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/positions_6nt_m1/peak-motifs_positions_6nt_m1.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/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=15; shift=2; ncol=17; --acACACrCACACrca ; Alignment reference a 0 0 2460 417 3456 98 3539 72 1434 73 3511 79 3438 73 998 561 1745 c 0 0 435 2532 54 3524 54 3551 73 3555 25 3556 91 3576 237 2074 601 g 0 0 560 284 179 63 121 74 2125 61 193 54 179 89 2345 565 858 t 0 0 350 572 116 120 91 108 173 116 76 116 97 67 225 605 601

klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)
; positions_6nt_m1 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/3; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score=0.541754; mmmmmCACCCmCrCm-- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0

klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)
; positions_6nt_m1 versus klu_SANGER_10_FBgn0013469_rc; m=2/3; ncol2=11; w=0; offset=2; strand=R; shift=4; score=0.535556; ----mCACCCmCrCa-- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0 0

CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)
; positions_6nt_m1 versus CG12029_SANGER_10_FBgn0035454_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=1; score=0.471629; -RCCACACCCac----- ; cor=; Ncor= a 0 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 0 c 0 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 0 g 0 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 0 t 0 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=15; shift=2; ncol=17; --acACACrCACACrca ; Alignment reference a 0 0 2460 417 3456 98 3539 72 1434 73 3511 79 3438 73 998 561 1745 c 0 0 435 2532 54 3524 54 3551 73 3555 25 3556 91 3576 237 2074 601 g 0 0 560 284 179 63 121 74 2125 61 193 54 179 89 2345 565 858 t 0 0 350 572 116 120 91 108 173 116 76 116 97 67 225 605 601
klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)				; positions_6nt_m1 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/3; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score=0.541754; mmmmmCACCCmCrCm-- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0
klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)				; positions_6nt_m1 versus klu_SANGER_10_FBgn0013469_rc; m=2/3; ncol2=11; w=0; offset=2; strand=R; shift=4; score=0.535556; ----mCACCCmCrCa-- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0 0
CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)				; positions_6nt_m1 versus CG12029_SANGER_10_FBgn0035454_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=1; score=0.471629; -RCCACACCCac----- ; cor=; Ncor= a 0 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 0 c 0 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 0 g 0 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 0 t 0 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0 0