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_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_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/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift4 ; 3 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_mkv4_m1_shift4 (oligos_6nt_mkv4_m1) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=4; ncol=14; ----wwCTTTTCwh
; Alignment reference
a 0 0 0 0 205 230 0 0 0 0 0 0 234 195
c 0 0 0 0 77 61 630 0 0 0 0 630 77 168
g 0 0 0 0 157 51 0 1 0 0 0 0 27 73
t 0 0 0 0 191 288 0 629 630 630 630 0 292 194
|
| MA0152.1_shift7 (NFATC2) |
 |
0.811 |
0.568 |
6.389 |
0.551 |
0.878 |
1.459 |
0.896 |
1 |
1 |
1 |
1 |
2 |
1 |
1 |
1.143 |
1 |
; oligos_6nt_mkv4_m1 versus MA0152.1 (NFATC2); m=1/2; ncol2=7; w=7; offset=3; strand=D; shift=7; score= 1.1429; -------TTTTCCA
; cor=0.811; Ncor=0.568; logoDP=6.389; NIcor=0.551; NsEucl=0.878; SSD=1.459; NSW=0.896; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.143; match_rank=1
a 0 0 0 0 0 0 0 3 1 1 0 1 0 18
c 0 0 0 0 0 0 0 1 2 1 0 25 26 3
g 0 0 0 0 0 0 0 2 2 0 0 0 0 1
t 0 0 0 0 0 0 0 20 21 24 26 0 0 4
|
| MA0029.1_rc_shift0 (Mecom_rc) |
 |
0.758 |
0.542 |
1.509 |
-0.029 |
0.888 |
2.506 |
0.875 |
2 |
2 |
2 |
2 |
1 |
2 |
2 |
1.857 |
2 |
; oligos_6nt_mkv4_m1 versus MA0029.1_rc (Mecom_rc); m=2/2; ncol2=14; w=10; offset=-4; strand=R; shift=0; score= 1.8571; tvTTATCTTrTCTt
; cor=0.758; Ncor=0.542; logoDP=1.509; NIcor=-0.029; NsEucl=0.888; SSD=2.506; NSW=0.875; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.857; match_rank=2
a 3 7 0 2 24 0 0 0 0 16 0 1 4 5
c 3 7 4 0 0 0 27 1 0 0 0 25 2 6
g 6 7 0 1 3 0 0 0 0 10 0 1 1 2
t 15 6 23 24 0 27 0 26 27 1 27 0 20 14
|