One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.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 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_Schmidt_CEBPa_motif
One-to-n matrix alignment; reference matrix: positions_7nt_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_7nt_m1_shift0 (positions_7nt_m1) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; wtATTTCACAATCwy
; Alignment reference
a 394 218 1344 6 10 132 6 1281 17 1366 1387 18 237 486 348
c 277 242 17 9 7 9 1392 26 1335 33 4 63 1048 300 369
g 313 341 33 4 46 166 3 48 5 1 6 13 43 155 231
t 419 602 9 1384 1340 1096 2 48 46 3 6 1309 75 462 455
|
| do560+do843_mmus_cebpa_liver_meme_top_m1_shift2 (do560+do843_mmus_cebpa_liver_meme_top_m1) |
 |
0.796 |
0.583 |
8.448 |
0.547 |
0.898 |
2.497 |
0.886 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m1 versus do560+do843_mmus_cebpa_liver_meme_top_m1; m=1/1; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 1; --rTTGCacMAym--
; cor=0.796; Ncor=0.583; logoDP=8.448; NIcor=0.547; NsEucl=0.898; SSD=2.497; NSW=0.886; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 204 0 0 35 0 259 80 300 431 1 143 0 0
c 0 0 69 0 0 0 431 48 258 130 0 169 145 0 0
g 0 0 138 0 0 365 0 85 0 0 0 78 60 0 0
t 0 0 20 431 431 31 0 39 93 1 0 183 83 0 0
|