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_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.2025-11-26.204716_2025-11-26.204716_g9CRAo/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=14; shift=0; ncol=14; caAACACACACmca ; Alignment reference a 665 1337 1976 2446 92 2530 67 2498 59 2477 62 891 527 1266 c 1305 637 478 94 2450 56 2487 87 2538 99 2482 1505 1329 555 g 367 345 63 67 43 57 48 47 32 30 70 152 464 441 t 356 374 176 86 108 50 91 61 64 87 79 145 373 431

CG5953_SANGER_5_FBgn0032587_shift3 (CG5953_SANGER_5_FBgn0032587)
; dyads_m9 versus CG5953_SANGER_5_FBgn0032587; m=1/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.414153; ---aCAAACAy--- ; cor=; Ncor= a 0 0 0 10 0 16 16 16 0 16 1 0 0 0 c 0 0 0 3 16 0 0 0 16 0 5 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 3 0 0 0 0 0 0 10 0 0 0

CG16778_SANGER_5_FBgn0003715_shift4 (CG16778_SANGER_5_FBgn0003715)
; dyads_m9 versus CG16778_SANGER_5_FBgn0003715; m=2/3; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.407586; ----CACAyAYG-- ; cor=; Ncor= a 0 0 0 0 0 18 0 20 0 17 0 0 0 0 c 0 0 0 0 15 1 20 0 9 0 6 1 0 0 g 0 0 0 0 2 0 0 0 0 3 0 18 0 0 t 0 0 0 0 1 0 0 0 11 0 14 1 0 0

Ara_Cell_FBgn0015904_shift0 (Ara_Cell_FBgn0015904)
; dyads_m9 versus Ara_Cell_FBgn0015904; m=3/3; ncol2=8; w=0; offset=0; strand=D; shift=0; score=0.40058; raAwwACA------ ; cor=; Ncor= a 12 16 24 14 23 34 0 34 0 0 0 0 0 0 c 5 7 1 0 0 0 34 0 0 0 0 0 0 0 g 10 6 1 5 0 0 0 0 0 0 0 0 0 0 t 7 5 8 15 11 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m9_shift0 (dyads_m9)				; dyads_m9; m=0 (reference); ncol1=14; shift=0; ncol=14; caAACACACACmca ; Alignment reference a 665 1337 1976 2446 92 2530 67 2498 59 2477 62 891 527 1266 c 1305 637 478 94 2450 56 2487 87 2538 99 2482 1505 1329 555 g 367 345 63 67 43 57 48 47 32 30 70 152 464 441 t 356 374 176 86 108 50 91 61 64 87 79 145 373 431
CG5953_SANGER_5_FBgn0032587_shift3 (CG5953_SANGER_5_FBgn0032587)				; dyads_m9 versus CG5953_SANGER_5_FBgn0032587; m=1/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.414153; ---aCAAACAy--- ; cor=; Ncor= a 0 0 0 10 0 16 16 16 0 16 1 0 0 0 c 0 0 0 3 16 0 0 0 16 0 5 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 3 0 0 0 0 0 0 10 0 0 0
CG16778_SANGER_5_FBgn0003715_shift4 (CG16778_SANGER_5_FBgn0003715)				; dyads_m9 versus CG16778_SANGER_5_FBgn0003715; m=2/3; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.407586; ----CACAyAYG-- ; cor=; Ncor= a 0 0 0 0 0 18 0 20 0 17 0 0 0 0 c 0 0 0 0 15 1 20 0 9 0 6 1 0 0 g 0 0 0 0 2 0 0 0 0 3 0 18 0 0 t 0 0 0 0 1 0 0 0 11 0 14 1 0 0
Ara_Cell_FBgn0015904_shift0 (Ara_Cell_FBgn0015904)				; dyads_m9 versus Ara_Cell_FBgn0015904; m=3/3; ncol2=8; w=0; offset=0; strand=D; shift=0; score=0.40058; raAwwACA------ ; cor=; Ncor= a 12 16 24 14 23 34 0 34 0 0 0 0 0 0 c 5 7 1 0 0 0 34 0 0 0 0 0 0 0 g 10 6 1 5 0 0 0 0 0 0 0 0 0 0 t 7 5 8 15 11 0 0 0 0 0 0 0 0 0