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_m5/peak-motifs_dyads_m5.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_m5/peak-motifs_dyads_m5_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=14; shift=0; ncol=14; agCAGCAGCAGCag ; Alignment reference a 3023 732 205 4256 205 120 4427 196 120 4310 275 188 3102 833 c 572 721 4047 152 229 4354 108 164 4365 138 232 4152 534 744 g 704 2845 257 245 4149 96 157 4245 93 192 4045 171 729 2643 t 468 469 258 114 184 197 75 162 189 127 215 256 402 547

odd_NAR_FBgn0002985_shift0 (odd_NAR_FBgn0002985)
; dyads_m5 versus odd_NAR_FBgn0002985; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.570072; mmCAGTAGCAv--- ; cor=; Ncor= a 7 10 0 12 0 0 15 0 0 11 5 0 0 0 c 5 5 14 0 0 0 0 0 15 3 4 0 0 0 g 0 0 1 3 15 0 0 15 0 1 6 0 0 0 t 3 0 0 0 0 15 0 0 0 0 0 0 0 0

odd_NBT_5_FBgn0002985_rc_shift0 (odd_NBT_5_FBgn0002985_rc)
; dyads_m5 versus odd_NBT_5_FBgn0002985_rc; m=2/5; ncol2=9; w=0; offset=0; strand=R; shift=0; score=0.46271; wMCAGTAGC----- ; cor=; Ncor= a 9 16 0 18 0 0 23 0 0 0 0 0 0 0 c 5 6 23 0 0 0 0 0 23 0 0 0 0 0 g 0 0 0 5 23 0 0 23 0 0 0 0 0 0 t 9 1 0 0 0 23 0 0 0 0 0 0 0 0

odd_NBT_1.5_FBgn0002985_rc_shift0 (odd_NBT_1.5_FBgn0002985_rc)
; dyads_m5 versus odd_NBT_1.5_FBgn0002985_rc; m=3/5; ncol2=9; w=0; offset=0; strand=R; shift=0; score=0.461044; wmCrGWAGC----- ; cor=; Ncor= a 8 6 1 12 0 6 20 0 0 0 0 0 0 0 c 2 11 21 0 0 0 0 2 19 0 0 0 0 0 g 2 2 0 10 22 0 0 20 1 0 0 0 0 0 t 10 3 0 0 0 16 2 0 2 0 0 0 0 0

CG11504_SANGER_5_FBgn0039733_shift5 (CG11504_SANGER_5_FBgn0039733)
; dyads_m5 versus CG11504_SANGER_5_FBgn0039733; m=4/5; ncol2=9; w=0; offset=5; strand=D; shift=5; score=0.453636; -----YmGCAACAT ; cor=; Ncor= a 0 0 0 0 0 0 11 0 1 20 19 1 20 2 c 0 0 0 0 0 14 5 1 19 0 0 19 0 4 g 0 0 0 0 0 0 1 19 0 0 0 0 0 0 t 0 0 0 0 0 6 3 0 0 0 1 0 0 14

bowl_SANGER_5_FBgn0004893_shift1 (bowl_SANGER_5_FBgn0004893)
; dyads_m5 versus bowl_SANGER_5_FBgn0004893; m=5/5; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.416262; -mCrGwAGY----- ; cor=; Ncor= a 0 4 0 7 0 5 12 0 0 0 0 0 0 0 c 0 7 12 1 0 0 0 0 8 0 0 0 0 0 g 0 0 0 4 12 1 0 12 0 0 0 0 0 0 t 0 0 0 0 0 6 0 0 3 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift0 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=14; shift=0; ncol=14; agCAGCAGCAGCag ; Alignment reference a 3023 732 205 4256 205 120 4427 196 120 4310 275 188 3102 833 c 572 721 4047 152 229 4354 108 164 4365 138 232 4152 534 744 g 704 2845 257 245 4149 96 157 4245 93 192 4045 171 729 2643 t 468 469 258 114 184 197 75 162 189 127 215 256 402 547
odd_NAR_FBgn0002985_shift0 (odd_NAR_FBgn0002985)				; dyads_m5 versus odd_NAR_FBgn0002985; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.570072; mmCAGTAGCAv--- ; cor=; Ncor= a 7 10 0 12 0 0 15 0 0 11 5 0 0 0 c 5 5 14 0 0 0 0 0 15 3 4 0 0 0 g 0 0 1 3 15 0 0 15 0 1 6 0 0 0 t 3 0 0 0 0 15 0 0 0 0 0 0 0 0
odd_NBT_5_FBgn0002985_rc_shift0 (odd_NBT_5_FBgn0002985_rc)				; dyads_m5 versus odd_NBT_5_FBgn0002985_rc; m=2/5; ncol2=9; w=0; offset=0; strand=R; shift=0; score=0.46271; wMCAGTAGC----- ; cor=; Ncor= a 9 16 0 18 0 0 23 0 0 0 0 0 0 0 c 5 6 23 0 0 0 0 0 23 0 0 0 0 0 g 0 0 0 5 23 0 0 23 0 0 0 0 0 0 t 9 1 0 0 0 23 0 0 0 0 0 0 0 0
odd_NBT_1.5_FBgn0002985_rc_shift0 (odd_NBT_1.5_FBgn0002985_rc)				; dyads_m5 versus odd_NBT_1.5_FBgn0002985_rc; m=3/5; ncol2=9; w=0; offset=0; strand=R; shift=0; score=0.461044; wmCrGWAGC----- ; cor=; Ncor= a 8 6 1 12 0 6 20 0 0 0 0 0 0 0 c 2 11 21 0 0 0 0 2 19 0 0 0 0 0 g 2 2 0 10 22 0 0 20 1 0 0 0 0 0 t 10 3 0 0 0 16 2 0 2 0 0 0 0 0
CG11504_SANGER_5_FBgn0039733_shift5 (CG11504_SANGER_5_FBgn0039733)				; dyads_m5 versus CG11504_SANGER_5_FBgn0039733; m=4/5; ncol2=9; w=0; offset=5; strand=D; shift=5; score=0.453636; -----YmGCAACAT ; cor=; Ncor= a 0 0 0 0 0 0 11 0 1 20 19 1 20 2 c 0 0 0 0 0 14 5 1 19 0 0 19 0 4 g 0 0 0 0 0 0 1 19 0 0 0 0 0 0 t 0 0 0 0 0 6 3 0 0 0 1 0 0 14
bowl_SANGER_5_FBgn0004893_shift1 (bowl_SANGER_5_FBgn0004893)				; dyads_m5 versus bowl_SANGER_5_FBgn0004893; m=5/5; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.416262; -mCrGwAGY----- ; cor=; Ncor= a 0 4 0 7 0 5 12 0 0 0 0 0 0 0 c 0 7 12 1 0 0 0 0 8 0 0 0 0 0 g 0 0 0 4 12 1 0 12 0 0 0 0 0 0 t 0 0 0 0 0 6 0 0 3 0 0 0 0 0