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_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_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_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_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 |
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| oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1) |
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; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; TykGGCCAGyCCAAAGTCCArGAy
; Alignment reference
a 0 0 0 0 0 0 0 2 0 0 0 0 2 2 2 0 0 0 0 2 1 0 2 0
c 0 1 0 0 0 2 2 0 0 1 2 2 0 0 0 0 0 2 2 0 0 0 0 1
g 0 0 1 2 2 0 0 0 2 0 0 0 0 0 0 2 0 0 0 0 1 2 0 0
t 2 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 0 0 0 0 0 1
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| MA0114.2_rc_shift6 (HNF4A_rc) |
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0.832 |
0.520 |
5.970 |
0.153 |
0.914 |
3.300 |
0.890 |
1 |
1 |
3 |
3 |
1 |
1 |
1 |
1.571 |
1 |
; oligos_7nt_test_vs_ctrl_m1 versus MA0114.2_rc (HNF4A_rc); m=1/3; ncol2=15; w=15; offset=6; strand=R; shift=6; score= 1.5714; ------rrGkyCAAAGkyCAg---
; cor=0.832; Ncor=0.520; logoDP=5.970; NIcor=0.153; NsEucl=0.914; SSD=3.300; NSW=0.890; rcor=1; rNcor=1; rlogoDP=3; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.571; match_rank=1
a 0 0 0 0 0 0 5247 7985 1769 3334 2413 128 16188 13586 15112 49 988 477 70 13410 4057 0 0 0
c 0 0 0 0 0 0 3001 415 352 1662 5340 15741 407 367 0 67 329 8370 15810 907 3974 0 0 0
g 0 0 0 0 0 0 6450 6498 13491 5653 3745 35 173 2637 1630 16535 4425 1846 51 720 5971 0 0 0
t 0 0 0 0 0 0 2070 1870 1156 6119 5270 864 0 178 26 117 11026 6075 837 1731 2766 0 0 0
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| MA0484.1_shift5 (HNF4G) |
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0.775 |
0.484 |
10.539 |
0.478 |
0.901 |
4.388 |
0.854 |
3 |
2 |
1 |
1 |
2 |
3 |
3 |
2.143 |
2 |
; oligos_7nt_test_vs_ctrl_m1 versus MA0484.1 (HNF4G); m=2/3; ncol2=15; w=15; offset=5; strand=D; shift=5; score= 2.1429; -----arrGkyCAAAGkyCA----
; cor=0.775; Ncor=0.484; logoDP=10.539; NIcor=0.478; NsEucl=0.901; SSD=4.388; NSW=0.854; rcor=3; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.143; match_rank=2
a 0 0 0 0 0 3514 3259 4696 1103 1944 1511 0 9343 7889 8464 99 324 225 159 6785 0 0 0 0
c 0 0 0 0 0 1864 1531 102 201 713 2870 8827 55 82 0 6 143 4338 8377 794 0 0 0 0
g 0 0 0 0 0 2011 3830 3811 7480 3301 2279 221 54 1481 938 9098 3624 1107 85 556 0 0 0 0
t 0 0 0 0 0 2063 832 843 668 3494 2792 404 0 0 50 249 5361 3782 831 1317 0 0 0 0
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| MA0114.1_shift7 (HNF4A) |
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0.801 |
0.434 |
6.718 |
0.434 |
0.897 |
3.573 |
0.863 |
2 |
3 |
2 |
2 |
3 |
2 |
2 |
2.286 |
3 |
; oligos_7nt_test_vs_ctrl_m1 versus MA0114.1 (HNF4A); m=3/3; ncol2=13; w=13; offset=7; strand=D; shift=7; score= 2.2857; -------rGgbCAAAGkyCa----
; cor=0.801; Ncor=0.434; logoDP=6.718; NIcor=0.434; NsEucl=0.897; SSD=3.573; NSW=0.863; rcor=2; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=2.286; match_rank=3
a 0 0 0 0 0 0 0 28 2 12 5 3 59 53 56 4 6 3 4 42 0 0 0 0
c 0 0 0 0 0 0 0 7 2 4 23 51 1 2 1 4 2 22 49 7 0 0 0 0
g 0 0 0 0 0 0 0 27 56 35 20 4 3 10 8 58 33 11 5 10 0 0 0 0
t 0 0 0 0 0 0 0 5 7 16 19 9 4 2 2 1 26 31 9 8 0 0 0 0
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