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/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_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/oligos_8nt_mkv6_m3/peak-motifs_oligos_8nt_mkv6_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m3_shift0 ; 5 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_m3_shift0 (oligos_8nt_mkv6_m3) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_8nt_mkv6_m3; m=0 (reference); ncol1=14; shift=0; ncol=15; wtATTGAGCAATaw-
; Alignment reference
a 1041 669 2747 14 15 176 2352 4 72 3314 3314 89 1418 955 0
c 573 505 180 6 5 9 210 10 3149 10 9 291 657 749 0
g 791 682 325 9 20 3053 96 3305 6 4 4 213 534 676 0
t 930 1479 83 3306 3295 97 677 16 108 7 8 2742 726 955 0
|
| MA0102.3_rc_shift1 (CEBPA_rc) |
 |
0.877 |
0.689 |
4.336 |
0.140 |
0.923 |
1.420 |
0.935 |
1 |
1 |
3 |
3 |
1 |
1 |
1 |
1.571 |
1 |
; oligos_8nt_mkv6_m3 versus MA0102.3_rc (CEBPA_rc); m=1/4; ncol2=11; w=11; offset=1; strand=R; shift=1; score= 1.5714; -krTTrTGCAAt---
; cor=0.877; Ncor=0.689; logoDP=4.336; NIcor=0.140; NsEucl=0.923; SSD=1.420; NSW=0.935; rcor=1; rNcor=1; rlogoDP=3; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.571; match_rank=1
a 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0
c 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0
g 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0
t 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0
|
| MA0466.1_rc_shift2 (CEBPB_rc) |
 |
0.872 |
0.685 |
2.615 |
-0.034 |
0.922 |
1.473 |
0.933 |
2 |
2 |
4 |
4 |
2 |
2 |
2 |
2.571 |
2 |
; oligos_8nt_mkv6_m3 versus MA0466.1_rc (CEBPB_rc); m=2/4; ncol2=11; w=11; offset=2; strand=R; shift=2; score= 2.5714; --rTkrTGCAATm--
; cor=0.872; Ncor=0.685; logoDP=2.615; NIcor=-0.034; NsEucl=0.922; SSD=1.473; NSW=0.933; rcor=2; rNcor=2; rlogoDP=4; rNIcor=4; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.571; match_rank=2
a 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0
c 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0
g 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0
t 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0
|
| MA0102.1_shift3 (Cebpa) |
 |
0.829 |
0.608 |
6.271 |
0.605 |
0.914 |
1.805 |
0.918 |
4 |
3 |
1 |
1 |
3 |
4 |
3 |
2.714 |
3 |
; oligos_8nt_mkv6_m3 versus MA0102.1 (Cebpa); m=3/4; ncol2=12; w=11; offset=3; strand=D; shift=3; score= 2.7143; ---TtkygCAAyvyb
; cor=0.829; Ncor=0.608; logoDP=6.271; NIcor=0.605; NsEucl=0.914; SSD=1.805; NSW=0.918; rcor=4; rNcor=3; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=4; rNSW=3; rank_mean=2.714; match_rank=3
a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1
c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6
g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5
t 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
|
| MA0102.2_shift3 (CEBPA) |
 |
0.843 |
0.542 |
6.270 |
0.533 |
0.898 |
1.680 |
0.907 |
3 |
4 |
2 |
2 |
4 |
3 |
4 |
3.143 |
4 |
; oligos_8nt_mkv6_m3 versus MA0102.2 (CEBPA); m=4/4; ncol2=9; w=9; offset=3; strand=D; shift=3; score= 3.1429; ---TtkygCAAy---
; cor=0.843; Ncor=0.542; logoDP=6.270; NIcor=0.533; NsEucl=0.898; SSD=1.680; NSW=0.907; rcor=3; rNcor=4; rlogoDP=2; rNIcor=2; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=3.143; match_rank=4
a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0
c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0
g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0
t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
|