One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_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/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_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 |
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oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4) |
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; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=13; shift=0; ncol=14; ttTTCTTTTCTtt-
; Alignment reference
a 284 285 145 199 3 0 6 8 4 1 7 298 281 0
c 250 209 51 47 1336 0 0 0 1 1338 14 258 292 0
g 215 182 43 30 0 11 1 0 0 0 46 236 177 0
t 590 663 1100 1063 0 1328 1332 1331 1334 0 1272 547 589 0
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MA0035.3_shift2 (Gata1) |
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0.767 |
0.649 |
9.313 |
0.658 |
0.896 |
2.612 |
0.881 |
2 |
1 |
1 |
1 |
1 |
3 |
1 |
1.429 |
1 |
; oligos_6nt_mkv4_m4 versus MA0035.3 (Gata1); m=1/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 1.4286; --tyCTTATCTsy-
; cor=0.767; Ncor=0.649; logoDP=9.313; NIcor=0.658; NsEucl=0.896; SSD=2.612; NSW=0.881; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=3; rNSW=1; rank_mean=1.429; match_rank=1
a 0 0 2035 506 0 0 0 17955 0 0 2166 2502 1886 0
c 0 0 4321 6406 14869 697 0 0 0 17955 0 6166 5072 0
g 0 0 2530 2792 437 0 0 0 0 0 0 6687 1598 0
t 0 0 9069 8251 2649 17258 17955 0 17955 0 15789 2600 9399 0
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MA0482.1_shift3 (Gata4) |
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0.757 |
0.541 |
8.933 |
0.552 |
0.887 |
2.546 |
0.873 |
3 |
2 |
2 |
2 |
2 |
2 |
2 |
2.143 |
2 |
; oligos_6nt_mkv4_m4 versus MA0482.1 (Gata4); m=2/3; ncol2=11; w=10; offset=3; strand=D; shift=3; score= 2.1429; ---yCTTATCTsyy
; cor=0.757; Ncor=0.541; logoDP=8.933; NIcor=0.552; NsEucl=0.887; SSD=2.546; NSW=0.873; rcor=3; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.143; match_rank=2
a 0 0 0 10 0 0 0 2707 0 0 547 0 601 386
c 0 0 0 1039 2165 89 0 39 0 2746 0 1240 1004 929
g 0 0 0 374 306 0 0 0 0 0 0 940 157 682
t 0 0 0 1323 275 2657 2746 0 2746 0 2199 566 984 749
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MA0037.2_rc_shift3 (GATA3_rc) |
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0.787 |
0.484 |
2.035 |
-0.076 |
0.867 |
2.253 |
0.859 |
1 |
3 |
3 |
3 |
3 |
1 |
3 |
2.429 |
3 |
; oligos_6nt_mkv4_m4 versus MA0037.2_rc (GATA3_rc); m=3/3; ncol2=8; w=8; offset=3; strand=R; shift=3; score= 2.4286; ---tYTTATCT---
; cor=0.787; Ncor=0.484; logoDP=2.035; NIcor=-0.076; NsEucl=0.867; SSD=2.253; NSW=0.859; rcor=1; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=1; rNSW=3; rank_mean=2.429; match_rank=3
a 0 0 0 0 0 0 0 4628 0 0 0 0 0 0
c 0 0 0 1120 3338 0 0 0 0 4628 0 0 0 0
g 0 0 0 712 0 0 0 0 0 0 0 0 0 0
t 0 0 0 2796 1290 4628 4628 0 4628 0 4628 0 0 0
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