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/dyads_m4/peak-motifs_dyads_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/dyads_m4/peak-motifs_dyads_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 2 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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| dyads_m4_shift0 (dyads_m4) |
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; dyads_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; awyAAATAAATAAAww
; Alignment reference
a 816 878 261 1523 1525 1523 37 1539 1545 1536 17 1531 1527 1524 565 769
c 357 125 635 13 8 9 27 9 9 8 28 11 20 10 156 222
g 180 136 26 10 26 21 21 13 8 19 16 16 8 12 105 130
t 214 428 645 21 8 14 1482 6 5 4 1506 9 12 21 741 446
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| MA0042.1_rc_shift3 (FOXI1_rc) |
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0.772 |
0.579 |
4.114 |
0.117 |
0.895 |
3.146 |
0.869 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; dyads_m4 versus MA0042.1_rc (FOXI1_rc); m=1/1; ncol2=12; w=12; offset=3; strand=R; shift=3; score= 1; ---AwAyAAAyAhsm-
; cor=0.772; Ncor=0.579; logoDP=4.114; NIcor=0.117; NsEucl=0.895; SSD=3.146; NSW=0.869; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 0 24 18 24 0 31 31 31 0 31 8 7 10 0
c 0 0 0 4 4 7 16 0 0 0 18 0 8 12 14 0
g 0 0 0 1 1 0 0 0 0 0 0 0 4 8 1 0
t 0 0 0 2 8 0 15 0 0 0 13 0 11 4 6 0
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