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/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_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/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift3 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=13; shift=3; ncol=16; ---caCACAcACACac ; Alignment reference a 0 0 0 1616 5949 121 8874 84 8611 2218 8784 54 8849 112 5929 1185 c 0 0 0 5506 794 8776 44 8848 265 5812 99 8906 48 8808 804 5541 g 0 0 0 663 1558 47 67 42 67 257 96 17 101 57 1381 1022 t 0 0 0 1242 726 83 42 53 84 740 48 50 29 50 913 1279

klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)
; oligos_7nt_mkv5_m4 versus klu_SANGER_10_FBgn0013469_rc; m=1/6; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.624937; ----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

klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)
; oligos_7nt_mkv5_m4 versus klu_SOLEXA_5_FBgn0013469_rc; m=2/6; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.534019; 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

CG5953_SANGER_5_FBgn0032587_shift6 (CG5953_SANGER_5_FBgn0032587)
; oligos_7nt_mkv5_m4 versus CG5953_SANGER_5_FBgn0032587; m=3/6; ncol2=8; w=0; offset=3; strand=D; shift=6; score=0.492643; ------aCAAACAy-- ; cor=; Ncor= a 0 0 0 0 0 0 10 0 16 16 16 0 16 1 0 0 c 0 0 0 0 0 0 3 16 0 0 0 16 0 5 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 3 0 0 0 0 0 0 10 0 0

Ci_SANGER_5_FBgn0004859_shift1 (Ci_SANGER_5_FBgn0004859)
; oligos_7nt_mkv5_m4 versus Ci_SANGER_5_FBgn0004859; m=4/6; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.433596; -rGMCCACMCAC---- ; cor=; Ncor= a 0 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 c 0 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 g 0 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 t 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0

CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)
; oligos_7nt_mkv5_m4 versus CG12029_SANGER_10_FBgn0035454_rc; m=5/6; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.43286; -RCCACACCCac---- ; cor=; Ncor= a 0 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 c 0 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 g 0 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 t 0 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0

CG16778_SANGER_5_FBgn0003715_shift9 (CG16778_SANGER_5_FBgn0003715)
; oligos_7nt_mkv5_m4 versus CG16778_SANGER_5_FBgn0003715; m=6/6; ncol2=8; w=0; offset=6; strand=D; shift=9; score=0.418046; ---------CACAyAY ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 18 0 20 0 17 0 c 0 0 0 0 0 0 0 0 0 15 1 20 0 9 0 6 g 0 0 0 0 0 0 0 0 0 2 0 0 0 0 3 0 t 0 0 0 0 0 0 0 0 0 1 0 0 0 11 0 14

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=13; shift=3; ncol=16; ---caCACAcACACac ; Alignment reference a 0 0 0 1616 5949 121 8874 84 8611 2218 8784 54 8849 112 5929 1185 c 0 0 0 5506 794 8776 44 8848 265 5812 99 8906 48 8808 804 5541 g 0 0 0 663 1558 47 67 42 67 257 96 17 101 57 1381 1022 t 0 0 0 1242 726 83 42 53 84 740 48 50 29 50 913 1279
klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)				; oligos_7nt_mkv5_m4 versus klu_SANGER_10_FBgn0013469_rc; m=1/6; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.624937; ----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
klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)				; oligos_7nt_mkv5_m4 versus klu_SOLEXA_5_FBgn0013469_rc; m=2/6; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.534019; 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
CG5953_SANGER_5_FBgn0032587_shift6 (CG5953_SANGER_5_FBgn0032587)				; oligos_7nt_mkv5_m4 versus CG5953_SANGER_5_FBgn0032587; m=3/6; ncol2=8; w=0; offset=3; strand=D; shift=6; score=0.492643; ------aCAAACAy-- ; cor=; Ncor= a 0 0 0 0 0 0 10 0 16 16 16 0 16 1 0 0 c 0 0 0 0 0 0 3 16 0 0 0 16 0 5 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 3 0 0 0 0 0 0 10 0 0
Ci_SANGER_5_FBgn0004859_shift1 (Ci_SANGER_5_FBgn0004859)				; oligos_7nt_mkv5_m4 versus Ci_SANGER_5_FBgn0004859; m=4/6; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.433596; -rGMCCACMCAC---- ; cor=; Ncor= a 0 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 c 0 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 g 0 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 t 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0
CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)				; oligos_7nt_mkv5_m4 versus CG12029_SANGER_10_FBgn0035454_rc; m=5/6; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.43286; -RCCACACCCac---- ; cor=; Ncor= a 0 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 c 0 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 g 0 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 t 0 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0
CG16778_SANGER_5_FBgn0003715_shift9 (CG16778_SANGER_5_FBgn0003715)				; oligos_7nt_mkv5_m4 versus CG16778_SANGER_5_FBgn0003715; m=6/6; ncol2=8; w=0; offset=6; strand=D; shift=9; score=0.418046; ---------CACAyAY ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 18 0 20 0 17 0 c 0 0 0 0 0 0 0 0 0 15 1 20 0 9 0 6 g 0 0 0 0 0 0 0 0 0 2 0 0 0 0 3 0 t 0 0 0 0 0 0 0 0 0 1 0 0 0 11 0 14