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.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9.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.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift0 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=13; shift=0; ncol=13; acATACACACmca ; Alignment reference a 1425 347 2251 103 2337 38 2277 26 2263 37 767 520 1082 c 426 1452 85 532 46 2255 72 2298 85 2267 1376 1114 522 g 318 252 52 45 26 51 36 34 26 65 149 430 440 t 266 384 47 1755 26 91 50 77 61 66 143 371 391

CG5953_SANGER_5_FBgn0032587_shift0 (CG5953_SANGER_5_FBgn0032587)
; dyads_m9 versus CG5953_SANGER_5_FBgn0032587; m=1/3; ncol2=8; w=0; offset=0; strand=D; shift=0; score=0.44298; aCAAACAy----- ; cor=; Ncor= a 10 0 16 16 16 0 16 1 0 0 0 0 0 c 3 16 0 0 0 16 0 5 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 t 3 0 0 0 0 0 0 10 0 0 0 0 0

Cf2-II_FlyReg_FBgn0000286_rc_shift0 (Cf2-II_FlyReg_FBgn0000286_rc)
; dyads_m9 versus Cf2-II_FlyReg_FBgn0000286_rc; m=2/3; ncol2=8; w=0; offset=0; strand=R; shift=0; score=0.437862; wTATACdy----- ; cor=; Ncor= a 1 0 3 0 3 0 1 0 0 0 0 0 0 c 0 0 0 0 0 3 0 2 0 0 0 0 0 g 0 0 0 0 0 0 1 0 0 0 0 0 0 t 2 3 0 3 0 0 1 1 0 0 0 0 0

CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715)
; dyads_m9 versus CG16778_SANGER_5_FBgn0003715; m=3/3; ncol2=8; w=0; offset=5; strand=D; shift=5; score=0.43251; -----CACAyAYG ; cor=; Ncor= a 0 0 0 0 0 0 18 0 20 0 17 0 0 c 0 0 0 0 0 15 1 20 0 9 0 6 1 g 0 0 0 0 0 2 0 0 0 0 3 0 18 t 0 0 0 0 0 1 0 0 0 11 0 14 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m9_shift0 (dyads_m9)				; dyads_m9; m=0 (reference); ncol1=13; shift=0; ncol=13; acATACACACmca ; Alignment reference a 1425 347 2251 103 2337 38 2277 26 2263 37 767 520 1082 c 426 1452 85 532 46 2255 72 2298 85 2267 1376 1114 522 g 318 252 52 45 26 51 36 34 26 65 149 430 440 t 266 384 47 1755 26 91 50 77 61 66 143 371 391
CG5953_SANGER_5_FBgn0032587_shift0 (CG5953_SANGER_5_FBgn0032587)				; dyads_m9 versus CG5953_SANGER_5_FBgn0032587; m=1/3; ncol2=8; w=0; offset=0; strand=D; shift=0; score=0.44298; aCAAACAy----- ; cor=; Ncor= a 10 0 16 16 16 0 16 1 0 0 0 0 0 c 3 16 0 0 0 16 0 5 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 t 3 0 0 0 0 0 0 10 0 0 0 0 0
Cf2-II_FlyReg_FBgn0000286_rc_shift0 (Cf2-II_FlyReg_FBgn0000286_rc)				; dyads_m9 versus Cf2-II_FlyReg_FBgn0000286_rc; m=2/3; ncol2=8; w=0; offset=0; strand=R; shift=0; score=0.437862; wTATACdy----- ; cor=; Ncor= a 1 0 3 0 3 0 1 0 0 0 0 0 0 c 0 0 0 0 0 3 0 2 0 0 0 0 0 g 0 0 0 0 0 0 1 0 0 0 0 0 0 t 2 3 0 3 0 0 1 1 0 0 0 0 0
CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715)				; dyads_m9 versus CG16778_SANGER_5_FBgn0003715; m=3/3; ncol2=8; w=0; offset=5; strand=D; shift=5; score=0.43251; -----CACAyAYG ; cor=; Ncor= a 0 0 0 0 0 0 18 0 20 0 17 0 0 c 0 0 0 0 0 15 1 20 0 9 0 6 1 g 0 0 0 0 0 2 0 0 0 0 3 0 18 t 0 0 0 0 0 1 0 0 0 11 0 14 1