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_m4/peak-motifs_oligos_8nt_test_vs_ctrl_m4.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_m4/peak-motifs_oligos_8nt_test_vs_ctrl_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_m4_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 |
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| oligos_8nt_test_vs_ctrl_m4_shift0 (oligos_8nt_test_vs_ctrl_m4) |
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; oligos_8nt_test_vs_ctrl_m4; m=0 (reference); ncol1=20; shift=0; ncol=20; hyCCCTGGACTTTGCCCTvb
; Alignment reference
a 12 8 4 4 0 3 0 1 37 0 1 0 0 1 0 1 0 6 11 6
c 15 12 28 30 34 1 0 2 2 39 1 4 0 3 33 38 37 0 11 10
g 3 8 3 2 0 0 40 36 0 0 0 1 2 34 3 0 0 1 13 10
t 10 12 5 4 6 36 0 1 1 1 38 35 38 2 4 1 3 33 5 14
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| MA0114.2_shift4 (HNF4A) |
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0.856 |
0.642 |
8.481 |
0.631 |
0.930 |
2.224 |
0.926 |
1 |
1 |
1 |
1 |
2 |
2 |
2 |
1.429 |
1 |
; oligos_8nt_test_vs_ctrl_m4 versus MA0114.2 (HNF4A); m=1/4; ncol2=15; w=15; offset=4; strand=D; shift=4; score= 1.4286; ----cTGrmCTTTGrmCyy-
; cor=0.856; Ncor=0.642; logoDP=8.481; NIcor=0.631; NsEucl=0.930; SSD=2.224; NSW=0.926; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.429; match_rank=1
a 0 0 0 0 2766 1731 837 6075 11026 117 26 178 0 864 5270 6119 1156 1870 2070 0
c 0 0 0 0 5971 720 51 1846 4425 16535 1630 2637 173 35 3745 5653 13491 6498 6450 0
g 0 0 0 0 3974 907 15810 8370 329 67 0 367 407 15741 5340 1662 352 415 3001 0
t 0 0 0 0 4057 13410 70 477 988 49 15112 13586 16188 128 2413 3334 1769 7985 5247 0
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| MA0484.1_rc_shift5 (HNF4G_rc) |
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0.853 |
0.640 |
0.743 |
-0.132 |
0.931 |
2.114 |
0.930 |
2 |
2 |
3 |
4 |
1 |
1 |
1 |
2.000 |
2 |
; oligos_8nt_test_vs_ctrl_m4 versus MA0484.1_rc (HNF4G_rc); m=2/4; ncol2=15; w=15; offset=5; strand=R; shift=5; score= 2; -----TGrmCTTTGrmCyyt
; cor=0.853; Ncor=0.640; logoDP=0.743; NIcor=-0.132; NsEucl=0.931; SSD=2.114; NSW=0.930; rcor=2; rNcor=2; rlogoDP=3; rNIcor=4; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.000; match_rank=2
a 0 0 0 0 0 1317 831 3782 5361 249 50 0 0 404 2792 3494 668 843 832 2063
c 0 0 0 0 0 556 85 1107 3624 9098 938 1481 54 221 2279 3301 7480 3811 3830 2011
g 0 0 0 0 0 794 8377 4338 143 6 0 82 55 8827 2870 713 201 102 1531 1864
t 0 0 0 0 0 6785 159 225 324 99 8464 7889 9343 0 1511 1944 1103 4696 3259 3514
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| MA0114.1_rc_shift5 (HNF4A_rc) |
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0.846 |
0.550 |
2.854 |
0.172 |
0.917 |
2.353 |
0.910 |
3 |
4 |
2 |
2 |
3 |
3 |
3 |
2.857 |
3 |
; oligos_8nt_test_vs_ctrl_m4 versus MA0114.1_rc (HNF4A_rc); m=3/4; ncol2=13; w=13; offset=5; strand=R; shift=5; score= 2.8571; -----tGrmCTTTGvcCy--
; cor=0.846; Ncor=0.550; logoDP=2.854; NIcor=0.172; NsEucl=0.917; SSD=2.353; NSW=0.910; rcor=3; rNcor=4; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.857; match_rank=3
a 0 0 0 0 0 8 9 31 26 1 2 2 4 9 19 16 7 5 0 0
c 0 0 0 0 0 10 5 11 33 58 8 10 3 4 20 35 56 27 0 0
g 0 0 0 0 0 7 49 22 2 4 1 2 1 51 23 4 2 7 0 0
t 0 0 0 0 0 42 4 3 6 4 56 53 59 3 5 12 2 28 0 0
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| MA0065.2_rc_shift5 (PPARG::RXRA_rc) |
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0.751 |
0.563 |
0.673 |
-0.122 |
0.913 |
3.368 |
0.888 |
4 |
3 |
4 |
3 |
4 |
4 |
4 |
3.714 |
4 |
; oligos_8nt_test_vs_ctrl_m4 versus MA0065.2_rc (PPARG::RXRA_rc); m=4/4; ncol2=15; w=15; offset=5; strand=R; shift=5; score= 3.7143; -----TgmCCTyTgcCCyas
; cor=0.751; Ncor=0.563; logoDP=0.673; NIcor=-0.122; NsEucl=0.913; SSD=3.368; NSW=0.888; rcor=4; rNcor=3; rlogoDP=4; rNIcor=3; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=3.714; match_rank=4
a 0 0 0 0 0 81 109 479 120 12 9 23 8 66 193 34 87 79 464 126
c 0 0 0 0 0 47 144 263 693 767 137 270 15 179 395 674 671 368 127 320
g 0 0 0 0 0 58 555 99 9 2 5 48 21 547 129 15 3 23 166 317
t 0 0 0 0 0 676 54 22 41 82 713 522 819 71 145 139 100 390 101 94
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