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_m2/peak-motifs_positions_7nt_m2.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_m2/peak-motifs_positions_7nt_m2_vs_db_Schmidt_CEBPa_motif
One-to-n matrix alignment; reference matrix: positions_7nt_m2_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_m2_shift0 (positions_7nt_m2) |
|
  |
  |
  |
  |
  |
  |
  |
  |
  |
  |
  |
  |
  |
  |
  |
  |
; positions_7nt_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; rmAGATTGCACAACTyt
; Alignment reference
a 94 132 260 16 314 0 0 10 2 311 7 331 333 6 35 67 73
c 71 85 4 10 5 0 0 0 330 11 318 3 0 296 15 105 76
g 95 77 9 277 13 1 2 309 1 1 1 0 0 7 2 77 54
t 74 40 61 31 2 333 332 15 1 11 8 0 1 25 282 85 131
|
do560+do843_mmus_cebpa_liver_meme_top_m1_shift4 (do560+do843_mmus_cebpa_liver_meme_top_m1) |
|
0.869 |
0.563 |
9.570 |
0.543 |
0.913 |
1.819 |
0.917 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m2 versus do560+do843_mmus_cebpa_liver_meme_top_m1; m=1/1; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 1; ----rTTGCacMAym--
; cor=0.869; Ncor=0.563; logoDP=9.570; NIcor=0.543; NsEucl=0.913; SSD=1.819; NSW=0.917; 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 0 204 0 0 35 0 259 80 300 431 1 143 0 0
c 0 0 0 0 69 0 0 0 431 48 258 130 0 169 145 0 0
g 0 0 0 0 138 0 0 365 0 85 0 0 0 78 60 0 0
t 0 0 0 0 20 431 431 31 0 39 93 1 0 183 83 0 0
|