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/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/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: dyads_m1_shift3 ; 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_shift3 (dyads_m1) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; dyads_m1; m=0 (reference); ncol1=16; shift=3; ncol=19; ---bwGTAAATATTTACwv
; Alignment reference
a 0 0 0 22 58 13 6 99 104 105 1 102 0 0 4 90 6 30 27
c 0 0 0 30 2 1 9 3 2 0 3 0 1 0 0 1 86 16 27
g 0 0 0 27 16 86 1 0 0 1 0 3 0 2 3 9 1 2 30
t 0 0 0 27 30 6 90 4 0 0 102 1 105 104 99 6 13 58 22
|
| MA0047.2_rc_shift0 (Foxa2_rc) |
 |
0.858 |
0.406 |
1.015 |
-0.082 |
0.912 |
1.255 |
0.930 |
1 |
2 |
2 |
2 |
1 |
1 |
1 |
1.429 |
1 |
; dyads_m1 versus MA0047.2_rc (Foxa2_rc); m=1/2; ncol2=12; w=9; offset=-3; strand=R; shift=0; score= 1.4286; ccwrwGTAAAYA-------
; cor=0.858; Ncor=0.406; logoDP=1.015; NIcor=-0.082; NsEucl=0.912; SSD=1.255; NSW=0.930; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.429; match_rank=1
a 189 140 360 436 391 81 3 634 769 806 3 805 0 0 0 0 0 0 0
c 290 482 24 58 3 2 67 175 36 1 582 1 0 0 0 0 0 0 0
g 195 53 6 265 77 725 4 1 3 1 3 1 0 0 0 0 0 0 0
t 129 131 417 50 338 2 736 1 1 1 221 1 0 0 0 0 0 0 0
|
| MA0047.1_shift7 (Foxa2) |
 |
0.791 |
0.593 |
6.324 |
0.564 |
0.908 |
2.456 |
0.898 |
2 |
1 |
1 |
1 |
2 |
2 |
2 |
1.571 |
2 |
; dyads_m1 versus MA0047.1 (Foxa2); m=2/2; ncol2=12; w=12; offset=4; strand=D; shift=7; score= 1.5714; -------mawTrTTkryTY
; cor=0.791; Ncor=0.593; logoDP=6.324; NIcor=0.564; NsEucl=0.908; SSD=2.456; NSW=0.898; 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 0 0 0 6 11 8 0 11 0 0 0 9 0 1 0
c 0 0 0 0 0 0 0 7 3 3 1 0 1 1 0 0 9 1 5
g 0 0 0 0 0 0 0 3 1 1 0 6 0 0 6 8 0 1 0
t 0 0 0 0 0 0 0 1 2 5 16 0 16 16 11 0 8 14 12
|