One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_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/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift3 ; 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 |
|---|
| oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssAGGGAGCcg
; Alignment reference
a 0 0 0 102 77 451 0 0 1 456 0 9 122 93
c 0 0 0 158 174 45 9 15 2 60 1 494 171 129
g 0 0 0 154 219 17 513 506 517 5 521 2 118 210
t 0 0 0 108 52 9 0 1 2 1 0 17 111 90
|
| MA0154.1_shift0 (EBF1) |
 |
0.884 |
0.442 |
5.690 |
0.454 |
0.912 |
0.766 |
0.945 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_6nt_test_vs_ctrl_m3 versus MA0154.1 (EBF1); m=1/1; ncol2=10; w=7; offset=-3; strand=D; shift=0; score= 1; mCyCmaGGGA----
; cor=0.884; Ncor=0.442; logoDP=5.690; NIcor=0.454; NsEucl=0.912; SSD=0.766; NSW=0.945; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 11 0 1 2 11 16 0 2 0 21 0 0 0 0
c 9 22 16 20 9 1 0 0 0 0 0 0 0 0
g 2 0 1 0 0 5 25 23 25 4 0 0 0 0
t 3 3 7 3 5 3 0 0 0 0 0 0 0 0
|