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.2025-04-28.203737_2025-04-28.203737_n2namY/results/discovered_motifs/dyads_m3/peak-motifs_dyads_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/2025/04/28/peak-motifs.2025-04-28.203737_2025-04-28.203737_n2namY/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_DMMPMM_drosophila

One-to-n matrix alignment; reference matrix: dyads_m3_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift1 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wrwAAAATAww ; Alignment reference a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11

hb_shift0 (hb)
; dyads_m3 versus hb; m=1/6; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.489914; 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

Antp_shift6 (Antp)
; dyads_m3 versus Antp; m=2/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.448324; ------mATAAw ; cor=; Ncor= a 0 0 0 0 0 0 10.5 18 0 16.5 18 7.5 c 0 0 0 0 0 0 4.5 0 0 0 0 0 g 0 0 0 0 0 0 3 0 0 1.5 0 0 t 0 0 0 0 0 0 0 0 18 0 0 10.5

pan_shift1 (pan)
; dyads_m3 versus pan; m=3/6; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.421604; -WtCAAA----- ; cor=; Ncor= a 0 18.72 5.2 3.12 20.8 23.92 23.92 0 0 0 0 0 c 0 0 4.16 20.8 0 1.04 0 0 0 0 0 0 g 0 0 0 1.04 0 0 0 0 0 0 0 0 t 0 7.28 16.64 1.04 5.2 1.04 2.08 0 0 0 0 0

ap_shift6 (ap)
; dyads_m3 versus ap; m=4/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.417999; ------AAThAt ; cor=; Ncor= a 0 0 0 0 0 0 14 14 0 5 13 2 c 0 0 0 0 0 0 0 0 1 4 0 1 g 0 0 0 0 0 0 0 0 1 1 1 3 t 0 0 0 0 0 0 0 0 12 4 0 8

br-Z3_rc_shift4 (br-Z3_rc)
; dyads_m3 versus br-Z3_rc; m=5/6; ncol2=11; w=0; offset=3; strand=R; shift=4; score=0.412983; ----AwAMTAdW ; cor=; Ncor= a 0 0 0 0 14 8 13 4 1 13 5 4 c 0 0 0 0 0 0 1 11 1 1 0 0 g 0 0 0 0 1 0 2 0 1 0 6 0 t 0 0 0 0 1 8 0 1 13 2 5 12

zen_shift6 (zen)
; dyads_m3 versus zen; m=6/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.411051; ------AATwAA ; cor=; Ncor= a 0 0 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 c 0 0 0 0 0 0 0.541667 0 1.08333 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift1 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wrwAAAATAww ; Alignment reference a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11
hb_shift0 (hb)				; dyads_m3 versus hb; m=1/6; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.489914; 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
Antp_shift6 (Antp)				; dyads_m3 versus Antp; m=2/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.448324; ------mATAAw ; cor=; Ncor= a 0 0 0 0 0 0 10.5 18 0 16.5 18 7.5 c 0 0 0 0 0 0 4.5 0 0 0 0 0 g 0 0 0 0 0 0 3 0 0 1.5 0 0 t 0 0 0 0 0 0 0 0 18 0 0 10.5
pan_shift1 (pan)				; dyads_m3 versus pan; m=3/6; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.421604; -WtCAAA----- ; cor=; Ncor= a 0 18.72 5.2 3.12 20.8 23.92 23.92 0 0 0 0 0 c 0 0 4.16 20.8 0 1.04 0 0 0 0 0 0 g 0 0 0 1.04 0 0 0 0 0 0 0 0 t 0 7.28 16.64 1.04 5.2 1.04 2.08 0 0 0 0 0
ap_shift6 (ap)				; dyads_m3 versus ap; m=4/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.417999; ------AAThAt ; cor=; Ncor= a 0 0 0 0 0 0 14 14 0 5 13 2 c 0 0 0 0 0 0 0 0 1 4 0 1 g 0 0 0 0 0 0 0 0 1 1 1 3 t 0 0 0 0 0 0 0 0 12 4 0 8
br-Z3_rc_shift4 (br-Z3_rc)				; dyads_m3 versus br-Z3_rc; m=5/6; ncol2=11; w=0; offset=3; strand=R; shift=4; score=0.412983; ----AwAMTAdW ; cor=; Ncor= a 0 0 0 0 14 8 13 4 1 13 5 4 c 0 0 0 0 0 0 1 11 1 1 0 0 g 0 0 0 0 1 0 2 0 1 0 6 0 t 0 0 0 0 1 8 0 1 13 2 5 12
zen_shift6 (zen)				; dyads_m3 versus zen; m=6/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.411051; ------AATwAA ; cor=; Ncor= a 0 0 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 c 0 0 0 0 0 0 0.541667 0 1.08333 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0