One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_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/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift2 ; 3 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_mkv5_m2_shift2 (oligos_7nt_mkv5_m2) |
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; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=2; ncol=15; --wwATTTTTAAaw-
; Alignment reference
a 0 0 733 697 2692 0 0 0 0 0 2692 2691 1303 989 0
c 0 0 574 667 0 0 0 0 0 0 0 1 332 343 0
g 0 0 419 398 0 0 0 0 0 0 0 0 578 427 0
t 0 0 966 930 0 2692 2692 2692 2692 2692 0 0 479 933 0
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| MA0151.1_rc_shift7 (ARID3A_rc) |
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0.820 |
0.410 |
6.330 |
0.335 |
0.864 |
1.339 |
0.888 |
1 |
2 |
1 |
1 |
2 |
1 |
1 |
1.286 |
1 |
; oligos_7nt_mkv5_m2 versus MA0151.1_rc (ARID3A_rc); m=1/2; ncol2=6; w=6; offset=5; strand=R; shift=7; score= 1.2857; -------TTTrAT--
; cor=0.820; Ncor=0.410; logoDP=6.330; NIcor=0.335; NsEucl=0.864; SSD=1.339; NSW=0.888; rcor=1; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a 0 0 0 0 0 0 0 6 0 0 17 27 0 0 0
c 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
g 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0
t 0 0 0 0 0 0 0 20 27 27 1 0 27 0 0
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| MA0497.1_rc_shift0 (MEF2C_rc) |
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0.751 |
0.601 |
2.167 |
-0.067 |
0.901 |
2.826 |
0.882 |
2 |
1 |
2 |
2 |
1 |
2 |
2 |
1.714 |
2 |
; oligos_7nt_mkv5_m2 versus MA0497.1_rc (MEF2C_rc); m=2/2; ncol2=15; w=12; offset=-2; strand=R; shift=0; score= 1.7143; wkCTATTTTTrgmhy
; cor=0.751; Ncor=0.601; logoDP=2.167; NIcor=-0.067; NsEucl=0.901; SSD=2.826; NSW=0.882; rcor=2; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.714; match_rank=2
a 624 250 29 0 2091 70 76 15 230 263 1224 337 760 752 507
c 126 148 1671 32 0 4 2 87 241 74 0 78 822 573 676
g 450 836 120 0 62 0 0 0 32 256 985 1412 196 151 321
t 1009 975 389 2177 56 2135 2131 2107 1706 1616 0 382 431 733 705
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