One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: positions_6nt_m1_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_m1_shift0 (positions_6nt_m1) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd
; Alignment reference
a | 338 299 421 1039 1054 828 0 0 0 3 8 840 779 305 274
c | 216 265 122 1 2 15 1 0 0 0 4 1 89 195 240
g | 316 275 453 11 13 223 1073 1071 1074 27 1 232 103 393 287
t | 204 235 78 23 5 8 0 3 0 1044 1061 1 103 181 273
|
| positions_7nt_m1_shift0 (positions_7nt_m1) |
 |
0.996 |
0.996 |
12.961 |
0.997 |
0.990 |
0.047 |
0.998 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_6nt_m1 versus positions_7nt_m1; m=1/1; ncol2=15; w=15; offset=0; strand=D; shift=0; score= 1; rrrAAAGGGTTAArd
; cor=0.996; Ncor=0.996; logoDP=12.961; NIcor=0.997; NsEucl=0.990; SSD=0.047; NSW=0.998; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a | 325 287 388 918 991 801 0 0 0 1 1 821 814 317 252
c | 201 244 235 0 1 5 0 0 0 0 0 0 49 162 228
g | 288 256 319 72 12 200 1008 1008 1008 10 0 187 73 370 271
t | 194 221 66 18 4 2 0 0 0 997 1007 0 72 159 257
|