Z1_rc; m=2/2; ncol2=8; w=8; offset=4; strand=R; shift=4; score= 1.7143; ----TTwGtAty
; cor=0.802; Ncor=0.535; logoDP=1.425; NIcor=0.089; NsEucl=0.901; SSD=1.244; NSW=0.922; rcor=2; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.714; match_rank=2
a | 0 0 0 0 0 0 7.41176 0 0 14.8235 3.17647 0
c | 0 0 0 0 0 0 0 2.11765 3.17647 1.05882 3.17647 7.41176
g | 0 0 0 0 0 2.11765 1.05882 12.7059 3.17647 0 0 0
t | 0 0 0 0 18 15.8824 9.52941 3.17647 11.6471 2.11765 11.6471 10.5882
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