One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.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/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift2 ; 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 |
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positions_6nt_m2_shift2 (positions_6nt_m2) |
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; positions_6nt_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --TCCCCTAGCGC
; Alignment reference
a 0 0 0 0 0 0 0 0 1 0 0 0 0
c 0 0 0 1 1 1 1 0 0 0 1 0 1
g 0 0 0 0 0 0 0 0 0 1 0 1 0
t 0 0 1 0 0 0 0 1 0 0 0 0 0
|
MA0056.1_rc_shift2 (MZF1_1-4_rc) |
|
0.878 |
0.479 |
0.037 |
-0.132 |
0.880 |
1.035 |
0.914 |
1 |
1 |
3 |
2 |
1 |
1 |
1 |
1.429 |
1 |
; positions_6nt_m2 versus MA0056.1_rc (MZF1_1-4_rc); m=1/3; ncol2=6; w=6; offset=0; strand=R; shift=2; score= 1.4286; --TCCCCr-----
; cor=0.878; Ncor=0.479; logoDP=0.037; NIcor=-0.132; NsEucl=0.880; SSD=1.035; NSW=0.914; rcor=1; rNcor=1; rlogoDP=3; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.429; match_rank=1
a 0 0 0 0 1 0 1 8 0 0 0 0 0
c 0 0 2 20 19 18 19 4 0 0 0 0 0
g 0 0 0 0 0 0 0 5 0 0 0 0 0
t 0 0 18 0 0 2 0 3 0 0 0 0 0
|
MA0057.1_rc_shift0 (MZF1_5-13_rc) |
|
0.755 |
0.465 |
0.728 |
-0.108 |
0.858 |
2.594 |
0.838 |
3 |
2 |
1 |
1 |
2 |
3 |
3 |
2.143 |
2 |
; positions_6nt_m2 versus MA0057.1_rc (MZF1_5-13_rc); m=2/3; ncol2=10; w=8; offset=-2; strand=R; shift=0; score= 2.1429; yymCCCMTmv---
; cor=0.755; Ncor=0.465; logoDP=0.728; NIcor=-0.108; NsEucl=0.858; SSD=2.594; NSW=0.838; rcor=3; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.143; match_rank=2
a 2 2 4 2 0 1 5 0 7 4 0 0 0
c 4 4 8 14 14 15 11 0 7 7 0 0 0
g 2 0 1 0 2 0 0 1 0 4 0 0 0
t 8 10 3 0 0 0 0 15 2 1 0 0 0
|
MA0081.1_rc_shift1 (SPIB_rc) |
|
0.801 |
0.401 |
0.209 |
-0.140 |
0.850 |
1.616 |
0.865 |
2 |
3 |
2 |
3 |
3 |
2 |
2 |
2.429 |
3 |
; positions_6nt_m2 versus MA0081.1_rc (SPIB_rc); m=3/3; ncol2=7; w=6; offset=-1; strand=R; shift=1; score= 2.4286; -TTCCksw-----
; cor=0.801; Ncor=0.401; logoDP=0.209; NIcor=-0.140; NsEucl=0.850; SSD=1.616; NSW=0.865; rcor=2; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=2.429; match_rank=3
a 0 2 1 1 0 2 2 18 0 0 0 0 0
c 0 0 0 47 47 7 29 0 0 0 0 0 0
g 0 0 0 0 0 16 14 0 0 0 0 0 0
t 0 47 48 1 2 24 4 31 0 0 0 0 0
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