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.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5.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.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift2 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift2 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --hrATAAATAwh ; Alignment reference a 0 0 19 19 52 1 51 44 48 0 53 17 17 c 0 0 14 8 2 1 2 2 1 2 1 10 14 g 0 0 6 16 1 4 0 4 6 0 1 9 8 t 0 0 16 12 0 49 2 5 0 53 0 19 16

br-Z4_rc_shift5 (br-Z4_rc)
; oligos_7nt_mkv2_m5 versus br-Z4_rc; m=1/9; ncol2=8; w=0; offset=3; strand=R; shift=5; score=0.589885; -----TAAhYAdT ; cor=; Ncor= a 0 0 0 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2 0 t 0 0 0 0 0 7 1 0 3 6 0 3 7

zen_shift3 (zen)
; oligos_7nt_mkv2_m5 versus zen; m=2/9; ncol2=6; w=0; offset=1; strand=D; shift=3; score=0.488425; ---AATwAA---- ; cor=; Ncor= a 0 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 0 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 0 t 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0

Antp_shift3 (Antp)
; oligos_7nt_mkv2_m5 versus Antp; m=3/9; ncol2=6; w=0; offset=1; strand=D; shift=3; score=0.477163; ---mATAAw---- ; cor=; Ncor= a 0 0 0 10.5 18 0 16.5 18 7.5 0 0 0 0 c 0 0 0 4.5 0 0 0 0 0 0 0 0 0 g 0 0 0 3 0 0 1.5 0 0 0 0 0 0 t 0 0 0 0 0 18 0 0 10.5 0 0 0 0

br-Z2_rc_shift5 (br-Z2_rc)
; oligos_7nt_mkv2_m5 versus br-Z2_rc; m=4/9; ncol2=7; w=0; offset=3; strand=R; shift=5; score=0.466547; -----twaaTAG- ; cor=; Ncor= a 0 0 0 0 0 5 9 12 11 0 21 1 0 c 0 0 0 0 0 4 1 3 3 0 0 0 0 g 0 0 0 0 0 0 3 1 3 0 0 20 0 t 0 0 0 0 0 12 8 5 4 21 0 0 0

abd-A_shift4 (abd-A)
; oligos_7nt_mkv2_m5 versus abd-A; m=5/9; ncol2=6; w=0; offset=2; strand=D; shift=4; score=0.456306; ----aTAAWT--- ; cor=; Ncor= a 0 0 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 0 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 0 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 0 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0

gt_shift1 (gt)
; oligos_7nt_mkv2_m5 versus gt; m=6/9; ncol2=7; w=-1; offset=-1; strand=D; shift=1; score=0.422784; -GTmAwAW----- ; cor=; Ncor= a 0 0 1 5 8 3 8 6 0 0 0 0 0 c 0 1 1 3 0 0 0 0 0 0 0 0 0 g 0 7 0 0 0 0 0 0 0 0 0 0 0 t 0 0 6 0 0 5 0 2 0 0 0 0 0

ap_shift7 (ap)
; oligos_7nt_mkv2_m5 versus ap; m=7/9; ncol2=6; w=0; offset=5; strand=D; shift=7; score=0.407629; -------AAThAt ; cor=; Ncor= a 0 0 0 0 0 0 0 14 14 0 5 13 2 c 0 0 0 0 0 0 0 0 0 1 4 0 1 g 0 0 0 0 0 0 0 0 0 1 1 1 3 t 0 0 0 0 0 0 0 0 0 12 4 0 8

vvl_rc_shift5 (vvl_rc)
; oligos_7nt_mkv2_m5 versus vvl_rc; m=8/9; ncol2=6; w=0; offset=3; strand=R; shift=5; score=0.40578; -----TgmwTA-- ; cor=; Ncor= a 0 0 0 0 0 0 2.36364 8.27273 5.90909 0 13 0 0 c 0 0 0 0 0 0 1.18182 4.72727 0 0 0 0 0 g 0 0 0 0 0 0 8.27273 0 0 1.18182 0 0 0 t 0 0 0 0 0 13 1.18182 0 7.09091 11.8182 0 0 0

cad_rc_shift0 (cad_rc)
; oligos_7nt_mkv2_m5 versus cad_rc; m=9/9; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.403226; WrtYrwAAA---- ; cor=; Ncor= a 9 8 1 0 7 4 12 11 11 0 0 0 0 c 0 1 3 9 1 2 0 2 0 0 0 0 0 g 0 4 3 0 5 1 1 0 0 0 0 0 0 t 4 0 6 4 0 6 0 0 2 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift2 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --hrATAAATAwh ; Alignment reference a 0 0 19 19 52 1 51 44 48 0 53 17 17 c 0 0 14 8 2 1 2 2 1 2 1 10 14 g 0 0 6 16 1 4 0 4 6 0 1 9 8 t 0 0 16 12 0 49 2 5 0 53 0 19 16
br-Z4_rc_shift5 (br-Z4_rc)				; oligos_7nt_mkv2_m5 versus br-Z4_rc; m=1/9; ncol2=8; w=0; offset=3; strand=R; shift=5; score=0.589885; -----TAAhYAdT ; cor=; Ncor= a 0 0 0 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2 0 t 0 0 0 0 0 7 1 0 3 6 0 3 7
zen_shift3 (zen)				; oligos_7nt_mkv2_m5 versus zen; m=2/9; ncol2=6; w=0; offset=1; strand=D; shift=3; score=0.488425; ---AATwAA---- ; cor=; Ncor= a 0 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 0 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 0 t 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0
Antp_shift3 (Antp)				; oligos_7nt_mkv2_m5 versus Antp; m=3/9; ncol2=6; w=0; offset=1; strand=D; shift=3; score=0.477163; ---mATAAw---- ; cor=; Ncor= a 0 0 0 10.5 18 0 16.5 18 7.5 0 0 0 0 c 0 0 0 4.5 0 0 0 0 0 0 0 0 0 g 0 0 0 3 0 0 1.5 0 0 0 0 0 0 t 0 0 0 0 0 18 0 0 10.5 0 0 0 0
br-Z2_rc_shift5 (br-Z2_rc)				; oligos_7nt_mkv2_m5 versus br-Z2_rc; m=4/9; ncol2=7; w=0; offset=3; strand=R; shift=5; score=0.466547; -----twaaTAG- ; cor=; Ncor= a 0 0 0 0 0 5 9 12 11 0 21 1 0 c 0 0 0 0 0 4 1 3 3 0 0 0 0 g 0 0 0 0 0 0 3 1 3 0 0 20 0 t 0 0 0 0 0 12 8 5 4 21 0 0 0
abd-A_shift4 (abd-A)				; oligos_7nt_mkv2_m5 versus abd-A; m=5/9; ncol2=6; w=0; offset=2; strand=D; shift=4; score=0.456306; ----aTAAWT--- ; cor=; Ncor= a 0 0 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 0 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 0 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 0 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0
gt_shift1 (gt)				; oligos_7nt_mkv2_m5 versus gt; m=6/9; ncol2=7; w=-1; offset=-1; strand=D; shift=1; score=0.422784; -GTmAwAW----- ; cor=; Ncor= a 0 0 1 5 8 3 8 6 0 0 0 0 0 c 0 1 1 3 0 0 0 0 0 0 0 0 0 g 0 7 0 0 0 0 0 0 0 0 0 0 0 t 0 0 6 0 0 5 0 2 0 0 0 0 0
ap_shift7 (ap)				; oligos_7nt_mkv2_m5 versus ap; m=7/9; ncol2=6; w=0; offset=5; strand=D; shift=7; score=0.407629; -------AAThAt ; cor=; Ncor= a 0 0 0 0 0 0 0 14 14 0 5 13 2 c 0 0 0 0 0 0 0 0 0 1 4 0 1 g 0 0 0 0 0 0 0 0 0 1 1 1 3 t 0 0 0 0 0 0 0 0 0 12 4 0 8
vvl_rc_shift5 (vvl_rc)				; oligos_7nt_mkv2_m5 versus vvl_rc; m=8/9; ncol2=6; w=0; offset=3; strand=R; shift=5; score=0.40578; -----TgmwTA-- ; cor=; Ncor= a 0 0 0 0 0 0 2.36364 8.27273 5.90909 0 13 0 0 c 0 0 0 0 0 0 1.18182 4.72727 0 0 0 0 0 g 0 0 0 0 0 0 8.27273 0 0 1.18182 0 0 0 t 0 0 0 0 0 13 1.18182 0 7.09091 11.8182 0 0 0
cad_rc_shift0 (cad_rc)				; oligos_7nt_mkv2_m5 versus cad_rc; m=9/9; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.403226; WrtYrwAAA---- ; cor=; Ncor= a 9 8 1 0 7 4 12 11 11 0 0 0 0 c 0 1 3 9 1 2 0 2 0 0 0 0 0 g 0 4 3 0 5 1 1 0 0 0 0 0 0 t 4 0 6 4 0 6 0 0 2 0 0 0 0