One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.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/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift0 ; 3 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_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4) |
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; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; ccyCCACCTCss
; Alignment reference
a 94 140 65 6 3 595 4 5 35 1 150 89
c 361 304 239 718 703 3 722 704 2 729 276 248
g 131 130 122 7 18 130 1 19 60 2 203 234
t 147 159 307 2 9 5 6 5 636 1 104 162
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| MA0130.1_shift1 (ZNF354C) |
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0.949 |
0.474 |
5.659 |
0.480 |
0.932 |
0.336 |
0.972 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_7nt_mkv5_m4 versus MA0130.1 (ZNF354C); m=1/2; ncol2=6; w=6; offset=1; strand=D; shift=1; score= 1; -mTCCAC-----
; cor=0.949; Ncor=0.474; logoDP=5.659; NIcor=0.480; NsEucl=0.932; SSD=0.336; NSW=0.972; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 7 3 0 0 16 0 0 0 0 0 0
c 0 6 2 16 16 0 15 0 0 0 0 0
g 0 3 0 0 0 0 1 0 0 0 0 0
t 0 0 11 0 0 0 0 0 0 0 0 0
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| MA0103.1_shift4 (ZEB1) |
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0.808 |
0.404 |
5.190 |
0.416 |
0.863 |
1.351 |
0.887 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; oligos_7nt_mkv5_m4 versus MA0103.1 (ZEB1); m=2/2; ncol2=6; w=6; offset=4; strand=D; shift=4; score= 2; ----CACCTk--
; cor=0.808; Ncor=0.404; logoDP=5.190; NIcor=0.416; NsEucl=0.863; SSD=1.351; NSW=0.887; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 0 0 0 1 38 0 0 0 10 0 0
c 0 0 0 0 34 0 40 38 1 1 0 0
g 0 0 0 0 1 2 1 3 0 16 0 0
t 0 0 0 0 5 1 0 0 40 14 0 0
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