One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6.tf -format2 tf -file2 $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.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/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: dyads_m6_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift1 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=13; shift=1; ncol=14; -camACACACAyac ; Alignment reference a 0 641 1787 1910 2920 40 2982 31 2973 30 2915 148 1847 393 c 0 1706 619 936 41 2945 17 2942 28 2937 41 987 432 1939 g 0 346 362 48 33 15 30 21 19 24 30 98 415 351 t 0 345 270 144 44 38 9 44 18 47 52 1805 344 355

CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715)
; dyads_m6 versus CG16778_SANGER_5_FBgn0003715; m=1/3; ncol2=8; w=0; offset=4; strand=D; shift=5; score=0.503517; -----CACAyAYG- ; cor=; Ncor= a 0 0 0 0 0 0 18 0 20 0 17 0 0 0 c 0 0 0 0 0 15 1 20 0 9 0 6 1 0 g 0 0 0 0 0 2 0 0 0 0 3 0 18 0 t 0 0 0 0 0 1 0 0 0 11 0 14 1 0

CG5953_SANGER_5_FBgn0032587_shift4 (CG5953_SANGER_5_FBgn0032587)
; dyads_m6 versus CG5953_SANGER_5_FBgn0032587; m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=4; score=0.486142; ----aCAAACAy-- ; cor=; Ncor= a 0 0 0 0 10 0 16 16 16 0 16 1 0 0 c 0 0 0 0 3 16 0 0 0 16 0 5 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 3 0 0 0 0 0 0 10 0 0

foxo_SANGER_10_FBgn0038197_rc_shift0 (foxo_SANGER_10_FBgn0038197_rc)
; dyads_m6 versus foxo_SANGER_10_FBgn0038197_rc; m=3/3; ncol2=9; w=-1; offset=-1; strand=R; shift=0; score=0.421793; ycrwAAACA----- ; cor=; Ncor= a 0 3 8 8 16 16 20 0 20 0 0 0 0 0 c 6 12 0 0 1 4 0 18 0 0 0 0 0 0 g 3 3 11 0 0 0 0 0 0 0 0 0 0 0 t 11 2 1 12 3 0 0 2 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m6_shift1 (dyads_m6)				; dyads_m6; m=0 (reference); ncol1=13; shift=1; ncol=14; -camACACACAyac ; Alignment reference a 0 641 1787 1910 2920 40 2982 31 2973 30 2915 148 1847 393 c 0 1706 619 936 41 2945 17 2942 28 2937 41 987 432 1939 g 0 346 362 48 33 15 30 21 19 24 30 98 415 351 t 0 345 270 144 44 38 9 44 18 47 52 1805 344 355
CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715)				; dyads_m6 versus CG16778_SANGER_5_FBgn0003715; m=1/3; ncol2=8; w=0; offset=4; strand=D; shift=5; score=0.503517; -----CACAyAYG- ; cor=; Ncor= a 0 0 0 0 0 0 18 0 20 0 17 0 0 0 c 0 0 0 0 0 15 1 20 0 9 0 6 1 0 g 0 0 0 0 0 2 0 0 0 0 3 0 18 0 t 0 0 0 0 0 1 0 0 0 11 0 14 1 0
CG5953_SANGER_5_FBgn0032587_shift4 (CG5953_SANGER_5_FBgn0032587)				; dyads_m6 versus CG5953_SANGER_5_FBgn0032587; m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=4; score=0.486142; ----aCAAACAy-- ; cor=; Ncor= a 0 0 0 0 10 0 16 16 16 0 16 1 0 0 c 0 0 0 0 3 16 0 0 0 16 0 5 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 3 0 0 0 0 0 0 10 0 0
foxo_SANGER_10_FBgn0038197_rc_shift0 (foxo_SANGER_10_FBgn0038197_rc)				; dyads_m6 versus foxo_SANGER_10_FBgn0038197_rc; m=3/3; ncol2=9; w=-1; offset=-1; strand=R; shift=0; score=0.421793; ycrwAAACA----- ; cor=; Ncor= a 0 3 8 8 16 16 20 0 20 0 0 0 0 0 c 6 12 0 0 1 4 0 18 0 0 0 0 0 0 g 3 3 11 0 0 0 0 0 0 0 0 0 0 0 t 11 2 1 12 3 0 0 2 0 0 0 0 0 0