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.2026-01-25.181000_2026-01-25.181000_CpuIe4/results/discovered_motifs/positions_6-8nt_m1/peak-motifs_positions_6-8nt_m1.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.2026-01-25.181000_2026-01-25.181000_CpuIe4/results/discovered_motifs/positions_6-8nt_m1/peak-motifs_positions_6-8nt_m1_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: positions_6-8nt_m1_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m1_shift2 (positions_6-8nt_m1)
; positions_6-8nt_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --aaAAAAAAaa ; Alignment reference a 0 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 c 0 0 497 454 0 0 0 0 0 0 384 419 g 0 0 434 419 0 0 0 0 0 0 382 393 t 0 0 449 427 0 12 10 7 9 0 535 501

hb_shift2 (hb)
; positions_6-8nt_m1 versus hb; m=1/4; ncol2=9; w=0; offset=0; strand=D; shift=2; score=0.733313; --mayAAAAAa- ; cor=; Ncor= a 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 c 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 g 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 t 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0

zen_shift4 (zen)
; positions_6-8nt_m1 versus zen; m=2/4; ncol2=6; w=0; offset=2; strand=D; shift=4; score=0.448429; ----AATwAA-- ; cor=; Ncor= a 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 c 0 0 0 0 0.541667 0 1.08333 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0

cad_rc_shift0 (cad_rc)
; positions_6-8nt_m1 versus cad_rc; m=3/4; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.416893; WrtYrwAAA--- ; cor=; Ncor= a 9 8 1 0 7 4 12 11 11 0 0 0 c 0 1 3 9 1 2 0 2 0 0 0 0 g 0 4 3 0 5 1 1 0 0 0 0 0 t 4 0 6 4 0 6 0 0 2 0 0 0

gt_shift1 (gt)
; positions_6-8nt_m1 versus gt; m=4/4; ncol2=7; w=-1; offset=-1; strand=D; shift=1; score=0.409894; -GTmAwAW---- ; cor=; Ncor= a 0 0 1 5 8 3 8 6 0 0 0 0 c 0 1 1 3 0 0 0 0 0 0 0 0 g 0 7 0 0 0 0 0 0 0 0 0 0 t 0 0 6 0 0 5 0 2 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m1_shift2 (positions_6-8nt_m1)				; positions_6-8nt_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --aaAAAAAAaa ; Alignment reference a 0 0 994 1074 2374 2362 2364 2367 2365 2374 1073 1061 c 0 0 497 454 0 0 0 0 0 0 384 419 g 0 0 434 419 0 0 0 0 0 0 382 393 t 0 0 449 427 0 12 10 7 9 0 535 501
hb_shift2 (hb)				; positions_6-8nt_m1 versus hb; m=1/4; ncol2=9; w=0; offset=0; strand=D; shift=2; score=0.733313; --mayAAAAAa- ; cor=; Ncor= a 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 c 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 g 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 t 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0
zen_shift4 (zen)				; positions_6-8nt_m1 versus zen; m=2/4; ncol2=6; w=0; offset=2; strand=D; shift=4; score=0.448429; ----AATwAA-- ; cor=; Ncor= a 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 c 0 0 0 0 0.541667 0 1.08333 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0
cad_rc_shift0 (cad_rc)				; positions_6-8nt_m1 versus cad_rc; m=3/4; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.416893; WrtYrwAAA--- ; cor=; Ncor= a 9 8 1 0 7 4 12 11 11 0 0 0 c 0 1 3 9 1 2 0 2 0 0 0 0 g 0 4 3 0 5 1 1 0 0 0 0 0 t 4 0 6 4 0 6 0 0 2 0 0 0
gt_shift1 (gt)				; positions_6-8nt_m1 versus gt; m=4/4; ncol2=7; w=-1; offset=-1; strand=D; shift=1; score=0.409894; -GTmAwAW---- ; cor=; Ncor= a 0 0 1 5 8 3 8 6 0 0 0 0 c 0 1 1 3 0 0 0 0 0 0 0 0 g 0 7 0 0 0 0 0 0 0 0 0 0 t 0 0 6 0 0 5 0 2 0 0 0 0