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_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_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_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift2 ; 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_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3) |
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; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=2; ncol=18; --mdGGGTCAGrr-----
; Alignment reference
a 0 0 425 502 0 0 0 0 0 1513 0 452 396 0 0 0 0 0
c 0 0 446 86 0 0 0 0 1513 0 0 285 256 0 0 0 0 0
g 0 0 284 466 1513 1513 1513 0 0 0 1513 477 526 0 0 0 0 0
t 0 0 358 459 0 0 0 1513 0 0 0 299 335 0 0 0 0 0
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MA0258.1_shift2 (ESR2) |
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0.848 |
0.518 |
6.561 |
0.507 |
0.920 |
1.531 |
0.930 |
1 |
2 |
4 |
2 |
1 |
2 |
1 |
1.857 |
1 |
; oligos_6nt_test_vs_ctrl_m3 versus MA0258.1 (ESR2); m=1/5; ncol2=18; w=11; offset=0; strand=D; shift=2; score= 1.8571; --cwrGGTCAsgkTGmCC
; cor=0.848; Ncor=0.518; logoDP=6.561; NIcor=0.507; NsEucl=0.920; SSD=1.531; NSW=0.930; rcor=1; rNcor=2; rlogoDP=4; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.857; match_rank=1
a 0 0 78 158 186 27 18 13 0 337 49 64 52 21 63 178 34 46
c 0 0 161 51 15 0 20 19 357 1 123 63 61 33 25 99 268 289
g 0 0 63 41 154 275 319 33 0 0 113 149 147 24 265 19 2 0
t 0 0 55 107 2 55 0 292 0 19 72 81 97 279 4 61 53 22
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MA0071.1_shift0 (RORA_1) |
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0.834 |
0.513 |
9.825 |
0.504 |
0.892 |
1.486 |
0.907 |
2 |
3 |
1 |
3 |
4 |
1 |
2 |
2.286 |
2 |
; oligos_6nt_test_vs_ctrl_m3 versus MA0071.1 (RORA_1); m=2/5; ncol2=10; w=8; offset=-2; strand=D; shift=0; score= 2.2857; wwcwAGGTCA--------
; cor=0.834; Ncor=0.513; logoDP=9.825; NIcor=0.504; NsEucl=0.892; SSD=1.486; NSW=0.907; rcor=2; rNcor=3; rlogoDP=1; rNIcor=3; rNsEucl=4; rSSD=1; rNSW=2; rank_mean=2.286; match_rank=2
a 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0
c 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0
g 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0
t 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0
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MA0504.1_shift2 (NR2C2) |
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0.775 |
0.568 |
6.381 |
0.530 |
0.904 |
2.216 |
0.899 |
5 |
1 |
5 |
1 |
2 |
5 |
4 |
3.286 |
3 |
; oligos_6nt_test_vs_ctrl_m3 versus MA0504.1 (NR2C2); m=3/5; ncol2=15; w=11; offset=0; strand=D; shift=2; score= 3.2857; --mgrGGTCArAGGTCA-
; cor=0.775; Ncor=0.568; logoDP=6.381; NIcor=0.530; NsEucl=0.904; SSD=2.216; NSW=0.899; rcor=5; rNcor=1; rlogoDP=5; rNIcor=1; rNsEucl=2; rSSD=5; rNSW=4; rank_mean=3.286; match_rank=3
a 0 0 129 82 193 0 10 3 6 343 187 324 10 11 0 9 290 0
c 0 0 126 70 6 8 3 0 309 0 0 0 0 0 27 315 0 0
g 0 0 90 221 195 366 355 79 54 48 208 71 385 336 89 35 92 0
t 0 0 50 22 1 21 27 313 26 4 0 0 0 48 279 36 13 0
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MA0258.2_shift4 (ESR2) |
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0.814 |
0.431 |
7.479 |
0.420 |
0.895 |
1.783 |
0.901 |
3 |
4 |
3 |
5 |
3 |
3 |
3 |
3.429 |
4 |
; oligos_6nt_test_vs_ctrl_m3 versus MA0258.2 (ESR2); m=4/5; ncol2=15; w=9; offset=2; strand=D; shift=4; score= 3.4286; ----rGGTCAsmstGaCC
; cor=0.814; Ncor=0.431; logoDP=7.479; NIcor=0.420; NsEucl=0.895; SSD=1.783; NSW=0.901; rcor=3; rNcor=4; rlogoDP=3; rNIcor=5; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.429; match_rank=4
a 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111
c 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854
g 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0
t 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278
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MA0074.1_shift4 (RXRA::VDR) |
|
0.798 |
0.423 |
8.578 |
0.442 |
0.890 |
1.954 |
0.891 |
4 |
5 |
2 |
4 |
5 |
4 |
5 |
4.143 |
5 |
; oligos_6nt_test_vs_ctrl_m3 versus MA0074.1 (RXRA::VDR); m=5/5; ncol2=15; w=9; offset=2; strand=D; shift=4; score= 4.1429; ----RGGTCAwcGrGTTC
; cor=0.798; Ncor=0.423; logoDP=8.578; NIcor=0.442; NsEucl=0.890; SSD=1.954; NSW=0.891; rcor=4; rNcor=5; rlogoDP=2; rNIcor=4; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.143; match_rank=5
a 0 0 0 0 3 0 0 0 0 9 4 2 2 5 0 0 1 0
c 0 0 0 0 0 0 0 0 9 0 2 4 0 0 0 0 0 9
g 0 0 0 0 7 10 9 0 0 1 0 2 8 5 10 0 0 0
t 0 0 0 0 0 0 1 10 1 0 4 2 0 0 0 10 9 1
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