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/oligos_7nt_mkv5_m6/peak-motifs_oligos_7nt_mkv5_m6.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/oligos_7nt_mkv5_m6/peak-motifs_oligos_7nt_mkv5_m6_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m6_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m6_shift0 (oligos_7nt_mkv5_m6)
; oligos_7nt_mkv5_m6; m=0 (reference); ncol1=17; shift=0; ncol=17; tgsTGCTGyTGCTGytg ; Alignment reference a 167 226 113 47 59 58 27 40 40 30 21 38 39 45 109 190 250 c 335 230 1115 82 31 1919 38 44 1312 37 40 1972 68 82 1155 261 291 g 355 1425 770 45 2066 113 50 2073 102 35 2098 89 51 2015 200 279 1342 t 1343 319 202 2026 44 110 2085 43 746 2098 41 101 2042 58 736 1470 317

odd_NAR_FBgn0002985_rc_shift5 (odd_NAR_FBgn0002985_rc)
; oligos_7nt_mkv5_m6 versus odd_NAR_FBgn0002985_rc; m=1/3; ncol2=11; w=0; offset=5; strand=R; shift=5; score=0.459648; -----bTGCTACTGkk- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 15 0 0 0 0 3 0 c 0 0 0 0 0 6 1 0 15 0 0 15 3 1 0 0 0 g 0 0 0 0 0 4 3 15 0 0 0 0 0 14 5 5 0 t 0 0 0 0 0 5 11 0 0 15 0 0 12 0 10 7 0

Aef1_SANGER_5_FBgn0005694_rc_shift1 (Aef1_SANGER_5_FBgn0005694_rc)
; oligos_7nt_mkv5_m6 versus Aef1_SANGER_5_FBgn0005694_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.453241; -GKTGTTGTTGy----- ; cor=; Ncor= a 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 g 0 9 3 0 12 0 0 12 0 0 12 2 0 0 0 0 0 t 0 2 9 12 0 12 12 0 12 12 0 6 0 0 0 0 0

CG11504_SANGER_5_FBgn0039733_rc_shift5 (CG11504_SANGER_5_FBgn0039733_rc)
; oligos_7nt_mkv5_m6 versus CG11504_SANGER_5_FBgn0039733_rc; m=3/3; ncol2=9; w=0; offset=5; strand=R; shift=5; score=0.406288; -----ATGTTGCkR--- ; cor=; Ncor= a 0 0 0 0 0 14 0 0 1 0 0 0 3 6 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 19 1 0 0 0 0 g 0 0 0 0 0 4 0 19 0 0 19 1 5 14 0 0 0 t 0 0 0 0 0 2 20 1 19 20 1 0 11 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m6_shift0 (oligos_7nt_mkv5_m6)				; oligos_7nt_mkv5_m6; m=0 (reference); ncol1=17; shift=0; ncol=17; tgsTGCTGyTGCTGytg ; Alignment reference a 167 226 113 47 59 58 27 40 40 30 21 38 39 45 109 190 250 c 335 230 1115 82 31 1919 38 44 1312 37 40 1972 68 82 1155 261 291 g 355 1425 770 45 2066 113 50 2073 102 35 2098 89 51 2015 200 279 1342 t 1343 319 202 2026 44 110 2085 43 746 2098 41 101 2042 58 736 1470 317
odd_NAR_FBgn0002985_rc_shift5 (odd_NAR_FBgn0002985_rc)				; oligos_7nt_mkv5_m6 versus odd_NAR_FBgn0002985_rc; m=1/3; ncol2=11; w=0; offset=5; strand=R; shift=5; score=0.459648; -----bTGCTACTGkk- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 15 0 0 0 0 3 0 c 0 0 0 0 0 6 1 0 15 0 0 15 3 1 0 0 0 g 0 0 0 0 0 4 3 15 0 0 0 0 0 14 5 5 0 t 0 0 0 0 0 5 11 0 0 15 0 0 12 0 10 7 0
Aef1_SANGER_5_FBgn0005694_rc_shift1 (Aef1_SANGER_5_FBgn0005694_rc)				; oligos_7nt_mkv5_m6 versus Aef1_SANGER_5_FBgn0005694_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.453241; -GKTGTTGTTGy----- ; cor=; Ncor= a 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 g 0 9 3 0 12 0 0 12 0 0 12 2 0 0 0 0 0 t 0 2 9 12 0 12 12 0 12 12 0 6 0 0 0 0 0
CG11504_SANGER_5_FBgn0039733_rc_shift5 (CG11504_SANGER_5_FBgn0039733_rc)				; oligos_7nt_mkv5_m6 versus CG11504_SANGER_5_FBgn0039733_rc; m=3/3; ncol2=9; w=0; offset=5; strand=R; shift=5; score=0.406288; -----ATGTTGCkR--- ; cor=; Ncor= a 0 0 0 0 0 14 0 0 1 0 0 0 3 6 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 19 1 0 0 0 0 g 0 0 0 0 0 4 0 19 0 0 19 1 5 14 0 0 0 t 0 0 0 0 0 2 20 1 19 20 1 0 11 0 0 0 0