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_m4/peak-motifs_dyads_m4.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_m4/peak-motifs_dyads_m4_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: dyads_m4_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift2 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=13; shift=2; ncol=15; --camACACACrCaC ; Alignment reference a 0 0 692 1932 1963 3124 46 3190 60 3155 31 986 38 2067 370 c 0 0 1862 667 1096 52 3156 14 3160 33 3190 50 3147 251 2240 g 0 0 346 403 68 60 25 53 18 45 21 2134 51 608 304 t 0 0 369 267 142 33 42 12 31 36 27 99 33 343 355

klu_SANGER_10_FBgn0013469_rc_shift3 (klu_SANGER_10_FBgn0013469_rc)
; dyads_m4 versus klu_SANGER_10_FBgn0013469_rc; m=1/5; ncol2=11; w=0; offset=1; strand=R; shift=3; score=0.601875; ---mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0

CG16778_SANGER_5_FBgn0003715_shift4 (CG16778_SANGER_5_FBgn0003715)
; dyads_m4 versus CG16778_SANGER_5_FBgn0003715; m=2/5; ncol2=8; w=0; offset=2; strand=D; shift=4; score=0.455999; ----CACAyAYG--- ; cor=; Ncor= a 0 0 0 0 0 18 0 20 0 17 0 0 0 0 0 c 0 0 0 0 15 1 20 0 9 0 6 1 0 0 0 g 0 0 0 0 2 0 0 0 0 3 0 18 0 0 0 t 0 0 0 0 1 0 0 0 11 0 14 1 0 0 0

Ci_SANGER_5_FBgn0004859_shift0 (Ci_SANGER_5_FBgn0004859)
; dyads_m4 versus Ci_SANGER_5_FBgn0004859; m=3/5; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.420771; rGMCCACMCAC---- ; cor=; Ncor= a 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 c 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 g 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 t 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0

foxo_SANGER_10_FBgn0038197_rc_shift1 (foxo_SANGER_10_FBgn0038197_rc)
; dyads_m4 versus foxo_SANGER_10_FBgn0038197_rc; m=4/5; ncol2=9; w=-1; offset=-1; strand=R; shift=1; score=0.420181; -ycrwAAACA----- ; cor=; Ncor= a 0 0 3 8 8 16 16 20 0 20 0 0 0 0 0 c 0 6 12 0 0 1 4 0 18 0 0 0 0 0 0 g 0 3 3 11 0 0 0 0 0 0 0 0 0 0 0 t 0 11 2 1 12 3 0 0 2 0 0 0 0 0 0

CG5953_SANGER_5_FBgn0032587_shift1 (CG5953_SANGER_5_FBgn0032587)
; dyads_m4 versus CG5953_SANGER_5_FBgn0032587; m=5/5; ncol2=8; w=-1; offset=-1; strand=D; shift=1; score=0.408791; -aCAAACAy------ ; cor=; Ncor= a 0 10 0 16 16 16 0 16 1 0 0 0 0 0 0 c 0 3 16 0 0 0 16 0 5 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 3 0 0 0 0 0 0 10 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift2 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=13; shift=2; ncol=15; --camACACACrCaC ; Alignment reference a 0 0 692 1932 1963 3124 46 3190 60 3155 31 986 38 2067 370 c 0 0 1862 667 1096 52 3156 14 3160 33 3190 50 3147 251 2240 g 0 0 346 403 68 60 25 53 18 45 21 2134 51 608 304 t 0 0 369 267 142 33 42 12 31 36 27 99 33 343 355
klu_SANGER_10_FBgn0013469_rc_shift3 (klu_SANGER_10_FBgn0013469_rc)				; dyads_m4 versus klu_SANGER_10_FBgn0013469_rc; m=1/5; ncol2=11; w=0; offset=1; strand=R; shift=3; score=0.601875; ---mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0
CG16778_SANGER_5_FBgn0003715_shift4 (CG16778_SANGER_5_FBgn0003715)				; dyads_m4 versus CG16778_SANGER_5_FBgn0003715; m=2/5; ncol2=8; w=0; offset=2; strand=D; shift=4; score=0.455999; ----CACAyAYG--- ; cor=; Ncor= a 0 0 0 0 0 18 0 20 0 17 0 0 0 0 0 c 0 0 0 0 15 1 20 0 9 0 6 1 0 0 0 g 0 0 0 0 2 0 0 0 0 3 0 18 0 0 0 t 0 0 0 0 1 0 0 0 11 0 14 1 0 0 0
Ci_SANGER_5_FBgn0004859_shift0 (Ci_SANGER_5_FBgn0004859)				; dyads_m4 versus Ci_SANGER_5_FBgn0004859; m=3/5; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.420771; rGMCCACMCAC---- ; cor=; Ncor= a 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 c 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 g 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 t 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0
foxo_SANGER_10_FBgn0038197_rc_shift1 (foxo_SANGER_10_FBgn0038197_rc)				; dyads_m4 versus foxo_SANGER_10_FBgn0038197_rc; m=4/5; ncol2=9; w=-1; offset=-1; strand=R; shift=1; score=0.420181; -ycrwAAACA----- ; cor=; Ncor= a 0 0 3 8 8 16 16 20 0 20 0 0 0 0 0 c 0 6 12 0 0 1 4 0 18 0 0 0 0 0 0 g 0 3 3 11 0 0 0 0 0 0 0 0 0 0 0 t 0 11 2 1 12 3 0 0 2 0 0 0 0 0 0
CG5953_SANGER_5_FBgn0032587_shift1 (CG5953_SANGER_5_FBgn0032587)				; dyads_m4 versus CG5953_SANGER_5_FBgn0032587; m=5/5; ncol2=8; w=-1; offset=-1; strand=D; shift=1; score=0.408791; -aCAAACAy------ ; cor=; Ncor= a 0 10 0 16 16 16 0 16 1 0 0 0 0 0 0 c 0 3 16 0 0 0 16 0 5 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 3 0 0 0 0 0 0 10 0 0 0 0 0 0