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_m7/peak-motifs_dyads_m7.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_m7/peak-motifs_dyads_m7_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: dyads_m7_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift1 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=15; shift=1; ncol=16; -camACACACACrCac ; Alignment reference a 0 746 2162 2054 3563 103 3664 76 3641 88 3518 93 1154 127 2089 496 c 0 2128 728 1297 97 3543 51 3629 30 3616 79 3585 176 3437 446 2402 g 0 453 495 139 100 64 94 52 113 38 139 81 2268 151 757 435 t 0 523 465 360 90 140 41 93 66 108 114 91 252 135 558 517

klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)
; dyads_m7 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/3; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.630841; mmmmmCACCCmCrCm- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0

klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)
; dyads_m7 versus klu_SANGER_10_FBgn0013469_rc; m=2/3; ncol2=11; w=0; offset=3; strand=R; shift=4; score=0.55567; ----mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0

CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715)
; dyads_m7 versus CG16778_SANGER_5_FBgn0003715; m=3/3; ncol2=8; w=0; offset=4; strand=D; shift=5; score=0.436799; -----CACAyAYG--- ; cor=; Ncor= a 0 0 0 0 0 0 18 0 20 0 17 0 0 0 0 0 c 0 0 0 0 0 15 1 20 0 9 0 6 1 0 0 0 g 0 0 0 0 0 2 0 0 0 0 3 0 18 0 0 0 t 0 0 0 0 0 1 0 0 0 11 0 14 1 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m7_shift1 (dyads_m7)				; dyads_m7; m=0 (reference); ncol1=15; shift=1; ncol=16; -camACACACACrCac ; Alignment reference a 0 746 2162 2054 3563 103 3664 76 3641 88 3518 93 1154 127 2089 496 c 0 2128 728 1297 97 3543 51 3629 30 3616 79 3585 176 3437 446 2402 g 0 453 495 139 100 64 94 52 113 38 139 81 2268 151 757 435 t 0 523 465 360 90 140 41 93 66 108 114 91 252 135 558 517
klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)				; dyads_m7 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/3; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.630841; mmmmmCACCCmCrCm- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0
klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)				; dyads_m7 versus klu_SANGER_10_FBgn0013469_rc; m=2/3; ncol2=11; w=0; offset=3; strand=R; shift=4; score=0.55567; ----mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0
CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715)				; dyads_m7 versus CG16778_SANGER_5_FBgn0003715; m=3/3; ncol2=8; w=0; offset=4; strand=D; shift=5; score=0.436799; -----CACAyAYG--- ; cor=; Ncor= a 0 0 0 0 0 0 18 0 20 0 17 0 0 0 0 0 c 0 0 0 0 0 15 1 20 0 9 0 6 1 0 0 0 g 0 0 0 0 0 2 0 0 0 0 3 0 18 0 0 0 t 0 0 0 0 0 1 0 0 0 11 0 14 1 0 0 0