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_8nt_m2/peak-motifs_positions_8nt_m2.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_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_footprintDB
One-to-n matrix alignment; reference matrix: positions_8nt_m2_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_8nt_m2_shift0 (positions_8nt_m2) |
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; positions_8nt_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; shTCGTTGGCTdv
; Alignment reference
a 1 5 1 0 0 1 2 1 2 1 1 4 5
c 8 4 0 15 0 0 1 0 1 15 2 2 5
g 4 3 1 0 16 0 0 14 12 0 1 6 4
t 3 4 14 1 0 15 13 1 1 0 12 4 2
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| 7524_NFIA+NFIB+NFIC+NFIX_si_HOCOMOCO_v9__shift5 (7524_NFIA+NFIB+NFIC+NFIX_si_HOCOMOCO_v9_) |
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0.908 |
0.419 |
3.530 |
0.410 |
0.914 |
0.537 |
0.955 |
1 |
2 |
2 |
2 |
1 |
1 |
1 |
1.429 |
1 |
; positions_8nt_m2 versus 7524_NFIA+NFIB+NFIC+NFIX_si_HOCOMOCO_v9_; m=1/2; ncol2=6; w=6; offset=5; strand=D; shift=5; score= 1.4286; -----TTGGCw--
; cor=0.908; Ncor=0.419; logoDP=3.530; NIcor=0.410; NsEucl=0.914; SSD=0.537; NSW=0.955; 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 15 2 3 8 14 118 0 0
c 0 0 0 0 0 46 1 1 3 235 34 0 0
g 0 0 0 0 0 2 14 255 253 12 37 0 0
t 0 0 0 0 0 202 248 6 1 4 76 0 0
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| 7282_WRKY45_ArabidopsisPBM_20140210__shift2 (7282_WRKY45_ArabidopsisPBM_20140210_) |
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0.756 |
0.582 |
6.829 |
0.558 |
0.890 |
2.426 |
0.879 |
2 |
1 |
1 |
1 |
2 |
2 |
2 |
1.571 |
2 |
; positions_8nt_m2 versus 7282_WRKY45_ArabidopsisPBM_20140210_; m=2/2; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 1.5714; --dCGTTGACya-
; cor=0.756; Ncor=0.582; logoDP=6.829; NIcor=0.558; NsEucl=0.890; SSD=2.426; NSW=0.879; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.571; match_rank=2
a 0 0 30 6 2 1 1 0 99 1 1 64 0
c 0 0 12 88 0 2 0 0 1 98 53 12 0
g 0 0 32 2 89 0 1 99 0 0 1 13 0
t 0 0 26 4 9 97 98 1 0 1 45 11 0
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