One-to-n alignments
Command: compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/custom_motif_file.tf -format2 transfac -strand DR -lth cor 0.7 -lth Ncor 0.4 -uth match_rank 50 -return cor,Ncor,logoDP,NsEucl,NSW,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2026/04/21/compare-matrices_2026-04-21.093227_5guD2o/compare-matrices.tab
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift1 ; 3 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NsEucl |
NSW |
rcor |
rNcor |
rlogoDP |
rNsEucl |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3) |
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; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -msGAGAGAArG
; Alignment reference
a 0 2 0 0 4 0 4 0 4 4 2 0
c 0 2 2 0 0 0 0 0 0 0 0 0
g 0 0 2 4 0 4 0 4 0 0 2 4
t 0 0 0 0 0 0 0 0 0 0 0 0
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| oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2) |
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0.759 |
0.759 |
12.071 |
0.888 |
0.861 |
1 |
1 |
2 |
1 |
1 |
1.200 |
1 |
; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1.2; -hmGAGAGGAms
; cor=0.759; Ncor=0.759; logoDP=12.071; NsEucl=0.888; NSW=0.861; rcor=1; rNcor=1; rlogoDP=2; rNsEucl=1; rNSW=1; rank_mean=1.200; match_rank=1
a 0 2 2 0 7 0 7 0 0 7 4 1
c 0 2 4 0 0 0 0 0 0 0 2 2
g 0 1 0 7 0 7 0 7 7 0 1 4
t 0 2 1 0 0 0 0 0 0 0 0 0
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| oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |
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0.729 |
0.617 |
12.706 |
0.878 |
0.835 |
2 |
2 |
1 |
2 |
2 |
1.800 |
2 |
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m1; m=2/2; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score= 1.8; hnMGAGAGGAAs
; cor=0.729; Ncor=0.617; logoDP=12.706; NsEucl=0.878; NSW=0.835; rcor=2; rNcor=2; rlogoDP=1; rNsEucl=2; rNSW=2; rank_mean=1.800; match_rank=2
a 2 1 1 0 4 0 4 0 0 4 4 0
c 1 1 3 0 0 0 0 0 0 0 0 2
g 0 1 0 4 0 4 0 4 4 0 0 2
t 1 1 0 0 0 0 0 0 0 0 0 0
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