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_m4/peak-motifs_oligos_8nt_mkv6_m4.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_m4/peak-motifs_oligos_8nt_mkv6_m4_vs_db_Schmidt_CEBPa_motif
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m4_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_m4_shift0 (oligos_8nt_mkv6_m4) |
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; oligos_8nt_mkv6_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; wrTTACACAATah
; Alignment reference
a 768 1278 9 3 2545 2 2026 1 2529 2545 143 934 674
c 372 377 3 0 0 2552 7 2516 4 1 447 595 648
g 562 670 8 10 10 2 516 0 21 8 179 403 433
t 862 239 2544 2551 9 8 15 47 10 10 1795 632 809
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| do560+do843_mmus_cebpa_liver_meme_top_m1_shift1 (do560+do843_mmus_cebpa_liver_meme_top_m1) |
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0.800 |
0.677 |
8.714 |
0.660 |
0.906 |
2.155 |
0.902 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_8nt_mkv6_m4 versus do560+do843_mmus_cebpa_liver_meme_top_m1; m=1/1; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 1; -rTTGCacMAym-
; cor=0.800; Ncor=0.677; logoDP=8.714; NIcor=0.660; NsEucl=0.906; SSD=2.155; NSW=0.902; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 204 0 0 35 0 259 80 300 431 1 143 0
c 0 69 0 0 0 431 48 258 130 0 169 145 0
g 0 138 0 0 365 0 85 0 0 0 78 60 0
t 0 20 431 431 31 0 39 93 1 0 183 83 0
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