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_m3/peak-motifs_oligos_8nt_test_vs_ctrl_m3.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_m3/peak-motifs_oligos_8nt_test_vs_ctrl_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_m3_shift3 ; 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 |
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| oligos_8nt_test_vs_ctrl_m3_shift3 (oligos_8nt_test_vs_ctrl_m3) |
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; oligos_8nt_test_vs_ctrl_m3; m=0 (reference); ncol1=17; shift=3; ncol=20; ---ksCCAGAGTCCAGGGwt
; Alignment reference
a 0 0 0 17 13 6 0 84 5 84 0 0 0 0 74 4 4 9 31 19
c 0 0 0 13 28 68 88 3 2 2 1 1 87 88 3 4 6 4 19 18
g 0 0 0 32 30 9 0 1 82 2 88 4 0 1 5 77 77 72 15 17
t 0 0 0 28 19 7 2 2 1 2 1 85 3 1 8 5 3 5 25 36
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| MA0114.2_rc_shift1 (HNF4A_rc) |
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0.784 |
0.537 |
3.897 |
0.157 |
0.913 |
2.587 |
0.900 |
1 |
1 |
2 |
2 |
1 |
2 |
1 |
1.429 |
1 |
; oligos_8nt_test_vs_ctrl_m3 versus MA0114.2_rc (HNF4A_rc); m=1/2; ncol2=15; w=13; offset=-2; strand=R; shift=1; score= 1.4286; -rrGkyCAAAGkyCAg----
; cor=0.784; Ncor=0.537; logoDP=3.897; NIcor=0.157; NsEucl=0.913; SSD=2.587; NSW=0.900; rcor=1; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.429; match_rank=1
a 0 5247 7985 1769 3334 2413 128 16188 13586 15112 49 988 477 70 13410 4057 0 0 0 0
c 0 3001 415 352 1662 5340 15741 407 367 0 67 329 8370 15810 907 3974 0 0 0 0
g 0 6450 6498 13491 5653 3745 35 173 2637 1630 16535 4425 1846 51 720 5971 0 0 0 0
t 0 2070 1870 1156 6119 5270 864 0 178 26 117 11026 6075 837 1731 2766 0 0 0 0
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| MA0484.1_shift0 (HNF4G) |
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0.774 |
0.464 |
6.915 |
0.438 |
0.906 |
2.521 |
0.895 |
2 |
2 |
1 |
1 |
2 |
1 |
2 |
1.571 |
2 |
; oligos_8nt_test_vs_ctrl_m3 versus MA0484.1 (HNF4G); m=2/2; ncol2=15; w=12; offset=-3; strand=D; shift=0; score= 1.5714; arrGkyCAAAGkyCA-----
; cor=0.774; Ncor=0.464; logoDP=6.915; NIcor=0.438; NsEucl=0.906; SSD=2.521; NSW=0.895; rcor=2; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=2; rank_mean=1.571; match_rank=2
a 3514 3259 4696 1103 1944 1511 0 9343 7889 8464 99 324 225 159 6785 0 0 0 0 0
c 1864 1531 102 201 713 2870 8827 55 82 0 6 143 4338 8377 794 0 0 0 0 0
g 2011 3830 3811 7480 3301 2279 221 54 1481 938 9098 3624 1107 85 556 0 0 0 0 0
t 2063 832 843 668 3494 2792 404 0 0 50 249 5361 3782 831 1317 0 0 0 0 0
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