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_6nt_m1/peak-motifs_positions_6nt_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_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_Schmidt_CEBPa_motif
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 |
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| positions_6nt_m1_shift0 (positions_6nt_m1) |
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; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; wwAGATTGTGAAAtm
; Alignment reference
a 357 259 768 43 865 5 8 36 26 3 721 847 870 59 359
c 127 176 19 23 8 5 2 2 40 1 79 31 2 182 239
g 172 215 31 695 16 3 17 850 7 885 6 5 14 114 107
t 237 243 75 132 4 880 866 5 820 4 87 10 7 538 188
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| do560+do843_mmus_cebpa_liver_meme_top_m1_rc_shift3 (do560+do843_mmus_cebpa_liver_meme_top_m1_rc) |
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0.795 |
0.583 |
3.785 |
0.125 |
0.901 |
2.363 |
0.893 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_6nt_m1 versus do560+do843_mmus_cebpa_liver_meme_top_m1_rc; m=1/1; ncol2=11; w=11; offset=3; strand=R; shift=3; score= 1; ---krTKgtGCAAy-
; cor=0.795; Ncor=0.583; logoDP=3.785; NIcor=0.125; NsEucl=0.901; SSD=2.363; NSW=0.893; 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 83 183 0 1 93 39 0 31 431 431 20 0
c 0 0 0 60 78 0 0 0 85 0 365 0 0 138 0
g 0 0 0 145 169 0 130 258 48 431 0 0 0 69 0
t 0 0 0 143 1 431 300 80 259 0 35 0 0 204 0
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