One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m3/peak-motifs_positions_6-8nt_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.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/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m3/peak-motifs_positions_6-8nt_m3_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: positions_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6-8nt_m3_shift0 (positions_6-8nt_m3) |
 |
|
|
; positions_6-8nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wwCGTCAAcr
; Alignment reference
a 246 282 0 0 0 0 809 964 223 279
c 211 209 983 0 0 983 6 9 288 214
g 243 208 0 983 0 0 29 5 232 265
t 283 284 0 0 983 0 139 5 240 225
|
| tin_rc_shift4 (tin_rc) |
 |
|
|
; positions_6-8nt_m3 versus tin_rc; m=1/1; ncol2=7; w=0; offset=4; strand=R; shift=4; score=0.416108; ----TCAAGT
; cor=; Ncor=
a 0 0 0 0 0 0 11 11 0 0
c 0 0 0 0 1 8 0 0 0 0
g 0 0 0 0 0 1 0 0 11 1
t 0 0 0 0 10 2 0 0 0 10
|