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_m2/peak-motifs_dyads_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/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 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_m2_shift0 (dyads_m2) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; dyads_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; taAWTAAATAAATAAAw
; Alignment reference
a 169 428 683 502 27 709 718 719 19 722 721 719 5 714 717 592 306
c 112 46 25 9 9 3 3 1 2 1 1 1 6 1 0 22 54
g 29 179 5 25 3 5 2 4 4 0 2 3 0 5 3 52 41
t 415 72 12 189 686 8 2 1 700 2 1 2 714 5 5 59 324
|
| MA0042.1_rc_shift5 (FOXI1_rc) |
 |
0.783 |
0.553 |
4.476 |
0.115 |
0.898 |
3.020 |
0.874 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; dyads_m2 versus MA0042.1_rc (FOXI1_rc); m=1/1; ncol2=12; w=12; offset=5; strand=R; shift=5; score= 1; -----AwAyAAAyAhsm
; cor=0.783; Ncor=0.553; logoDP=4.476; NIcor=0.115; NsEucl=0.898; SSD=3.020; NSW=0.874; 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 24 18 24 0 31 31 31 0 31 8 7 10
c 0 0 0 0 0 4 4 7 16 0 0 0 18 0 8 12 14
g 0 0 0 0 0 1 1 0 0 0 0 0 0 0 4 8 1
t 0 0 0 0 0 2 8 0 15 0 0 0 13 0 11 4 6
|