One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_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/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_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 |
|---|
| oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=13; yyCTGCCTCmg--
; Alignment reference
a 136 100 1 20 14 7 1 13 2 315 114 0 0
c 256 419 890 62 1 865 869 1 890 252 202 0 0
g 133 118 2 27 877 1 21 30 0 162 401 0 0
t 368 256 0 784 1 20 2 849 1 164 176 0 0
|
| MA0003.1_shift4 (TFAP2A) |
 |
0.773 |
0.416 |
5.145 |
0.401 |
0.878 |
1.454 |
0.896 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_7nt_mkv5_m2 versus MA0003.1 (TFAP2A); m=1/1; ncol2=9; w=7; offset=4; strand=D; shift=4; score= 1; ----GCCcbrrGs
; cor=0.773; Ncor=0.416; logoDP=5.145; NIcor=0.401; NsEucl=0.878; SSD=1.454; NSW=0.896; 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 0 0 22 19 55 53 19 9
c 0 0 0 0 0 185 185 71 57 44 30 16 78
g 0 0 0 0 185 0 0 46 61 67 91 137 79
t 0 0 0 0 0 0 0 46 48 19 11 13 19
|