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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: dyads_m3_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 |
|---|
| dyads_m3_shift0 (dyads_m3) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; dyads_m3; m=0 (reference); ncol1=10; shift=0; ncol=12; wdTTGCAAhw--
; Alignment reference
a 3278 3895 0 0 0 0 12984 12984 4097 5695 0 0
c 1633 1516 0 0 0 12984 0 0 3476 2378 0 0
g 2378 3476 0 0 12984 0 0 0 1516 1633 0 0
t 5695 4097 12984 12984 0 0 0 0 3895 3278 0 0
|
| MA0019.1_shift0 (Ddit3::Cebpa) |
 |
0.778 |
0.648 |
7.559 |
0.663 |
0.902 |
1.936 |
0.903 |
2 |
1 |
1 |
1 |
1 |
2 |
1 |
1.286 |
1 |
; dyads_m3 versus MA0019.1 (Ddit3::Cebpa); m=1/3; ncol2=12; w=10; offset=0; strand=D; shift=0; score= 1.2857; rrrTGCAATmcc
; cor=0.778; Ncor=0.648; logoDP=7.559; NIcor=0.663; NsEucl=0.902; SSD=1.936; NSW=0.903; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.286; match_rank=1
a 14 11 18 0 0 4 38 36 0 14 4 0
c 7 7 3 1 0 33 1 2 6 17 23 26
g 12 14 15 0 38 0 0 1 0 5 9 6
t 6 7 3 38 1 2 0 0 33 3 3 7
|
| MA0133.1_shift4 (BRCA1) |
 |
0.779 |
0.425 |
3.282 |
0.420 |
0.870 |
1.212 |
0.899 |
1 |
3 |
3 |
3 |
3 |
1 |
2 |
2.286 |
2 |
; dyads_m3 versus MA0133.1 (BRCA1); m=2/3; ncol2=7; w=6; offset=4; strand=D; shift=4; score= 2.2857; ----mCAAcms-
; cor=0.779; Ncor=0.425; logoDP=3.282; NIcor=0.420; NsEucl=0.870; SSD=1.212; NSW=0.899; rcor=1; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=2.286; match_rank=2
a 0 0 0 0 15 4 41 36 7 19 3 0
c 0 0 0 0 11 35 1 2 29 14 22 0
g 0 0 0 0 10 2 1 4 6 7 15 0
t 0 0 0 0 7 2 0 1 1 3 3 0
|
| MA0102.3_shift1 (CEBPA) |
 |
0.756 |
0.567 |
7.319 |
0.532 |
0.883 |
2.233 |
0.876 |
3 |
2 |
2 |
2 |
2 |
3 |
3 |
2.429 |
3 |
; dyads_m3 versus MA0102.3 (CEBPA); m=3/3; ncol2=11; w=9; offset=1; strand=D; shift=1; score= 2.4286; -aTTGCAyAAym
; cor=0.756; Ncor=0.567; logoDP=7.319; NIcor=0.532; NsEucl=0.883; SSD=2.233; NSW=0.876; rcor=3; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.429; match_rank=3
a 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804
c 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963
g 0 3635 0 0 11304 0 1066 0 0 0 1804 890
t 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
|