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/oligos_6-8nt_m9/peak-motifs_oligos_6-8nt_m9.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/oligos_6-8nt_m9/peak-motifs_oligos_6-8nt_m9_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m9_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m9_shift0 (oligos_6-8nt_m9)
; oligos_6-8nt_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; waAATGAAaw ; Alignment reference a 700 1027 2381 2381 0 0 2381 2381 1101 836 c 482 452 0 0 0 0 0 0 337 368 g 529 495 0 0 0 2381 0 0 374 440 t 670 407 0 0 2381 0 0 0 569 737

en_rc_shift1 (en_rc)
; oligos_6-8nt_m9 versus en_rc; m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.609738; -yAATtAah- ; cor=; Ncor= a 0 10.125 58.5 57.375 1.125 5.625 51.75 31.5 18 0 c 0 31.5 3.375 2.25 0 14.625 4.5 11.25 21.375 0 g 0 1.125 0 1.125 1.125 6.75 6.75 12.375 0 0 t 0 20.25 1.125 2.25 60.75 36 0 7.875 23.625 0

sd_rc_shift1 (sd_rc)
; oligos_6-8nt_m9 versus sd_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.537557; -mAAwGdAAT ; cor=; Ncor= a 0 8 16 14 7 0 9 13 15 1 c 0 7 0 0 0 4 0 3 0 1 g 0 4 0 1 2 14 5 0 3 1 t 0 0 3 4 10 1 5 3 1 16

zen_shift2 (zen)
; oligos_6-8nt_m9 versus zen; m=3/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.484903; --AATwAA-- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 c 0 0 0.541667 0 1.08333 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 t 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0

ap_shift2 (ap)
; oligos_6-8nt_m9 versus ap; m=4/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.422116; --AAThAt-- ; cor=; Ncor= a 0 0 14 14 0 5 13 2 0 0 c 0 0 0 0 1 4 0 1 0 0 g 0 0 0 0 1 1 1 3 0 0 t 0 0 0 0 12 4 0 8 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m9_shift0 (oligos_6-8nt_m9)				; oligos_6-8nt_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; waAATGAAaw ; Alignment reference a 700 1027 2381 2381 0 0 2381 2381 1101 836 c 482 452 0 0 0 0 0 0 337 368 g 529 495 0 0 0 2381 0 0 374 440 t 670 407 0 0 2381 0 0 0 569 737
en_rc_shift1 (en_rc)				; oligos_6-8nt_m9 versus en_rc; m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.609738; -yAATtAah- ; cor=; Ncor= a 0 10.125 58.5 57.375 1.125 5.625 51.75 31.5 18 0 c 0 31.5 3.375 2.25 0 14.625 4.5 11.25 21.375 0 g 0 1.125 0 1.125 1.125 6.75 6.75 12.375 0 0 t 0 20.25 1.125 2.25 60.75 36 0 7.875 23.625 0
sd_rc_shift1 (sd_rc)				; oligos_6-8nt_m9 versus sd_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.537557; -mAAwGdAAT ; cor=; Ncor= a 0 8 16 14 7 0 9 13 15 1 c 0 7 0 0 0 4 0 3 0 1 g 0 4 0 1 2 14 5 0 3 1 t 0 0 3 4 10 1 5 3 1 16
zen_shift2 (zen)				; oligos_6-8nt_m9 versus zen; m=3/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.484903; --AATwAA-- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 c 0 0 0.541667 0 1.08333 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 t 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0
ap_shift2 (ap)				; oligos_6-8nt_m9 versus ap; m=4/4; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.422116; --AAThAt-- ; cor=; Ncor= a 0 0 14 14 0 5 13 2 0 0 c 0 0 0 0 1 4 0 1 0 0 g 0 0 0 0 1 1 1 3 0 0 t 0 0 0 0 12 4 0 8 0 0