One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_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.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m1_shift0 ; 6 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 |
|---|
| oligos_8nt_mkv6_m1_shift0 (oligos_8nt_mkv6_m1) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_8nt_mkv6_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; atGGTTGCACAACwh
; Alignment reference
a 991 446 177 354 1 2 76 3 2057 59 2210 2207 18 1073 570
c 349 252 30 55 10 0 3 2211 43 2086 12 4 1847 418 624
g 470 340 1759 1769 1 4 2107 4 72 10 1 6 50 136 460
t 414 1186 258 46 2212 2218 38 6 52 69 1 7 309 597 570
|
| MA0102.3_shift3 (CEBPA) |
 |
0.882 |
0.647 |
9.868 |
0.623 |
0.922 |
1.461 |
0.934 |
1 |
1 |
1 |
1 |
1 |
2 |
2 |
1.286 |
1 |
; oligos_8nt_mkv6_m1 versus MA0102.3 (CEBPA); m=1/5; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 1.2857; ---aTTGCAyAAym-
; cor=0.882; Ncor=0.647; logoDP=9.868; NIcor=0.623; NsEucl=0.922; SSD=1.461; NSW=0.934; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.286; match_rank=1
a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0
c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0
g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0
t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
|
| MA0133.1_shift8 (BRCA1) |
 |
0.874 |
0.408 |
3.200 |
0.412 |
0.910 |
0.795 |
0.943 |
2 |
5 |
3 |
3 |
2 |
1 |
1 |
2.429 |
2 |
; oligos_8nt_mkv6_m1 versus MA0133.1 (BRCA1); m=2/5; ncol2=7; w=7; offset=8; strand=D; shift=8; score= 2.4286; --------mCAAcms
; cor=0.874; Ncor=0.408; logoDP=3.200; NIcor=0.412; NsEucl=0.910; SSD=0.795; NSW=0.943; rcor=2; rNcor=5; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=2.429; match_rank=2
a 0 0 0 0 0 0 0 0 15 4 41 36 7 19 3
c 0 0 0 0 0 0 0 0 11 35 1 2 29 14 22
g 0 0 0 0 0 0 0 0 10 2 1 4 6 7 15
t 0 0 0 0 0 0 0 0 7 2 0 1 1 3 3
|
| MA0466.1_shift2 (CEBPB) |
 |
0.823 |
0.604 |
9.656 |
0.567 |
0.904 |
2.211 |
0.900 |
3 |
3 |
2 |
2 |
3 |
4 |
3 |
2.857 |
3 |
; oligos_8nt_mkv6_m1 versus MA0466.1 (CEBPB); m=3/5; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 2.8571; --kATTGCAymAy--
; cor=0.823; Ncor=0.604; logoDP=9.656; NIcor=0.567; NsEucl=0.904; SSD=2.211; NSW=0.900; rcor=3; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=4; rNSW=3; rank_mean=2.857; match_rank=3
a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0
c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0
g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0
t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
|
| MA0102.2_rc_shift3 (CEBPA_rc) |
 |
0.814 |
0.488 |
2.586 |
0.051 |
0.887 |
2.067 |
0.885 |
4 |
4 |
4 |
4 |
5 |
3 |
5 |
4.143 |
4 |
; oligos_8nt_mkv6_m1 versus MA0102.2_rc (CEBPA_rc); m=4/5; ncol2=9; w=9; offset=3; strand=R; shift=3; score= 4.1429; ---rTTGcrmaA---
; cor=0.814; Ncor=0.488; logoDP=2.586; NIcor=0.051; NsEucl=0.887; SSD=2.067; NSW=0.885; rcor=4; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=5; rSSD=3; rNSW=5; rank_mean=4.143; match_rank=4
a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0
c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0
g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0
t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
|
| MA0102.1_rc_shift0 (Cebpa_rc) |
 |
0.770 |
0.616 |
0.329 |
-0.164 |
0.903 |
2.689 |
0.888 |
5 |
2 |
5 |
5 |
4 |
5 |
4 |
4.286 |
5 |
; oligos_8nt_mkv6_m1 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=12; offset=0; strand=R; shift=0; score= 4.2857; vrbrTTGcrmaA---
; cor=0.770; Ncor=0.616; logoDP=0.329; NIcor=-0.164; NsEucl=0.903; SSD=2.689; NSW=0.888; rcor=5; rNcor=2; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=5; rNSW=4; rank_mean=4.286; match_rank=5
a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0
c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0
g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0
t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0
|