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_6nt_mkv4_m6/peak-motifs_oligos_6nt_mkv4_m6.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DrosophilaTFs/DrosophilaTFs_2015-11-06.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_6nt_mkv4_m6/peak-motifs_oligos_6nt_mkv4_m6_vs_db_DrosophilaTFs

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m6_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m6_shift3 (oligos_6nt_mkv4_m6)
; oligos_6nt_mkv4_m6; m=0 (reference); ncol1=12; shift=3; ncol=15; ---yyCTTATCagym ; Alignment reference a 0 0 0 258 185 81 30 34 1157 9 27 667 140 266 331 c 0 0 0 411 359 1020 64 33 44 19 1173 127 207 383 328 g 0 0 0 231 277 65 39 16 8 37 9 266 679 226 283 t 0 0 0 339 418 73 1106 1156 30 1174 30 179 213 364 297

4988_srp_DrosophilaTF_1.1__rc_shift3 (4988_srp_DrosophilaTF_1.1__rc)
; oligos_6nt_mkv4_m6 versus 4988_srp_DrosophilaTF_1.1__rc; m=1/3; ncol2=10; w=0; offset=0; strand=R; shift=3; score=0.760079; ---rysTTATCrm-- ; cor=; Ncor= a 0 0 0 28 3 9 0 0 1 0 0 37 28 0 0 c 0 0 0 19 41 56 3 0 0 0 1 0 50 0 0 g 0 0 0 34 9 35 0 0 0 0 0 44 13 0 0 t 0 0 0 19 47 0 97 1 0 1 0 19 9 0 0

4978_pnr_DrosophilaTF_1.1__rc_shift0 (4978_pnr_DrosophilaTF_1.1__rc)
; oligos_6nt_mkv4_m6 versus 4978_pnr_DrosophilaTF_1.1__rc; m=2/3; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.625142; vbcyscTTATCdsmm ; cor=; Ncor= a 42 17 23 20 6 16 10 0 1 0 0 42 22 40 33 c 25 33 31 40 50 63 10 0 0 0 1 0 34 27 34 g 25 25 23 7 31 21 10 0 0 0 0 32 33 13 13 t 8 25 23 33 13 0 70 1 0 1 0 26 11 20 20

4945_TFAM_DrosophilaTF_1.1__shift6 (4945_TFAM_DrosophilaTF_1.1_)
; oligos_6nt_mkv4_m6 versus 4945_TFAM_DrosophilaTF_1.1_; m=3/3; ncol2=5; w=0; offset=3; strand=D; shift=6; score=0.412265; ------TTATC---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 82 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 t 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m6_shift3 (oligos_6nt_mkv4_m6)				; oligos_6nt_mkv4_m6; m=0 (reference); ncol1=12; shift=3; ncol=15; ---yyCTTATCagym ; Alignment reference a 0 0 0 258 185 81 30 34 1157 9 27 667 140 266 331 c 0 0 0 411 359 1020 64 33 44 19 1173 127 207 383 328 g 0 0 0 231 277 65 39 16 8 37 9 266 679 226 283 t 0 0 0 339 418 73 1106 1156 30 1174 30 179 213 364 297
4988_srp_DrosophilaTF_1.1__rc_shift3 (4988_srp_DrosophilaTF_1.1__rc)				; oligos_6nt_mkv4_m6 versus 4988_srp_DrosophilaTF_1.1__rc; m=1/3; ncol2=10; w=0; offset=0; strand=R; shift=3; score=0.760079; ---rysTTATCrm-- ; cor=; Ncor= a 0 0 0 28 3 9 0 0 1 0 0 37 28 0 0 c 0 0 0 19 41 56 3 0 0 0 1 0 50 0 0 g 0 0 0 34 9 35 0 0 0 0 0 44 13 0 0 t 0 0 0 19 47 0 97 1 0 1 0 19 9 0 0
4978_pnr_DrosophilaTF_1.1__rc_shift0 (4978_pnr_DrosophilaTF_1.1__rc)				; oligos_6nt_mkv4_m6 versus 4978_pnr_DrosophilaTF_1.1__rc; m=2/3; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.625142; vbcyscTTATCdsmm ; cor=; Ncor= a 42 17 23 20 6 16 10 0 1 0 0 42 22 40 33 c 25 33 31 40 50 63 10 0 0 0 1 0 34 27 34 g 25 25 23 7 31 21 10 0 0 0 0 32 33 13 13 t 8 25 23 33 13 0 70 1 0 1 0 26 11 20 20
4945_TFAM_DrosophilaTF_1.1__shift6 (4945_TFAM_DrosophilaTF_1.1_)				; oligos_6nt_mkv4_m6 versus 4945_TFAM_DrosophilaTF_1.1_; m=3/3; ncol2=5; w=0; offset=3; strand=D; shift=6; score=0.412265; ------TTATC---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 82 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 t 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0