One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.203737_2025-04-28.203737_n2namY/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_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/2025/04/28/peak-motifs.2025-04-28.203737_2025-04-28.203737_n2namY/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; twaATAAATAww ; Alignment reference a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12

br-Z4_rc_shift4 (br-Z4_rc)
; oligos_7nt_mkv2_m3 versus br-Z4_rc; m=1/6; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.526082; ----TAAhYAdT ; cor=; Ncor= a 0 0 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 0 t 0 0 0 0 7 1 0 3 6 0 3 7

zen_shift2 (zen)
; oligos_7nt_mkv2_m3 versus zen; m=2/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.473161; --AATwAA---- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 0 0 0.541667 0 1.08333 0 0 0 0 0 0 0 g 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

gt_shift0 (gt)
; oligos_7nt_mkv2_m3 versus gt; m=3/6; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.445613; GTmAwAW----- ; cor=; Ncor= a 0 1 5 8 3 8 6 0 0 0 0 0 c 1 1 3 0 0 0 0 0 0 0 0 0 g 7 0 0 0 0 0 0 0 0 0 0 0 t 0 6 0 0 5 0 2 0 0 0 0 0

Antp_shift2 (Antp)
; oligos_7nt_mkv2_m3 versus Antp; m=4/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.432536; --mATAAw---- ; cor=; Ncor= a 0 0 10.5 18 0 16.5 18 7.5 0 0 0 0 c 0 0 4.5 0 0 0 0 0 0 0 0 0 g 0 0 3 0 0 1.5 0 0 0 0 0 0 t 0 0 0 0 18 0 0 10.5 0 0 0 0

br-Z2_rc_shift4 (br-Z2_rc)
; oligos_7nt_mkv2_m3 versus br-Z2_rc; m=5/6; ncol2=7; w=0; offset=4; strand=R; shift=4; score=0.414599; ----twaaTAG- ; cor=; Ncor= a 0 0 0 0 5 9 12 11 0 21 1 0 c 0 0 0 0 4 1 3 3 0 0 0 0 g 0 0 0 0 0 3 1 3 0 0 20 0 t 0 0 0 0 12 8 5 4 21 0 0 0

abd-A_shift3 (abd-A)
; oligos_7nt_mkv2_m3 versus abd-A; m=6/6; ncol2=6; w=0; offset=3; strand=D; shift=3; score=0.407691; ---aTAAWT--- ; cor=; Ncor= a 0 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; twaATAAATAww ; Alignment reference a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12
br-Z4_rc_shift4 (br-Z4_rc)				; oligos_7nt_mkv2_m3 versus br-Z4_rc; m=1/6; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.526082; ----TAAhYAdT ; cor=; Ncor= a 0 0 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 0 t 0 0 0 0 7 1 0 3 6 0 3 7
zen_shift2 (zen)				; oligos_7nt_mkv2_m3 versus zen; m=2/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.473161; --AATwAA---- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 0 0 0.541667 0 1.08333 0 0 0 0 0 0 0 g 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
gt_shift0 (gt)				; oligos_7nt_mkv2_m3 versus gt; m=3/6; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.445613; GTmAwAW----- ; cor=; Ncor= a 0 1 5 8 3 8 6 0 0 0 0 0 c 1 1 3 0 0 0 0 0 0 0 0 0 g 7 0 0 0 0 0 0 0 0 0 0 0 t 0 6 0 0 5 0 2 0 0 0 0 0
Antp_shift2 (Antp)				; oligos_7nt_mkv2_m3 versus Antp; m=4/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.432536; --mATAAw---- ; cor=; Ncor= a 0 0 10.5 18 0 16.5 18 7.5 0 0 0 0 c 0 0 4.5 0 0 0 0 0 0 0 0 0 g 0 0 3 0 0 1.5 0 0 0 0 0 0 t 0 0 0 0 18 0 0 10.5 0 0 0 0
br-Z2_rc_shift4 (br-Z2_rc)				; oligos_7nt_mkv2_m3 versus br-Z2_rc; m=5/6; ncol2=7; w=0; offset=4; strand=R; shift=4; score=0.414599; ----twaaTAG- ; cor=; Ncor= a 0 0 0 0 5 9 12 11 0 21 1 0 c 0 0 0 0 4 1 3 3 0 0 0 0 g 0 0 0 0 0 3 1 3 0 0 20 0 t 0 0 0 0 12 8 5 4 21 0 0 0
abd-A_shift3 (abd-A)				; oligos_7nt_mkv2_m3 versus abd-A; m=6/6; ncol2=6; w=0; offset=3; strand=D; shift=3; score=0.407691; ---aTAAWT--- ; cor=; Ncor= a 0 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0