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/positions_6-8nt_m6/peak-motifs_positions_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.2026-01-25.184326_2026-01-25.184326_ptOhrJ/results/discovered_motifs/positions_6-8nt_m6/peak-motifs_positions_6-8nt_m6_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: positions_6-8nt_m6_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m6_shift0 (positions_6-8nt_m6)
; positions_6-8nt_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; arTAAACAAAaa ; Alignment reference a 142 141 61 384 385 389 34 390 386 376 168 172 c 90 78 38 17 16 9 345 12 17 15 81 72 g 86 113 17 5 5 11 8 7 6 12 66 84 t 99 85 301 11 11 8 30 8 8 14 102 89

hb_shift0 (hb)
; positions_6-8nt_m6 versus hb; m=1/3; ncol2=9; w=0; offset=0; strand=D; shift=0; score=0.584528; mayAAAAAa--- ; cor=; Ncor= a 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0 c 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0 g 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0 t 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0

zen_shift0 (zen)
; positions_6-8nt_m6 versus zen; m=2/3; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.414317; AATwAA------ ; cor=; Ncor= a 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 0 c 0.541667 0 1.08333 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0 0 0

pan_shift4 (pan)
; positions_6-8nt_m6 versus pan; m=3/3; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.412932; ----WtCAAA-- ; cor=; Ncor= a 0 0 0 0 18.72 5.2 3.12 20.8 23.92 23.92 0 0 c 0 0 0 0 0 4.16 20.8 0 1.04 0 0 0 g 0 0 0 0 0 0 1.04 0 0 0 0 0 t 0 0 0 0 7.28 16.64 1.04 5.2 1.04 2.08 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m6_shift0 (positions_6-8nt_m6)				; positions_6-8nt_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; arTAAACAAAaa ; Alignment reference a 142 141 61 384 385 389 34 390 386 376 168 172 c 90 78 38 17 16 9 345 12 17 15 81 72 g 86 113 17 5 5 11 8 7 6 12 66 84 t 99 85 301 11 11 8 30 8 8 14 102 89
hb_shift0 (hb)				; positions_6-8nt_m6 versus hb; m=1/3; ncol2=9; w=0; offset=0; strand=D; shift=0; score=0.584528; mayAAAAAa--- ; cor=; Ncor= a 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0 c 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0 g 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0 t 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0
zen_shift0 (zen)				; positions_6-8nt_m6 versus zen; m=2/3; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.414317; AATwAA------ ; cor=; Ncor= a 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 0 0 c 0.541667 0 1.08333 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0 0 0
pan_shift4 (pan)				; positions_6-8nt_m6 versus pan; m=3/3; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.412932; ----WtCAAA-- ; cor=; Ncor= a 0 0 0 0 18.72 5.2 3.12 20.8 23.92 23.92 0 0 c 0 0 0 0 0 4.16 20.8 0 1.04 0 0 0 g 0 0 0 0 0 0 1.04 0 0 0 0 0 t 0 0 0 0 7.28 16.64 1.04 5.2 1.04 2.08 0 0