One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.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/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: dyads_m1_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 |
|---|
| dyads_m1_shift0 (dyads_m1) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; dyads_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; wwTATtdhdhaATAww
; Alignment reference
a 3310 3022 0 9626 0 1996 2451 2724 2823 3484 4759 9626 0 9626 3102 3127
c 1582 1807 0 0 0 1020 1192 2568 1511 2499 1851 0 0 0 1695 1607
g 1607 1695 0 0 0 1851 2499 1511 2568 1192 1020 0 0 0 1807 1582
t 3127 3102 9626 0 9626 4759 3484 2823 2724 2451 1996 0 9626 0 3022 3310
|
| MA0033.1_shift6 (FOXL1) |
 |
0.924 |
0.462 |
4.378 |
0.472 |
0.947 |
0.357 |
0.978 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; dyads_m1 versus MA0033.1 (FOXL1); m=1/2; ncol2=8; w=8; offset=6; strand=D; shift=6; score= 1; ------wwdayATA--
; cor=0.924; Ncor=0.462; logoDP=4.378; NIcor=0.472; NsEucl=0.947; SSD=0.357; NSW=0.978; 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 0 0 7 10 6 13 4 21 0 22 0 0
c 0 0 0 0 0 0 1 4 3 4 10 0 2 1 0 0
g 0 0 0 0 0 0 4 2 6 4 2 2 0 0 0 0
t 0 0 0 0 0 0 11 7 8 2 7 0 21 0 0 0
|
| MA0102.2_shift4 (CEBPA) |
 |
0.750 |
0.422 |
3.504 |
0.385 |
0.906 |
1.445 |
0.920 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; dyads_m1 versus MA0102.2 (CEBPA); m=2/2; ncol2=9; w=9; offset=4; strand=D; shift=4; score= 2; ----TtkygCAAy---
; cor=0.750; Ncor=0.422; logoDP=3.504; NIcor=0.385; NsEucl=0.906; SSD=1.445; NSW=0.920; 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 3 1 4 2 4 2 18 18 0 0 0 0
c 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0
g 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0
t 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
|