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.2026-01-25.180941_2026-01-25.180941_K9UVGH/results/discovered_motifs/oligos_6-8nt_m6/peak-motifs_oligos_6-8nt_m6.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.2026-01-25.180941_2026-01-25.180941_K9UVGH/results/discovered_motifs/oligos_6-8nt_m6/peak-motifs_oligos_6-8nt_m6_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m6_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)
; oligos_6-8nt_m6; m=0 (reference); ncol1=13; shift=0; ncol=13; wwaATAAATAAww ; Alignment reference a 383 486 767 825 67 1043 981 1032 38 1058 875 464 404 c 205 174 85 76 46 25 47 38 47 22 66 185 183 g 191 175 100 91 18 20 34 22 30 25 55 181 171 t 373 317 200 160 1021 64 90 60 1037 47 156 322 394

hb_shift2 (hb)
; oligos_6-8nt_m6 versus hb; m=1/6; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.502525; --mayAAAAAa-- ; cor=; Ncor= a 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 c 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 g 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 t 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0

br-Z4_rc_shift4 (br-Z4_rc)
; oligos_6-8nt_m6 versus br-Z4_rc; m=2/6; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.490747; ----TAAhYAdT- ; cor=; Ncor= a 0 0 0 0 1 7 8 2 0 8 3 1 0 c 0 0 0 0 0 0 0 3 2 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 0 0 t 0 0 0 0 7 1 0 3 6 0 3 7 0

zen_shift2 (zen)
; oligos_6-8nt_m6 versus zen; m=3/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.441955; --AATwAA----- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 c 0 0 0.541667 0 1.08333 0 0 0 0 0 0 0 0 g 0 0 0 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 0 0 0

Dfd_rc_shift3 (Dfd_rc)
; oligos_6-8nt_m6 versus Dfd_rc; m=4/6; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.436099; ---rymATTAA-- ; cor=; Ncor= a 0 0 0 9 2 10 16 0 0 15 11 0 0 c 0 0 0 2 6 5 0 0 0 0 2 0 0 g 0 0 0 5 0 0 0 1 1 0 2 0 0 t 0 0 0 0 8 1 0 15 15 1 1 0 0

Antp_shift6 (Antp)
; oligos_6-8nt_m6 versus Antp; m=5/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.43327; ------mATAAw- ; cor=; Ncor= a 0 0 0 0 0 0 10.5 18 0 16.5 18 7.5 0 c 0 0 0 0 0 0 4.5 0 0 0 0 0 0 g 0 0 0 0 0 0 3 0 0 1.5 0 0 0 t 0 0 0 0 0 0 0 0 18 0 0 10.5 0

ap_shift6 (ap)
; oligos_6-8nt_m6 versus ap; m=6/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.400727; ------AAThAt- ; cor=; Ncor= a 0 0 0 0 0 0 14 14 0 5 13 2 0 c 0 0 0 0 0 0 0 0 1 4 0 1 0 g 0 0 0 0 0 0 0 0 1 1 1 3 0 t 0 0 0 0 0 0 0 0 12 4 0 8 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6)				; oligos_6-8nt_m6; m=0 (reference); ncol1=13; shift=0; ncol=13; wwaATAAATAAww ; Alignment reference a 383 486 767 825 67 1043 981 1032 38 1058 875 464 404 c 205 174 85 76 46 25 47 38 47 22 66 185 183 g 191 175 100 91 18 20 34 22 30 25 55 181 171 t 373 317 200 160 1021 64 90 60 1037 47 156 322 394
hb_shift2 (hb)				; oligos_6-8nt_m6 versus hb; m=1/6; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.502525; --mayAAAAAa-- ; cor=; Ncor= a 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 c 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 g 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 t 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0
br-Z4_rc_shift4 (br-Z4_rc)				; oligos_6-8nt_m6 versus br-Z4_rc; m=2/6; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.490747; ----TAAhYAdT- ; cor=; Ncor= a 0 0 0 0 1 7 8 2 0 8 3 1 0 c 0 0 0 0 0 0 0 3 2 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 0 0 t 0 0 0 0 7 1 0 3 6 0 3 7 0
zen_shift2 (zen)				; oligos_6-8nt_m6 versus zen; m=3/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.441955; --AATwAA----- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 c 0 0 0.541667 0 1.08333 0 0 0 0 0 0 0 0 g 0 0 0 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 0 0 0
Dfd_rc_shift3 (Dfd_rc)				; oligos_6-8nt_m6 versus Dfd_rc; m=4/6; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.436099; ---rymATTAA-- ; cor=; Ncor= a 0 0 0 9 2 10 16 0 0 15 11 0 0 c 0 0 0 2 6 5 0 0 0 0 2 0 0 g 0 0 0 5 0 0 0 1 1 0 2 0 0 t 0 0 0 0 8 1 0 15 15 1 1 0 0
Antp_shift6 (Antp)				; oligos_6-8nt_m6 versus Antp; m=5/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.43327; ------mATAAw- ; cor=; Ncor= a 0 0 0 0 0 0 10.5 18 0 16.5 18 7.5 0 c 0 0 0 0 0 0 4.5 0 0 0 0 0 0 g 0 0 0 0 0 0 3 0 0 1.5 0 0 0 t 0 0 0 0 0 0 0 0 18 0 0 10.5 0
ap_shift6 (ap)				; oligos_6-8nt_m6 versus ap; m=6/6; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.400727; ------AAThAt- ; cor=; Ncor= a 0 0 0 0 0 0 14 14 0 5 13 2 0 c 0 0 0 0 0 0 0 0 1 4 0 1 0 g 0 0 0 0 0 0 0 0 1 1 1 3 0 t 0 0 0 0 0 0 0 0 12 4 0 8 0