One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.091816_2025-06-19.091816_x3rpdD/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.091816_2025-06-19.091816_x3rpdD/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift9 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m5_shift9 (oligos_6-8nt_m5) |
 |
|
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; oligos_6-8nt_m5; m=0 (reference); ncol1=12; shift=9; ncol=21; ---------csCCACGCCCcc
; Alignment reference
a 0 0 0 0 0 0 0 0 0 26 17 1 1 123 9 9 3 6 4 36 30
c 0 0 0 0 0 0 0 0 0 62 67 141 152 14 124 4 138 142 146 65 56
g 0 0 0 0 0 0 0 0 0 38 40 11 2 9 13 136 13 4 2 31 31
t 0 0 0 0 0 0 0 0 0 29 31 2 0 9 9 6 1 3 3 23 38
|