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/positions_7nt_m5/peak-motifs_positions_7nt_m5.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/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m5_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 |
|---|
| positions_7nt_m5_shift0 (positions_7nt_m5) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; positions_7nt_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; wmACATTGCACAACTsy
; Alignment reference
a 73 84 193 16 219 0 0 4 0 221 11 226 224 2 20 52 44
c 48 64 6 163 4 0 0 0 227 3 213 1 0 205 12 64 62
g 45 44 16 18 0 0 3 206 0 1 1 0 1 4 0 58 48
t 62 36 13 31 5 228 225 18 1 3 3 1 3 17 196 54 74
|
| MA0102.3_shift4 (CEBPA) |
 |
0.883 |
0.571 |
10.162 |
0.554 |
0.918 |
1.644 |
0.925 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m5 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 1; ----aTTGCAyAAym--
; cor=0.883; Ncor=0.571; logoDP=10.162; NIcor=0.554; NsEucl=0.918; SSD=1.644; NSW=0.925; 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 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0
c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0
g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0
t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
|
| MA0466.1_shift3 (CEBPB) |
 |
0.855 |
0.553 |
10.041 |
0.543 |
0.911 |
1.913 |
0.913 |
2 |
3 |
2 |
2 |
2 |
2 |
2 |
2.143 |
2 |
; positions_7nt_m5 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 2.1429; ---kATTGCAymAy---
; cor=0.855; Ncor=0.553; logoDP=10.041; NIcor=0.543; NsEucl=0.911; SSD=1.913; NSW=0.913; rcor=2; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.143; match_rank=2
a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0
c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0
g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0
t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
|
| MA0102.2_rc_shift4 (CEBPA_rc) |
 |
0.829 |
0.439 |
2.792 |
0.031 |
0.888 |
2.029 |
0.887 |
3 |
4 |
3 |
3 |
4 |
3 |
4 |
3.429 |
3 |
; positions_7nt_m5 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score= 3.4286; ----rTTGcrmaA----
; cor=0.829; Ncor=0.439; logoDP=2.792; NIcor=0.031; NsEucl=0.888; SSD=2.029; NSW=0.887; rcor=3; rNcor=4; rlogoDP=3; rNIcor=3; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=3.429; match_rank=3
a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 0
c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 0
g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 0
t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0 0
|
| MA0102.1_rc_shift1 (Cebpa_rc) |
 |
0.805 |
0.568 |
0.267 |
-0.193 |
0.906 |
2.565 |
0.893 |
4 |
2 |
4 |
4 |
3 |
4 |
3 |
3.429 |
4 |
; positions_7nt_m5 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 3.4286; -vrbrTTGcrmaA----
; cor=0.805; Ncor=0.568; logoDP=0.267; NIcor=-0.193; NsEucl=0.906; SSD=2.565; NSW=0.893; rcor=4; rNcor=2; rlogoDP=4; rNIcor=4; rNsEucl=3; rSSD=4; rNSW=3; rank_mean=3.429; match_rank=4
a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0
c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0
g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0
t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0
|