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.2026-01-25.201729_2026-01-25.201729_P12xBT/results/discovered_motifs/oligos_6nt_mkv3_m9/peak-motifs_oligos_6nt_mkv3_m9.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.2026-01-25.201729_2026-01-25.201729_P12xBT/results/discovered_motifs/oligos_6nt_mkv3_m9/peak-motifs_oligos_6nt_mkv3_m9_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m9_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; waTAwATAtw ; Alignment reference a 74 122 0 245 151 236 0 248 51 106 c 30 27 0 0 15 8 0 0 51 39 g 33 44 0 2 15 4 0 0 34 29 t 111 55 248 1 67 0 248 0 112 74

br-Z4_rc_shift2 (br-Z4_rc)
; oligos_6nt_mkv3_m9 versus br-Z4_rc; m=1/6; ncol2=8; w=0; offset=2; strand=R; shift=2; score=0.619645; --TAAhYAdT ; cor=; Ncor= a 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 2 0 t 0 0 7 1 0 3 6 0 3 7

br-Z2_rc_shift2 (br-Z2_rc)
; oligos_6nt_mkv3_m9 versus br-Z2_rc; m=2/6; ncol2=7; w=0; offset=2; strand=R; shift=2; score=0.501528; --twaaTAG- ; cor=; Ncor= a 0 0 5 9 12 11 0 21 1 0 c 0 0 4 1 3 3 0 0 0 0 g 0 0 0 3 1 3 0 0 20 0 t 0 0 12 8 5 4 21 0 0 0

abd-A_shift1 (abd-A)
; oligos_6nt_mkv3_m9 versus abd-A; m=3/6; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.48587; -aTAAWT--- ; cor=; Ncor= a 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0

Antp_shift4 (Antp)
; oligos_6nt_mkv3_m9 versus Antp; m=4/6; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.484807; ----mATAAw ; cor=; Ncor= a 0 0 0 0 10.5 18 0 16.5 18 7.5 c 0 0 0 0 4.5 0 0 0 0 0 g 0 0 0 0 3 0 0 1.5 0 0 t 0 0 0 0 0 0 18 0 0 10.5

zen_shift0 (zen)
; oligos_6nt_mkv3_m9 versus zen; m=5/6; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.482115; AATwAA---- ; cor=; Ncor= a 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 0.541667 0 1.08333 0 0 0 0 0 0 0 g 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

vvl_rc_shift2 (vvl_rc)
; oligos_6nt_mkv3_m9 versus vvl_rc; m=6/6; ncol2=6; w=0; offset=2; strand=R; shift=2; score=0.443719; --TgmwTA-- ; cor=; Ncor= a 0 0 0 2.36364 8.27273 5.90909 0 13 0 0 c 0 0 0 1.18182 4.72727 0 0 0 0 0 g 0 0 0 8.27273 0 0 1.18182 0 0 0 t 0 0 13 1.18182 0 7.09091 11.8182 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; waTAwATAtw ; Alignment reference a 74 122 0 245 151 236 0 248 51 106 c 30 27 0 0 15 8 0 0 51 39 g 33 44 0 2 15 4 0 0 34 29 t 111 55 248 1 67 0 248 0 112 74
br-Z4_rc_shift2 (br-Z4_rc)				; oligos_6nt_mkv3_m9 versus br-Z4_rc; m=1/6; ncol2=8; w=0; offset=2; strand=R; shift=2; score=0.619645; --TAAhYAdT ; cor=; Ncor= a 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 2 0 t 0 0 7 1 0 3 6 0 3 7
br-Z2_rc_shift2 (br-Z2_rc)				; oligos_6nt_mkv3_m9 versus br-Z2_rc; m=2/6; ncol2=7; w=0; offset=2; strand=R; shift=2; score=0.501528; --twaaTAG- ; cor=; Ncor= a 0 0 5 9 12 11 0 21 1 0 c 0 0 4 1 3 3 0 0 0 0 g 0 0 0 3 1 3 0 0 20 0 t 0 0 12 8 5 4 21 0 0 0
abd-A_shift1 (abd-A)				; oligos_6nt_mkv3_m9 versus abd-A; m=3/6; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.48587; -aTAAWT--- ; cor=; Ncor= a 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0
Antp_shift4 (Antp)				; oligos_6nt_mkv3_m9 versus Antp; m=4/6; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.484807; ----mATAAw ; cor=; Ncor= a 0 0 0 0 10.5 18 0 16.5 18 7.5 c 0 0 0 0 4.5 0 0 0 0 0 g 0 0 0 0 3 0 0 1.5 0 0 t 0 0 0 0 0 0 18 0 0 10.5
zen_shift0 (zen)				; oligos_6nt_mkv3_m9 versus zen; m=5/6; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.482115; AATwAA---- ; cor=; Ncor= a 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 0.541667 0 1.08333 0 0 0 0 0 0 0 g 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
vvl_rc_shift2 (vvl_rc)				; oligos_6nt_mkv3_m9 versus vvl_rc; m=6/6; ncol2=6; w=0; offset=2; strand=R; shift=2; score=0.443719; --TgmwTA-- ; cor=; Ncor= a 0 0 0 2.36364 8.27273 5.90909 0 13 0 0 c 0 0 0 1.18182 4.72727 0 0 0 0 0 g 0 0 0 8.27273 0 0 1.18182 0 0 0 t 0 0 13 1.18182 0 7.09091 11.8182 0 0 0