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_m5/peak-motifs_positions_7nt_m5.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_m5/peak-motifs_positions_7nt_m5_vs_db_Schmidt_CEBPa_motif
One-to-n matrix alignment; reference matrix: positions_7nt_m5_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_m5_shift0 (positions_7nt_m5) |
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; positions_7nt_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; wmACATTGCACAACTsy
; Alignment reference
a 73 84 193 16 219 0 0 4 0 221 11 226 224 2 20 52 44
c 48 64 6 163 4 0 0 0 227 3 213 1 0 205 12 64 62
g 45 44 16 18 0 0 3 206 0 1 1 0 1 4 0 58 48
t 62 36 13 31 5 228 225 18 1 3 3 1 3 17 196 54 74
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| do560+do843_mmus_cebpa_liver_meme_top_m1_shift4 (do560+do843_mmus_cebpa_liver_meme_top_m1) |
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0.863 |
0.558 |
9.473 |
0.537 |
0.911 |
1.916 |
0.913 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m5 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=0.863; Ncor=0.558; logoDP=9.473; NIcor=0.537; NsEucl=0.911; SSD=1.916; NSW=0.913; 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
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