One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.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/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_footprintDB
One-to-n matrix alignment; reference matrix: positions_7nt_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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| positions_7nt_m4_shift0 (positions_7nt_m4) |
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; positions_7nt_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; dymCCCyAGCCAyy
; Alignment reference
a 3 1 5 1 0 1 0 11 1 0 0 11 1 2
c 1 4 3 9 10 8 5 0 0 11 11 0 4 6
g 4 1 1 0 0 1 1 0 10 0 0 0 1 0
t 3 5 2 1 1 1 5 0 0 0 0 0 5 3
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| 2547_MA0285.1_JASPAR_CORE_2009__shift4 (2547_MA0285.1_JASPAR_CORE_2009_) |
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0.766 |
0.492 |
5.956 |
0.478 |
0.890 |
1.972 |
0.890 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m4 versus 2547_MA0285.1_JASPAR_CORE_2009_; m=1/2; ncol2=9; w=9; offset=4; strand=D; shift=4; score= 1; ----cwmmGCCmC-
; cor=0.766; Ncor=0.492; logoDP=5.956; NIcor=0.478; NsEucl=0.890; SSD=1.972; NSW=0.890; 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 20 28 37 63 0 0 0 42 7 0
c 0 0 0 0 48 22 30 36 0 100 99 30 76 0
g 0 0 0 0 18 17 22 1 100 0 0 7 8 0
t 0 0 0 0 14 32 11 1 0 0 0 21 8 0
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| 2733_PF0046.1_JASPAR_CORE_2009__rc_shift6 (2733_PF0046.1_JASPAR_CORE_2009__rc) |
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0.753 |
0.430 |
0.184 |
-0.133 |
0.865 |
2.349 |
0.853 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; positions_7nt_m4 versus 2733_PF0046.1_JASPAR_CORE_2009__rc; m=2/2; ncol2=8; w=8; offset=6; strand=R; shift=6; score= 2; ------CAGCCAAW
; cor=0.753; Ncor=0.430; logoDP=0.184; NIcor=-0.133; NsEucl=0.865; SSD=2.349; NSW=0.853; 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 0 0 0 2172 0 529 0 2172 2172 548
c 0 0 0 0 0 0 2172 0 0 1643 2172 0 0 0
g 0 0 0 0 0 0 0 0 2172 0 0 0 0 0
t 0 0 0 0 0 0 0 0 0 0 0 0 0 1624
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