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_m4/peak-motifs_positions_7nt_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/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_Schmidt_CEBPa_motif
One-to-n matrix alignment; reference matrix: positions_7nt_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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| positions_7nt_m4_shift0 (positions_7nt_m4) |
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; positions_7nt_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; wyCTCTTGCACAACTbh
; Alignment reference
a 53 47 13 1 20 0 1 2 0 180 11 195 197 3 6 36 50
c 42 60 160 8 160 0 0 0 198 8 185 2 1 178 15 53 54
g 45 38 9 0 18 0 1 189 1 3 1 1 0 3 3 54 24
t 59 54 17 190 1 199 197 8 0 8 2 1 1 15 175 56 71
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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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0.834 |
0.540 |
9.481 |
0.527 |
0.906 |
2.141 |
0.903 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m4 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=0.834; Ncor=0.540; logoDP=9.481; NIcor=0.527; NsEucl=0.906; SSD=2.141; NSW=0.903; 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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