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_m3/peak-motifs_positions_6-8nt_m3.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_m3/peak-motifs_positions_6-8nt_m3_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: positions_6-8nt_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6-8nt_m3_shift0 (positions_6-8nt_m3)
; positions_6-8nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; ktAGATTAth ; Alignment reference a 37 37 144 0 146 7 6 154 23 53 c 35 16 4 6 0 7 1 1 37 40 g 39 33 6 112 7 12 0 1 24 23 t 45 70 2 38 3 130 149 0 72 40

bcd_shift1 (bcd)
; positions_6-8nt_m3 versus bcd; m=1/5; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.624778; -vrGMTTAd- ; cor=; Ncor= a 0 13.2708 15.3125 5.10417 33.6875 0 1.02083 36.75 16.3333 0 c 0 18.375 2.04167 0 15.3125 0 2.04167 1.02083 2.04167 0 g 0 12.25 29.6042 42.875 0 0 0 3.0625 18.375 0 t 0 5.10417 2.04167 1.02083 0 49 45.9375 8.16667 12.25 0

Antp_rc_shift4 (Antp_rc)
; positions_6-8nt_m3 versus Antp_rc; m=2/5; ncol2=6; w=0; offset=4; strand=R; shift=4; score=0.505137; ----wTTATk ; cor=; Ncor= a 0 0 0 0 10.5 0 0 18 0 0 c 0 0 0 0 0 0 1.5 0 0 3 g 0 0 0 0 0 0 0 0 0 4.5 t 0 0 0 0 7.5 18 16.5 0 18 10.5

abd-A_rc_shift3 (abd-A_rc)
; positions_6-8nt_m3 versus abd-A_rc; m=3/5; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.454221; ---AWTTAt- ; cor=; Ncor= a 0 0 0 35.122 30.7317 4.39024 0 40.6098 7.68293 0 c 0 0 0 6.58537 0 0 3.29268 1.09756 4.39024 0 g 0 0 0 3.29268 0 0 1.09756 3.29268 5.4878 0 t 0 0 0 0 14.2683 40.6098 40.6098 0 27.439 0

Ubx_shift2 (Ubx)
; positions_6-8nt_m3 versus Ubx; m=4/5; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.446863; --mmATTA-- ; cor=; Ncor= a 0 0 21 42 67.6667 3.5 1.16667 58.3333 0 0 c 0 0 36.1667 17.5 2.33333 0 4.66667 2.33333 0 0 g 0 0 3.5 3.5 0 0 0 0 0 0 t 0 0 9.33333 7 0 66.5 64.1667 9.33333 0 0

prd_rc_shift4 (prd_rc)
; positions_6-8nt_m3 versus prd_rc; m=5/5; ncol2=8; w=0; offset=4; strand=R; shift=4; score= 0.401; ----wTTrtC ; cor=; Ncor= a 0 0 0 0 6 0 0 7 2 1 c 0 0 0 0 0 0 0 0 1 9 g 0 0 0 0 2 0 1 3 2 1 t 0 0 0 0 3 11 10 1 6 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6-8nt_m3_shift0 (positions_6-8nt_m3)				; positions_6-8nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; ktAGATTAth ; Alignment reference a 37 37 144 0 146 7 6 154 23 53 c 35 16 4 6 0 7 1 1 37 40 g 39 33 6 112 7 12 0 1 24 23 t 45 70 2 38 3 130 149 0 72 40
bcd_shift1 (bcd)				; positions_6-8nt_m3 versus bcd; m=1/5; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.624778; -vrGMTTAd- ; cor=; Ncor= a 0 13.2708 15.3125 5.10417 33.6875 0 1.02083 36.75 16.3333 0 c 0 18.375 2.04167 0 15.3125 0 2.04167 1.02083 2.04167 0 g 0 12.25 29.6042 42.875 0 0 0 3.0625 18.375 0 t 0 5.10417 2.04167 1.02083 0 49 45.9375 8.16667 12.25 0
Antp_rc_shift4 (Antp_rc)				; positions_6-8nt_m3 versus Antp_rc; m=2/5; ncol2=6; w=0; offset=4; strand=R; shift=4; score=0.505137; ----wTTATk ; cor=; Ncor= a 0 0 0 0 10.5 0 0 18 0 0 c 0 0 0 0 0 0 1.5 0 0 3 g 0 0 0 0 0 0 0 0 0 4.5 t 0 0 0 0 7.5 18 16.5 0 18 10.5
abd-A_rc_shift3 (abd-A_rc)				; positions_6-8nt_m3 versus abd-A_rc; m=3/5; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.454221; ---AWTTAt- ; cor=; Ncor= a 0 0 0 35.122 30.7317 4.39024 0 40.6098 7.68293 0 c 0 0 0 6.58537 0 0 3.29268 1.09756 4.39024 0 g 0 0 0 3.29268 0 0 1.09756 3.29268 5.4878 0 t 0 0 0 0 14.2683 40.6098 40.6098 0 27.439 0
Ubx_shift2 (Ubx)				; positions_6-8nt_m3 versus Ubx; m=4/5; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.446863; --mmATTA-- ; cor=; Ncor= a 0 0 21 42 67.6667 3.5 1.16667 58.3333 0 0 c 0 0 36.1667 17.5 2.33333 0 4.66667 2.33333 0 0 g 0 0 3.5 3.5 0 0 0 0 0 0 t 0 0 9.33333 7 0 66.5 64.1667 9.33333 0 0
prd_rc_shift4 (prd_rc)				; positions_6-8nt_m3 versus prd_rc; m=5/5; ncol2=8; w=0; offset=4; strand=R; shift=4; score= 0.401; ----wTTrtC ; cor=; Ncor= a 0 0 0 0 6 0 0 7 2 1 c 0 0 0 0 0 0 0 0 1 9 g 0 0 0 0 2 0 1 3 2 1 t 0 0 0 0 3 11 10 1 6 0