One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_8nt_test_vs_ctrl_m1/peak-motifs_oligos_8nt_test_vs_ctrl_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/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_8nt_test_vs_ctrl_m1/peak-motifs_oligos_8nt_test_vs_ctrl_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_m1_shift0 ; 4 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_test_vs_ctrl_m1_shift0 (oligos_8nt_test_vs_ctrl_m1) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_8nt_test_vs_ctrl_m1; m=0 (reference); ncol1=21; shift=0; ncol=21; ymAAGTCCAAAGTCCAGGGrw
; Alignment reference
a 3 5 15 18 0 1 0 0 18 17 16 0 0 0 2 15 1 3 0 6 6
c 6 7 0 0 0 1 18 18 0 0 0 2 1 18 16 0 1 0 0 3 4
g 3 4 2 0 17 1 0 0 0 1 2 15 3 0 0 0 14 14 15 7 3
t 6 2 1 0 1 15 0 0 0 0 0 1 14 0 0 3 2 1 3 2 5
|
| MA0484.1_shift1 (HNF4G) |
 |
0.841 |
0.600 |
8.171 |
0.570 |
0.925 |
2.513 |
0.916 |
2 |
2 |
1 |
1 |
1 |
1 |
1 |
1.286 |
1 |
; oligos_8nt_test_vs_ctrl_m1 versus MA0484.1 (HNF4G); m=1/3; ncol2=15; w=15; offset=1; strand=D; shift=1; score= 1.2857; -arrGkyCAAAGkyCA-----
; cor=0.841; Ncor=0.600; logoDP=8.171; NIcor=0.570; NsEucl=0.925; SSD=2.513; NSW=0.916; rcor=2; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a 0 3514 3259 4696 1103 1944 1511 0 9343 7889 8464 99 324 225 159 6785 0 0 0 0 0
c 0 1864 1531 102 201 713 2870 8827 55 82 0 6 143 4338 8377 794 0 0 0 0 0
g 0 2011 3830 3811 7480 3301 2279 221 54 1481 938 9098 3624 1107 85 556 0 0 0 0 0
t 0 2063 832 843 668 3494 2792 404 0 0 50 249 5361 3782 831 1317 0 0 0 0 0
|
| MA0114.2_rc_shift2 (HNF4A_rc) |
 |
0.843 |
0.602 |
4.672 |
0.155 |
0.924 |
2.580 |
0.914 |
1 |
1 |
3 |
3 |
2 |
2 |
2 |
2.000 |
2 |
; oligos_8nt_test_vs_ctrl_m1 versus MA0114.2_rc (HNF4A_rc); m=2/3; ncol2=15; w=15; offset=2; strand=R; shift=2; score= 2; --rrGkyCAAAGkyCAg----
; cor=0.843; Ncor=0.602; logoDP=4.672; NIcor=0.155; NsEucl=0.924; SSD=2.580; NSW=0.914; rcor=1; rNcor=1; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 0 5247 7985 1769 3334 2413 128 16188 13586 15112 49 988 477 70 13410 4057 0 0 0 0
c 0 0 3001 415 352 1662 5340 15741 407 367 0 67 329 8370 15810 907 3974 0 0 0 0
g 0 0 6450 6498 13491 5653 3745 35 173 2637 1630 16535 4425 1846 51 720 5971 0 0 0 0
t 0 0 2070 1870 1156 6119 5270 864 0 178 26 117 11026 6075 837 1731 2766 0 0 0 0
|
| MA0114.1_shift3 (HNF4A) |
 |
0.799 |
0.495 |
5.209 |
0.470 |
0.906 |
2.964 |
0.886 |
3 |
3 |
2 |
2 |
3 |
3 |
3 |
2.714 |
3 |
; oligos_8nt_test_vs_ctrl_m1 versus MA0114.1 (HNF4A); m=3/3; ncol2=13; w=13; offset=3; strand=D; shift=3; score= 2.7143; ---rGgbCAAAGkyCa-----
; cor=0.799; Ncor=0.495; logoDP=5.209; NIcor=0.470; NsEucl=0.906; SSD=2.964; NSW=0.886; rcor=3; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.714; match_rank=3
a 0 0 0 28 2 12 5 3 59 53 56 4 6 3 4 42 0 0 0 0 0
c 0 0 0 7 2 4 23 51 1 2 1 4 2 22 49 7 0 0 0 0 0
g 0 0 0 27 56 35 20 4 3 10 8 58 33 11 5 10 0 0 0 0 0
t 0 0 0 5 7 16 19 9 4 2 2 1 26 31 9 8 0 0 0 0 0
|