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_m2/peak-motifs_oligos_7nt_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_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_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 |
|---|
| oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; CACCTGCCCTTTGACCTGGCCACG
; Alignment reference
a 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0
c 1 0 1 1 0 0 1 1 1 0 0 0 0 0 1 1 0 0 0 1 1 0 1 0
g 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 1
t 0 0 0 0 1 0 0 0 0 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0
|
| MA0504.1_rc_shift4 (NR2C2_rc) |
 |
0.787 |
0.492 |
3.742 |
0.013 |
0.902 |
4.336 |
0.855 |
2 |
1 |
1 |
2 |
1 |
2 |
2 |
1.571 |
1 |
; oligos_7nt_test_vs_ctrl_m2 versus MA0504.1_rc (NR2C2_rc); m=1/3; ncol2=15; w=15; offset=4; strand=R; shift=4; score= 1.5714; ----TGACCTyTGACCyck-----
; cor=0.787; Ncor=0.492; logoDP=3.742; NIcor=0.013; NsEucl=0.902; SSD=4.336; NSW=0.855; rcor=2; rNcor=1; rlogoDP=1; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.571; match_rank=1
a 0 0 0 0 13 36 279 48 0 0 0 4 26 313 27 21 1 22 50 0 0 0 0 0
c 0 0 0 0 92 35 89 336 385 71 208 48 54 79 355 366 195 221 90 0 0 0 0 0
g 0 0 0 0 0 315 27 0 0 0 0 0 309 0 3 8 6 70 126 0 0 0 0 0
t 0 0 0 0 290 9 0 11 10 324 187 343 6 3 10 0 193 82 129 0 0 0 0 0
|
| MA0114.1_rc_shift4 (HNF4A_rc) |
 |
0.822 |
0.445 |
3.550 |
0.112 |
0.897 |
3.566 |
0.863 |
1 |
3 |
2 |
1 |
3 |
1 |
1 |
1.714 |
2 |
; oligos_7nt_test_vs_ctrl_m2 versus MA0114.1_rc (HNF4A_rc); m=2/3; ncol2=13; w=13; offset=4; strand=R; shift=4; score= 1.7143; ----tGrmCTTTGvcCy-------
; cor=0.822; Ncor=0.445; logoDP=3.550; NIcor=0.112; NsEucl=0.897; SSD=3.566; NSW=0.863; rcor=1; rNcor=3; rlogoDP=2; rNIcor=1; rNsEucl=3; rSSD=1; rNSW=1; rank_mean=1.714; match_rank=2
a 0 0 0 0 8 9 31 26 1 2 2 4 9 19 16 7 5 0 0 0 0 0 0 0
c 0 0 0 0 10 5 11 33 58 8 10 3 4 20 35 56 27 0 0 0 0 0 0 0
g 0 0 0 0 7 49 22 2 4 1 2 1 51 23 4 2 7 0 0 0 0 0 0 0
t 0 0 0 0 42 4 3 6 4 56 53 59 3 5 12 2 28 0 0 0 0 0 0 0
|
| MA0065.2_rc_shift4 (PPARG::RXRA_rc) |
 |
0.779 |
0.487 |
1.791 |
-0.076 |
0.898 |
4.682 |
0.844 |
3 |
2 |
3 |
3 |
2 |
3 |
3 |
2.714 |
3 |
; oligos_7nt_test_vs_ctrl_m2 versus MA0065.2_rc (PPARG::RXRA_rc); m=3/3; ncol2=15; w=15; offset=4; strand=R; shift=4; score= 2.7143; ----TgmCCTyTgcCCyas-----
; cor=0.779; Ncor=0.487; logoDP=1.791; NIcor=-0.076; NsEucl=0.898; SSD=4.682; NSW=0.844; rcor=3; rNcor=2; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.714; match_rank=3
a 0 0 0 0 81 109 479 120 12 9 23 8 66 193 34 87 79 464 126 0 0 0 0 0
c 0 0 0 0 47 144 263 693 767 137 270 15 179 395 674 671 368 127 320 0 0 0 0 0
g 0 0 0 0 58 555 99 9 2 5 48 21 547 129 15 3 23 166 317 0 0 0 0 0
t 0 0 0 0 676 54 22 41 82 713 522 819 71 145 139 100 390 101 94 0 0 0 0 0
|