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_m2/peak-motifs_oligos_8nt_test_vs_ctrl_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/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_8nt_test_vs_ctrl_m2/peak-motifs_oligos_8nt_test_vs_ctrl_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_m2_shift0 ; 6 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_8nt_test_vs_ctrl_m2_shift0 (oligos_8nt_test_vs_ctrl_m2) |
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; oligos_8nt_test_vs_ctrl_m2; m=0 (reference); ncol1=23; shift=0; ncol=23; myTCCArrGmCCAAAGGkCAGvh
; Alignment reference
a 2 0 0 0 0 3 2 2 0 2 0 0 3 3 3 0 0 0 0 3 0 1 1
c 1 2 0 3 3 0 0 0 0 1 3 3 0 0 0 0 0 0 3 0 0 1 1
g 0 0 0 0 0 0 1 1 3 0 0 0 0 0 0 3 3 1 0 0 3 1 0
t 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1
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MA0512.1_shift11 (Rxra) |
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0.905 |
0.433 |
10.330 |
0.424 |
0.925 |
1.352 |
0.939 |
1 |
5 |
1 |
3 |
1 |
1 |
1 |
1.857 |
1 |
; oligos_8nt_test_vs_ctrl_m2 versus MA0512.1 (Rxra); m=1/5; ncol2=11; w=11; offset=11; strand=D; shift=11; score= 1.8571; -----------CArAGKTCAgd-
; cor=0.905; Ncor=0.433; logoDP=10.330; NIcor=0.424; NsEucl=0.925; SSD=1.352; NSW=0.939; rcor=1; rNcor=5; rlogoDP=1; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.857; match_rank=1
a 0 0 0 0 0 0 0 0 0 0 0 278 4154 2623 4877 0 0 0 0 5348 1150 1640 0
c 0 0 0 0 0 0 0 0 0 0 0 4521 418 252 0 0 0 583 5348 0 1070 742 0
g 0 0 0 0 0 0 0 0 0 0 0 305 9 2473 471 5348 3882 643 0 0 2336 1569 0
t 0 0 0 0 0 0 0 0 0 0 0 244 767 0 0 0 1466 4122 0 0 792 1397 0
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MA0484.1_shift5 (HNF4G) |
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0.818 |
0.534 |
10.149 |
0.530 |
0.916 |
3.212 |
0.893 |
3 |
1 |
2 |
1 |
2 |
4 |
4 |
2.429 |
2 |
; oligos_8nt_test_vs_ctrl_m2 versus MA0484.1 (HNF4G); m=2/5; ncol2=15; w=15; offset=5; strand=D; shift=5; score= 2.4286; -----arrGkyCAAAGkyCA---
; cor=0.818; Ncor=0.534; logoDP=10.149; NIcor=0.530; NsEucl=0.916; SSD=3.212; NSW=0.893; rcor=3; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=2; rSSD=4; rNSW=4; rank_mean=2.429; 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
c 0 0 0 0 0 1864 1531 102 201 713 2870 8827 55 82 0 6 143 4338 8377 794 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
t 0 0 0 0 0 2063 832 843 668 3494 2792 404 0 0 50 249 5361 3782 831 1317 0 0 0
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MA0114.1_shift7 (HNF4A) |
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0.862 |
0.487 |
6.666 |
0.497 |
0.914 |
2.491 |
0.904 |
2 |
4 |
3 |
2 |
3 |
2 |
2 |
2.571 |
3 |
; oligos_8nt_test_vs_ctrl_m2 versus MA0114.1 (HNF4A); m=3/5; ncol2=13; w=13; offset=7; strand=D; shift=7; score= 2.5714; -------rGgbCAAAGkyCa---
; cor=0.862; Ncor=0.487; logoDP=6.666; NIcor=0.497; NsEucl=0.914; SSD=2.491; NSW=0.904; rcor=2; rNcor=4; rlogoDP=3; rNIcor=2; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=2.571; 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
c 0 0 0 0 0 0 0 7 2 4 23 51 1 2 1 4 2 22 49 7 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
t 0 0 0 0 0 0 0 5 7 16 19 9 4 2 2 1 26 31 9 8 0 0 0
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MA0017.1_rc_shift6 (NR2F1_rc) |
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0.817 |
0.497 |
3.603 |
-0.066 |
0.914 |
2.905 |
0.896 |
4 |
3 |
5 |
5 |
4 |
3 |
3 |
3.857 |
4 |
; oligos_8nt_test_vs_ctrl_m2 versus MA0017.1_rc (NR2F1_rc); m=4/5; ncol2=14; w=14; offset=6; strand=R; shift=6; score= 3.8571; ------arGkkCAAAGkTCA---
; cor=0.817; Ncor=0.497; logoDP=3.603; NIcor=-0.066; NsEucl=0.914; SSD=2.905; NSW=0.896; rcor=4; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=3; rNSW=3; rank_mean=3.857; match_rank=4
a 0 0 0 0 0 0 7 4 1 1 0 0 12 11 10 0 0 0 0 11 0 0 0
c 0 0 0 0 0 0 3 0 1 1 3 11 0 0 0 0 0 1 12 2 0 0 0
g 0 0 0 0 0 0 3 6 10 5 4 0 0 2 3 13 7 0 0 0 0 0 0
t 0 0 0 0 0 0 0 3 1 6 6 2 1 0 0 0 6 12 1 0 0 0 0
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MA0114.2_rc_shift6 (HNF4A_rc) |
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0.795 |
0.519 |
5.945 |
0.175 |
0.912 |
3.514 |
0.883 |
5 |
2 |
4 |
4 |
5 |
5 |
5 |
4.286 |
5 |
; oligos_8nt_test_vs_ctrl_m2 versus MA0114.2_rc (HNF4A_rc); m=5/5; ncol2=15; w=15; offset=6; strand=R; shift=6; score= 4.2857; ------rrGkyCAAAGkyCAg--
; cor=0.795; Ncor=0.519; logoDP=5.945; NIcor=0.175; NsEucl=0.912; SSD=3.514; NSW=0.883; rcor=5; rNcor=2; rlogoDP=4; rNIcor=4; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=4.286; match_rank=5
a 0 0 0 0 0 0 5247 7985 1769 3334 2413 128 16188 13586 15112 49 988 477 70 13410 4057 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
g 0 0 0 0 0 0 6450 6498 13491 5653 3745 35 173 2637 1630 16535 4425 1846 51 720 5971 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
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