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_m5/peak-motifs_oligos_7nt_mkv5_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.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift3 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=14; shift=3; ncol=17; ---caCACGCACACmca ; Alignment reference a 0 0 0 460 1509 205 2555 45 520 37 2687 35 2652 46 968 624 1177 c 0 0 0 1722 359 2317 95 2713 96 2718 45 2733 70 2700 1562 1283 628 g 0 0 0 280 595 123 87 48 2153 40 64 21 60 67 155 526 545 t 0 0 0 389 388 206 114 45 82 56 55 62 69 38 166 418 501

klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)
; oligos_7nt_mkv5_m5 versus klu_SANGER_10_FBgn0013469_rc; m=1/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.585532; ----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

klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)
; oligos_7nt_mkv5_m5 versus klu_SOLEXA_5_FBgn0013469_rc; m=2/7; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.532574; 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

tgo_ss_SANGER_5_FBgn0003513_rc_shift3 (tgo_ss_SANGER_5_FBgn0003513_rc)
; oligos_7nt_mkv5_m5 versus tgo_ss_SANGER_5_FBgn0003513_rc; m=3/7; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.44245; ---GTCACGCA------ ; cor=; Ncor= a 0 0 0 2 0 0 10 0 1 0 9 0 0 0 0 0 0 c 0 0 0 0 0 10 0 9 0 10 0 0 0 0 0 0 0 g 0 0 0 8 0 0 0 1 9 0 1 0 0 0 0 0 0 t 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0

tgo_ss_SANGER_5_FBgn0015014_rc_shift3 (tgo_ss_SANGER_5_FBgn0015014_rc)
; oligos_7nt_mkv5_m5 versus tgo_ss_SANGER_5_FBgn0015014_rc; m=4/7; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.44245; ---GTCACGCA------ ; cor=; Ncor= a 0 0 0 2 0 0 10 0 1 0 9 0 0 0 0 0 0 c 0 0 0 0 0 10 0 9 0 10 0 0 0 0 0 0 0 g 0 0 0 8 0 0 0 1 9 0 1 0 0 0 0 0 0 t 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0

CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)
; oligos_7nt_mkv5_m5 versus CG12029_SANGER_10_FBgn0035454_rc; m=5/7; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.424923; -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

Ci_SANGER_5_FBgn0004859_shift1 (Ci_SANGER_5_FBgn0004859)
; oligos_7nt_mkv5_m5 versus Ci_SANGER_5_FBgn0004859; m=6/7; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.412168; -rGMCCACMCAC----- ; cor=; Ncor= a 0 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 0 c 0 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 0 g 0 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 0 t 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0

CG16778_SANGER_5_FBgn0003715_shift9 (CG16778_SANGER_5_FBgn0003715)
; oligos_7nt_mkv5_m5 versus CG16778_SANGER_5_FBgn0003715; m=7/7; ncol2=8; w=0; offset=6; strand=D; shift=9; score=0.405763; ---------CACAyAYG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 18 0 20 0 17 0 0 c 0 0 0 0 0 0 0 0 0 15 1 20 0 9 0 6 1 g 0 0 0 0 0 0 0 0 0 2 0 0 0 0 3 0 18 t 0 0 0 0 0 0 0 0 0 1 0 0 0 11 0 14 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m5_shift3 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=14; shift=3; ncol=17; ---caCACGCACACmca ; Alignment reference a 0 0 0 460 1509 205 2555 45 520 37 2687 35 2652 46 968 624 1177 c 0 0 0 1722 359 2317 95 2713 96 2718 45 2733 70 2700 1562 1283 628 g 0 0 0 280 595 123 87 48 2153 40 64 21 60 67 155 526 545 t 0 0 0 389 388 206 114 45 82 56 55 62 69 38 166 418 501
klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)				; oligos_7nt_mkv5_m5 versus klu_SANGER_10_FBgn0013469_rc; m=1/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.585532; ----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
klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)				; oligos_7nt_mkv5_m5 versus klu_SOLEXA_5_FBgn0013469_rc; m=2/7; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.532574; 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
tgo_ss_SANGER_5_FBgn0003513_rc_shift3 (tgo_ss_SANGER_5_FBgn0003513_rc)				; oligos_7nt_mkv5_m5 versus tgo_ss_SANGER_5_FBgn0003513_rc; m=3/7; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.44245; ---GTCACGCA------ ; cor=; Ncor= a 0 0 0 2 0 0 10 0 1 0 9 0 0 0 0 0 0 c 0 0 0 0 0 10 0 9 0 10 0 0 0 0 0 0 0 g 0 0 0 8 0 0 0 1 9 0 1 0 0 0 0 0 0 t 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0
tgo_ss_SANGER_5_FBgn0015014_rc_shift3 (tgo_ss_SANGER_5_FBgn0015014_rc)				; oligos_7nt_mkv5_m5 versus tgo_ss_SANGER_5_FBgn0015014_rc; m=4/7; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.44245; ---GTCACGCA------ ; cor=; Ncor= a 0 0 0 2 0 0 10 0 1 0 9 0 0 0 0 0 0 c 0 0 0 0 0 10 0 9 0 10 0 0 0 0 0 0 0 g 0 0 0 8 0 0 0 1 9 0 1 0 0 0 0 0 0 t 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0
CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)				; oligos_7nt_mkv5_m5 versus CG12029_SANGER_10_FBgn0035454_rc; m=5/7; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.424923; -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
Ci_SANGER_5_FBgn0004859_shift1 (Ci_SANGER_5_FBgn0004859)				; oligos_7nt_mkv5_m5 versus Ci_SANGER_5_FBgn0004859; m=6/7; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.412168; -rGMCCACMCAC----- ; cor=; Ncor= a 0 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 0 c 0 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 0 g 0 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 0 t 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0
CG16778_SANGER_5_FBgn0003715_shift9 (CG16778_SANGER_5_FBgn0003715)				; oligos_7nt_mkv5_m5 versus CG16778_SANGER_5_FBgn0003715; m=7/7; ncol2=8; w=0; offset=6; strand=D; shift=9; score=0.405763; ---------CACAyAYG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 18 0 20 0 17 0 0 c 0 0 0 0 0 0 0 0 0 15 1 20 0 9 0 6 1 g 0 0 0 0 0 0 0 0 0 2 0 0 0 0 3 0 18 t 0 0 0 0 0 0 0 0 0 1 0 0 0 11 0 14 1