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_m2/peak-motifs_positions_6nt_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_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_Schmidt_CEBPa_motif
One-to-n matrix alignment; reference matrix: positions_6nt_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 |
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| positions_6nt_m2_shift0 (positions_6nt_m2) |
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; positions_6nt_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; dkATTACGCAAGArw
; Alignment reference
a 201 156 603 2 1 580 30 65 11 668 668 9 620 178 200
c 107 113 23 2 2 3 534 20 638 1 0 57 15 145 138
g 172 198 33 1 11 48 28 569 1 0 1 531 14 185 143
t 189 202 10 664 655 38 77 15 19 0 0 72 20 161 188
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| do560+do843_mmus_cebpa_liver_meme_top_m1_rc_shift1 (do560+do843_mmus_cebpa_liver_meme_top_m1_rc) |
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0.768 |
0.563 |
4.172 |
0.096 |
0.898 |
2.497 |
0.886 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_6nt_m2 versus do560+do843_mmus_cebpa_liver_meme_top_m1_rc; m=1/1; ncol2=11; w=11; offset=1; strand=R; shift=1; score= 1; -krTKgtGCAAy---
; cor=0.768; Ncor=0.563; logoDP=4.172; NIcor=0.096; 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 83 183 0 1 93 39 0 31 431 431 20 0 0 0
c 0 60 78 0 0 0 85 0 365 0 0 138 0 0 0
g 0 145 169 0 130 258 48 431 0 0 0 69 0 0 0
t 0 143 1 431 300 80 259 0 35 0 0 204 0 0 0
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