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/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3.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/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_vs_db_Schmidt_CEBPa_motif
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m3_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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| oligos_8nt_mkv6_m3_shift0 (oligos_8nt_mkv6_m3) |
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; oligos_8nt_mkv6_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; wtATTGAGCAATaw
; Alignment reference
a 1041 669 2747 14 15 176 2352 4 72 3314 3314 89 1418 955
c 573 505 180 6 5 9 210 10 3149 10 9 291 657 749
g 791 682 325 9 20 3053 96 3305 6 4 4 213 534 676
t 930 1479 83 3306 3295 97 677 16 108 7 8 2742 726 955
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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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0.881 |
0.692 |
4.135 |
0.136 |
0.925 |
1.378 |
0.937 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_8nt_mkv6_m3 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=0.881; Ncor=0.692; logoDP=4.135; NIcor=0.136; NsEucl=0.925; SSD=1.378; NSW=0.937; 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
c 0 60 78 0 0 0 85 0 365 0 0 138 0 0
g 0 145 169 0 130 258 48 431 0 0 0 69 0 0
t 0 143 1 431 300 80 259 0 35 0 0 204 0 0
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