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.2026-01-25.184326_2026-01-25.184326_ptOhrJ/results/discovered_motifs/oligos_6-8nt_m8/peak-motifs_oligos_6-8nt_m8.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.2026-01-25.184326_2026-01-25.184326_ptOhrJ/results/discovered_motifs/oligos_6-8nt_m8/peak-motifs_oligos_6-8nt_m8_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m8_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)
; oligos_6-8nt_m8; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATAAATAwww ; Alignment reference a 232 183 433 17 573 471 548 10 575 267 221 205 c 94 108 38 12 15 47 23 22 16 105 105 119 g 123 109 76 24 10 28 29 17 16 81 117 93 t 176 225 78 572 27 79 25 576 18 172 182 208

br-Z4_rc_shift3 (br-Z4_rc)
; oligos_6-8nt_m8 versus br-Z4_rc; m=1/5; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.540736; ---TAAhYAdT- ; cor=; Ncor= a 0 0 0 1 7 8 2 0 8 3 1 0 c 0 0 0 0 0 0 3 2 0 0 0 0 g 0 0 0 0 0 0 0 0 0 2 0 0 t 0 0 0 7 1 0 3 6 0 3 7 0

Antp_shift5 (Antp)
; oligos_6-8nt_m8 versus Antp; m=2/5; ncol2=6; w=0; offset=5; strand=D; shift=5; score=0.443294; -----mATAAw- ; cor=; Ncor= a 0 0 0 0 0 10.5 18 0 16.5 18 7.5 0 c 0 0 0 0 0 4.5 0 0 0 0 0 0 g 0 0 0 0 0 3 0 0 1.5 0 0 0 t 0 0 0 0 0 0 0 18 0 0 10.5 0

zen_shift1 (zen)
; oligos_6-8nt_m8 versus zen; m=3/5; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.436814; -AATwAA----- ; cor=; Ncor= a 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 c 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 t 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0 0

abd-A_shift2 (abd-A)
; oligos_6-8nt_m8 versus abd-A; m=4/5; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.426345; --aTAAWT---- ; cor=; Ncor= a 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 0 c 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 0 g 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 0 t 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0 0

br-Z2_rc_shift3 (br-Z2_rc)
; oligos_6-8nt_m8 versus br-Z2_rc; m=5/5; ncol2=7; w=0; offset=3; strand=R; shift=3; score=0.417786; ---twaaTAG-- ; cor=; Ncor= a 0 0 0 5 9 12 11 0 21 1 0 0 c 0 0 0 4 1 3 3 0 0 0 0 0 g 0 0 0 0 3 1 3 0 0 20 0 0 t 0 0 0 12 8 5 4 21 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8)				; oligos_6-8nt_m8; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATAAATAwww ; Alignment reference a 232 183 433 17 573 471 548 10 575 267 221 205 c 94 108 38 12 15 47 23 22 16 105 105 119 g 123 109 76 24 10 28 29 17 16 81 117 93 t 176 225 78 572 27 79 25 576 18 172 182 208
br-Z4_rc_shift3 (br-Z4_rc)				; oligos_6-8nt_m8 versus br-Z4_rc; m=1/5; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.540736; ---TAAhYAdT- ; cor=; Ncor= a 0 0 0 1 7 8 2 0 8 3 1 0 c 0 0 0 0 0 0 3 2 0 0 0 0 g 0 0 0 0 0 0 0 0 0 2 0 0 t 0 0 0 7 1 0 3 6 0 3 7 0
Antp_shift5 (Antp)				; oligos_6-8nt_m8 versus Antp; m=2/5; ncol2=6; w=0; offset=5; strand=D; shift=5; score=0.443294; -----mATAAw- ; cor=; Ncor= a 0 0 0 0 0 10.5 18 0 16.5 18 7.5 0 c 0 0 0 0 0 4.5 0 0 0 0 0 0 g 0 0 0 0 0 3 0 0 1.5 0 0 0 t 0 0 0 0 0 0 0 18 0 0 10.5 0
zen_shift1 (zen)				; oligos_6-8nt_m8 versus zen; m=3/5; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.436814; -AATwAA----- ; cor=; Ncor= a 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 c 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 t 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0 0
abd-A_shift2 (abd-A)				; oligos_6-8nt_m8 versus abd-A; m=4/5; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.426345; --aTAAWT---- ; cor=; Ncor= a 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 0 c 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 0 g 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 0 t 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0 0
br-Z2_rc_shift3 (br-Z2_rc)				; oligos_6-8nt_m8 versus br-Z2_rc; m=5/5; ncol2=7; w=0; offset=3; strand=R; shift=3; score=0.417786; ---twaaTAG-- ; cor=; Ncor= a 0 0 0 5 9 12 11 0 21 1 0 0 c 0 0 0 4 1 3 3 0 0 0 0 0 g 0 0 0 0 3 1 3 0 0 20 0 0 t 0 0 0 12 8 5 4 21 0 0 0 0