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.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4.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.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: positions_6-8nt_m4_shift0 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m4_shift0 (positions_6-8nt_m4)
; positions_6-8nt_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wwAATAATAAww ; Alignment reference a 2260 2331 5328 5299 723 5275 5253 631 5235 5243 2150 2257 c 934 1129 123 92 337 100 119 399 124 137 1086 991 g 1004 801 121 97 127 122 104 194 117 127 767 866 t 1546 1483 172 256 4557 247 268 4520 268 237 1741 1630

br-Z1_shift2 (br-Z1)
; positions_6-8nt_m4 versus br-Z1; m=1/9; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.504114; --raTaCwAA-- ; cor=; Ncor= a 0 0 10.5882 11.6471 2.11765 11.6471 3.17647 9.52941 15.8824 18 0 0 c 0 0 0 0 0 3.17647 12.7059 1.05882 2.11765 0 0 0 g 0 0 7.41176 3.17647 1.05882 3.17647 2.11765 0 0 0 0 0 t 0 0 0 3.17647 14.8235 0 0 7.41176 0 0 0 0

en_rc_shift4 (en_rc)
; positions_6-8nt_m4 versus en_rc; m=2/9; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.488582; ----yAATtAah ; cor=; Ncor= a 0 0 0 0 10.125 58.5 57.375 1.125 5.625 51.75 31.5 18 c 0 0 0 0 31.5 3.375 2.25 0 14.625 4.5 11.25 21.375 g 0 0 0 0 1.125 0 1.125 1.125 6.75 6.75 12.375 0 t 0 0 0 0 20.25 1.125 2.25 60.75 36 0 7.875 23.625

eve_shift2 (eve)
; positions_6-8nt_m4 versus eve; m=3/9; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.484153; --mACaaTwA-- ; cor=; Ncor= a 0 0 8 18 1 13 13 0 9 19 0 0 c 0 0 9 0 16 3 0 1 1 0 0 0 g 0 0 3 2 0 4 3 0 1 0 0 0 t 0 0 0 0 3 0 4 19 9 1 0 0

br-Z4_rc_shift0 (br-Z4_rc)
; positions_6-8nt_m4 versus br-Z4_rc; m=4/9; ncol2=8; w=0; offset=0; strand=R; shift=0; score=0.472675; TAAhYAdT---- ; cor=; Ncor= a 1 7 8 2 0 8 3 1 0 0 0 0 c 0 0 0 3 2 0 0 0 0 0 0 0 g 0 0 0 0 0 0 2 0 0 0 0 0 t 7 1 0 3 6 0 3 7 0 0 0 0

Antp_shift5 (Antp)
; positions_6-8nt_m4 versus Antp; m=5/9; ncol2=6; w=0; offset=5; strand=D; shift=5; score=0.46758; -----mATAAw- ; cor=; Ncor= a 0 0 0 0 0 10.5 18 0 16.5 18 7.5 0 c 0 0 0 0 0 4.5 0 0 0 0 0 0 g 0 0 0 0 0 3 0 0 1.5 0 0 0 t 0 0 0 0 0 0 0 18 0 0 10.5 0

ap_shift2 (ap)
; positions_6-8nt_m4 versus ap; m=6/9; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.453183; --AAThAt---- ; cor=; Ncor= a 0 0 14 14 0 5 13 2 0 0 0 0 c 0 0 0 0 1 4 0 1 0 0 0 0 g 0 0 0 0 1 1 1 3 0 0 0 0 t 0 0 0 0 12 4 0 8 0 0 0 0

zen_shift5 (zen)
; positions_6-8nt_m4 versus zen; m=7/9; ncol2=6; w=0; offset=5; strand=D; shift=5; score=0.446892; -----AATwAA- ; cor=; Ncor= a 0 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 0 c 0 0 0 0 0 0.541667 0 1.08333 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0

gt_shift0 (gt)
; positions_6-8nt_m4 versus gt; m=8/9; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.44646; 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

abd-A_shift6 (abd-A)
; positions_6-8nt_m4 versus abd-A; m=9/9; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.421067; ------aTAAWT ; cor=; Ncor= a 0 0 0 0 0 0 27.439 0 40.6098 40.6098 14.2683 0 c 0 0 0 0 0 0 5.4878 3.29268 1.09756 0 0 3.29268 g 0 0 0 0 0 0 4.39024 1.09756 3.29268 0 0 6.58537 t 0 0 0 0 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m4_shift0 (positions_6-8nt_m4)				; positions_6-8nt_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wwAATAATAAww ; Alignment reference a 2260 2331 5328 5299 723 5275 5253 631 5235 5243 2150 2257 c 934 1129 123 92 337 100 119 399 124 137 1086 991 g 1004 801 121 97 127 122 104 194 117 127 767 866 t 1546 1483 172 256 4557 247 268 4520 268 237 1741 1630
br-Z1_shift2 (br-Z1)				; positions_6-8nt_m4 versus br-Z1; m=1/9; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.504114; --raTaCwAA-- ; cor=; Ncor= a 0 0 10.5882 11.6471 2.11765 11.6471 3.17647 9.52941 15.8824 18 0 0 c 0 0 0 0 0 3.17647 12.7059 1.05882 2.11765 0 0 0 g 0 0 7.41176 3.17647 1.05882 3.17647 2.11765 0 0 0 0 0 t 0 0 0 3.17647 14.8235 0 0 7.41176 0 0 0 0
en_rc_shift4 (en_rc)				; positions_6-8nt_m4 versus en_rc; m=2/9; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.488582; ----yAATtAah ; cor=; Ncor= a 0 0 0 0 10.125 58.5 57.375 1.125 5.625 51.75 31.5 18 c 0 0 0 0 31.5 3.375 2.25 0 14.625 4.5 11.25 21.375 g 0 0 0 0 1.125 0 1.125 1.125 6.75 6.75 12.375 0 t 0 0 0 0 20.25 1.125 2.25 60.75 36 0 7.875 23.625
eve_shift2 (eve)				; positions_6-8nt_m4 versus eve; m=3/9; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.484153; --mACaaTwA-- ; cor=; Ncor= a 0 0 8 18 1 13 13 0 9 19 0 0 c 0 0 9 0 16 3 0 1 1 0 0 0 g 0 0 3 2 0 4 3 0 1 0 0 0 t 0 0 0 0 3 0 4 19 9 1 0 0
br-Z4_rc_shift0 (br-Z4_rc)				; positions_6-8nt_m4 versus br-Z4_rc; m=4/9; ncol2=8; w=0; offset=0; strand=R; shift=0; score=0.472675; TAAhYAdT---- ; cor=; Ncor= a 1 7 8 2 0 8 3 1 0 0 0 0 c 0 0 0 3 2 0 0 0 0 0 0 0 g 0 0 0 0 0 0 2 0 0 0 0 0 t 7 1 0 3 6 0 3 7 0 0 0 0
Antp_shift5 (Antp)				; positions_6-8nt_m4 versus Antp; m=5/9; ncol2=6; w=0; offset=5; strand=D; shift=5; score=0.46758; -----mATAAw- ; cor=; Ncor= a 0 0 0 0 0 10.5 18 0 16.5 18 7.5 0 c 0 0 0 0 0 4.5 0 0 0 0 0 0 g 0 0 0 0 0 3 0 0 1.5 0 0 0 t 0 0 0 0 0 0 0 18 0 0 10.5 0
ap_shift2 (ap)				; positions_6-8nt_m4 versus ap; m=6/9; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.453183; --AAThAt---- ; cor=; Ncor= a 0 0 14 14 0 5 13 2 0 0 0 0 c 0 0 0 0 1 4 0 1 0 0 0 0 g 0 0 0 0 1 1 1 3 0 0 0 0 t 0 0 0 0 12 4 0 8 0 0 0 0
zen_shift5 (zen)				; positions_6-8nt_m4 versus zen; m=7/9; ncol2=6; w=0; offset=5; strand=D; shift=5; score=0.446892; -----AATwAA- ; cor=; Ncor= a 0 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 0 c 0 0 0 0 0 0.541667 0 1.08333 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0
gt_shift0 (gt)				; positions_6-8nt_m4 versus gt; m=8/9; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.44646; 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
abd-A_shift6 (abd-A)				; positions_6-8nt_m4 versus abd-A; m=9/9; ncol2=6; w=0; offset=6; strand=D; shift=6; score=0.421067; ------aTAAWT ; cor=; Ncor= a 0 0 0 0 0 0 27.439 0 40.6098 40.6098 14.2683 0 c 0 0 0 0 0 0 5.4878 3.29268 1.09756 0 0 3.29268 g 0 0 0 0 0 0 4.39024 1.09756 3.29268 0 0 6.58537 t 0 0 0 0 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122