One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.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/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/oligos_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift0 ; 4 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 |
|---|
| oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2) |
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; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; rwrTGAsTCATty
; Alignment reference
a 169 181 354 0 0 602 45 0 87 602 16 139 146
c 139 111 41 0 0 1 263 0 516 0 63 133 174
g 162 146 192 0 603 0 243 1 0 1 41 148 115
t 133 165 16 603 0 0 52 602 0 0 483 183 168
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| MA0099.2_rc_shift3 (AP1_rc) |
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0.951 |
0.512 |
6.533 |
0.518 |
0.933 |
0.441 |
0.969 |
1 |
1 |
1 |
1 |
1 |
2 |
2 |
1.286 |
1 |
; oligos_7nt_mkv4_m2 versus MA0099.2_rc (AP1_rc); m=1/3; ncol2=7; w=7; offset=3; strand=R; shift=3; score= 1.2857; ---TGAkTCA---
; cor=0.951; Ncor=0.512; logoDP=6.533; NIcor=0.518; NsEucl=0.933; SSD=0.441; NSW=0.969; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.286; match_rank=1
a 0 0 0 1 0 14 0 0 3 17 0 0 0
c 0 0 0 1 3 1 1 0 15 0 0 0 0
g 0 0 0 0 15 0 12 2 0 1 0 0 0
t 0 0 0 16 0 3 5 16 0 0 0 0 0
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| MA0089.1_rc_shift6 (NFE2L1::MafG_rc) |
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0.942 |
0.435 |
0.077 |
-0.104 |
0.931 |
0.340 |
0.972 |
2 |
3 |
3 |
2 |
2 |
1 |
1 |
2.000 |
2 |
; oligos_7nt_mkv4_m2 versus MA0089.1_rc (NFE2L1::MafG_rc); m=2/3; ncol2=6; w=6; offset=6; strand=R; shift=6; score= 2; ------GTCATs-
; cor=0.942; Ncor=0.435; logoDP=0.077; NIcor=-0.104; NsEucl=0.931; SSD=0.340; NSW=0.972; rcor=2; rNcor=3; rlogoDP=3; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=2.000; match_rank=2
a 0 0 0 0 0 0 6 0 1 34 0 6 0
c 0 0 0 0 0 0 2 0 32 0 3 10 0
g 0 0 0 0 0 0 26 0 0 0 2 11 0
t 0 0 0 0 0 0 0 34 1 0 29 7 0
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| MA0067.1_rc_shift0 (Pax2_rc) |
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0.767 |
0.472 |
0.370 |
-0.142 |
0.896 |
1.379 |
0.914 |
3 |
2 |
2 |
3 |
3 |
3 |
3 |
2.714 |
3 |
; oligos_7nt_mkv4_m2 versus MA0067.1_rc (Pax2_rc); m=3/3; ncol2=8; w=8; offset=0; strand=R; shift=0; score= 2.7143; vmrTGAcw-----
; cor=0.767; Ncor=0.472; logoDP=0.370; NIcor=-0.142; NsEucl=0.896; SSD=1.379; NSW=0.914; rcor=3; rNcor=2; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.714; match_rank=3
a 8 10 11 1 2 26 2 9 0 0 0 0 0
c 11 19 1 3 1 0 21 5 0 0 0 0 0
g 11 0 17 1 28 2 1 7 0 0 0 0 0
t 1 2 2 26 0 3 7 10 0 0 0 0 0
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