One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.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/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_vs_db_footprintDB
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_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_8nt_mkv2_shift0 (oligos_8nt_mkv2) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_8nt_mkv2; m=0 (reference); ncol1=12; shift=0; ncol=13; rwAGAGGGAGws-
; Alignment reference
a 2 2 3 0 3 0 0 0 3 0 1 0 0
c 0 0 0 0 0 0 0 0 0 0 0 2 0
g 1 0 0 3 0 3 3 3 0 3 0 1 0
t 0 1 0 0 0 0 0 0 0 0 2 0 0
|
| 6513_2v2t_A_3D-footprint_20130124__shift5 (6513_2v2t_A_3D-footprint_20130124_) |
 |
0.860 |
0.430 |
4.825 |
0.409 |
0.876 |
1.103 |
0.908 |
1 |
2 |
2 |
2 |
2 |
1 |
1 |
1.571 |
1 |
; oligos_8nt_mkv2 versus 6513_2v2t_A_3D-footprint_20130124_; m=1/3; ncol2=6; w=6; offset=5; strand=D; shift=5; score= 1.5714; -----GGgAnT--
; cor=0.860; Ncor=0.430; logoDP=4.825; NIcor=0.409; NsEucl=0.876; SSD=1.103; NSW=0.908; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.571; match_rank=1
a 0 0 0 0 0 0 0 17 69 24 11 0 0
c 0 0 0 0 0 0 0 10 11 24 8 0 0
g 0 0 0 0 0 96 96 61 8 24 8 0 0
t 0 0 0 0 0 0 0 8 8 24 69 0 0
|
| 6322_1svc_P_3D-footprint_20130124__rc_shift5 (6322_1svc_P_3D-footprint_20130124__rc) |
 |
0.829 |
0.483 |
0.244 |
-0.041 |
0.881 |
1.387 |
0.901 |
2 |
1 |
3 |
3 |
1 |
2 |
2 |
2.000 |
2 |
; oligos_8nt_mkv2 versus 6322_1svc_P_3D-footprint_20130124__rc; m=2/3; ncol2=7; w=7; offset=5; strand=R; shift=5; score= 2; -----gGGAnnc-
; cor=0.829; Ncor=0.483; logoDP=0.244; NIcor=-0.041; NsEucl=0.881; SSD=1.387; NSW=0.901; rcor=2; rNcor=1; rlogoDP=3; rNIcor=3; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 0 0 0 0 13 0 0 96 24 24 13 0
c 0 0 0 0 0 13 0 0 0 24 24 54 0
g 0 0 0 0 0 54 96 96 0 24 24 16 0
t 0 0 0 0 0 16 0 0 0 24 24 13 0
|
| 2711_PF0024.1_JASPAR_CORE_2009__shift5 (2711_PF0024.1_JASPAR_CORE_2009_) |
 |
0.758 |
0.408 |
9.734 |
0.441 |
0.849 |
2.222 |
0.841 |
3 |
3 |
1 |
1 |
3 |
3 |
3 |
2.429 |
3 |
; oligos_8nt_mkv2 versus 2711_PF0024.1_JASPAR_CORE_2009_; m=3/3; ncol2=8; w=7; offset=5; strand=D; shift=5; score= 2.4286; -----GGGAGGrG
; cor=0.758; Ncor=0.408; logoDP=9.734; NIcor=0.441; NsEucl=0.849; SSD=2.222; NSW=0.841; rcor=3; rNcor=3; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.429; match_rank=3
a 0 0 0 0 0 0 0 0 11176 0 0 3724 2525
c 0 0 0 0 0 0 0 0 0 0 0 0 0
g 0 0 0 0 0 11176 11176 11176 0 11176 11176 7452 8651
t 0 0 0 0 0 0 0 0 0 0 0 0 0
|