One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.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 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_jaspar_core_insects
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 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 |
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| oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1) |
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; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wkCTTATsArw
; Alignment reference
a | 474 394 0 0 0 1796 0 0 1796 611 473
c | 435 355 1796 0 0 0 0 1203 0 347 443
g | 342 496 0 0 0 0 0 593 0 458 295
t | 545 551 0 1796 1796 0 1796 0 0 380 585
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| MA0199.1_rc_shift4 (Optix_rc) |
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0.957 |
0.435 |
2.664 |
0.084 |
0.924 |
0.289 |
0.971 |
1 |
1 |
2 |
2 |
1 |
1 |
1 |
1.286 |
1 |
; oligos_6nt_mkv4_m1 versus MA0199.1_rc (Optix_rc); m=1/2; ncol2=5; w=5; offset=4; strand=R; shift=4; score= 1.2857; ----TATCA--
; cor=0.957; Ncor=0.435; logoDP=2.664; NIcor=0.084; NsEucl=0.924; SSD=0.289; NSW=0.971; rcor=1; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a | 0 0 0 0 0 27 0 0 22 0 0
c | 0 0 0 0 1 0 0 27 0 0 0
g | 0 0 0 0 0 0 0 0 5 0 0
t | 0 0 0 0 26 0 27 0 0 0 0
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| MA0246.1_rc_shift3 (so_rc) |
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0.768 |
0.419 |
5.200 |
0.225 |
0.839 |
1.868 |
0.844 |
2 |
2 |
1 |
1 |
2 |
2 |
2 |
1.714 |
2 |
; oligos_6nt_mkv4_m1 versus MA0246.1_rc (so_rc); m=2/2; ncol2=6; w=6; offset=3; strand=R; shift=3; score= 1.7143; ---GTATCA--
; cor=0.768; Ncor=0.419; logoDP=5.200; NIcor=0.225; NsEucl=0.839; SSD=1.868; NSW=0.844; rcor=2; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.714; match_rank=2
a | 0 0 0 3 0 26 0 0 26 0 0
c | 0 0 0 0 0 1 0 27 1 0 0
g | 0 0 0 10 0 0 0 0 0 0 0
t | 0 0 0 0 27 0 27 0 0 0 0
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