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/positions_6nt_m3/peak-motifs_positions_6nt_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/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_jaspar_core_insects
One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 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 |
|---|
| positions_6nt_m3_shift0 (positions_6nt_m3) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; positions_6nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wrCAGGTAra
; Alignment reference
a | 1036 986 0 3557 0 0 0 3557 1228 1214
c | 764 745 3557 0 0 0 0 0 538 770
g | 860 1059 0 0 3557 3557 0 0 1249 762
t | 897 767 0 0 0 0 3557 0 542 811
|
| MA0086.1_shift2 (sna) |
 |
0.777 |
0.466 |
8.354 |
0.471 |
0.837 |
1.924 |
0.840 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_6nt_m3 versus MA0086.1 (sna); m=1/1; ncol2=6; w=6; offset=2; strand=D; shift=2; score= 1; --CAGGTG--
; cor=0.777; Ncor=0.466; logoDP=8.354; NIcor=0.471; NsEucl=0.837; SSD=1.924; NSW=0.840; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a | 0 0 0 39 3 2 0 0 0 0
c | 0 0 39 0 0 0 0 0 0 0
g | 0 0 1 0 37 38 0 38 0 0
t | 0 0 0 1 0 0 40 2 0 0
|