One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5.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/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/positions_6nt_m5/peak-motifs_positions_6nt_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_6nt_m5_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_6nt_m5_shift0 (positions_6nt_m5) |
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; positions_6nt_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; wwAATGTCATGwy
; Alignment reference
a 127 136 335 387 8 9 13 10 395 18 45 135 102
c 66 70 28 7 1 3 7 384 6 14 27 66 111
g 80 60 27 9 8 402 2 11 7 14 319 75 73
t 144 151 27 14 400 3 395 12 9 371 26 141 131
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| MA0089.1_rc_shift5 (NFE2L1::MafG_rc) |
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0.948 |
0.437 |
0.234 |
-0.132 |
0.930 |
0.355 |
0.970 |
1 |
2 |
2 |
2 |
1 |
1 |
1 |
1.429 |
1 |
; positions_6nt_m5 versus MA0089.1_rc (NFE2L1::MafG_rc); m=1/2; ncol2=6; w=6; offset=5; strand=R; shift=5; score= 1.4286; -----GTCATs--
; cor=0.948; Ncor=0.437; logoDP=0.234; NIcor=-0.132; NsEucl=0.930; SSD=0.355; NSW=0.970; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.429; match_rank=1
a 0 0 0 0 0 6 0 1 34 0 6 0 0
c 0 0 0 0 0 2 0 32 0 3 10 0 0
g 0 0 0 0 0 26 0 0 0 2 11 0 0
t 0 0 0 0 0 0 34 1 0 29 7 0 0
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| MA0067.1_shift4 (Pax2) |
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0.789 |
0.486 |
3.014 |
0.484 |
0.889 |
1.586 |
0.901 |
2 |
1 |
1 |
1 |
2 |
2 |
2 |
1.571 |
2 |
; positions_6nt_m5 versus MA0067.1 (Pax2); m=2/2; ncol2=8; w=8; offset=4; strand=D; shift=4; score= 1.5714; ----wgTCAykb-
; cor=0.789; Ncor=0.486; logoDP=3.014; NIcor=0.484; NsEucl=0.889; SSD=1.586; NSW=0.901; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.571; match_rank=2
a 0 0 0 0 10 7 3 0 26 2 2 1 0
c 0 0 0 0 7 1 2 28 1 17 0 11 0
g 0 0 0 0 5 21 0 1 3 1 19 11 0
t 0 0 0 0 9 2 26 2 1 11 10 8 0
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