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/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/idmmpmm_PCM.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_vs_db/peak-motifs_motifs_vs_db_IDMMPMM_drosophila.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m6_shift0 (oligos_6nt_mkv4_m6)				; oligos_6nt_mkv4_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; yyCTTATCagym ; Alignment reference a 258 185 81 30 34 1157 9 27 667 140 266 331 c 411 359 1020 64 33 44 19 1173 127 207 383 328 g 231 277 65 39 16 8 37 9 266 679 226 283 t 339 418 73 1106 1156 30 1174 30 179 213 364 297
srp_rc_shift1 (srp_rc)				; oligos_6nt_mkv4_m6 versus srp_rc; m=1/1; ncol2=9; w=0; offset=1; strand=R; shift=1; score=0.634094; -yvYTATCgm-- ; cor=; Ncor= a 0 0.5625 10.6875 0 0 31.5 0 0 6.75 14.0625 0 0 c 0 11.8125 14.625 9.5625 0 0 0 36 0 18 0 0 g 0 6.1875 10.6875 0 0 0 0 0 21.375 2.25 0 0 t 0 17.4375 0 26.4375 36 4.5 36 0 7.875 1.6875 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift3 ; 2 matrices ; sort_field=Ncor

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m1_shift3 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=3; ncol=14; ---maAACACAAmm ; Alignment reference a 0 0 0 623 573 1802 1747 96 1720 81 1680 1767 555 640 c 0 0 0 544 437 1 22 1609 67 1586 57 20 518 599 g 0 0 0 384 449 28 54 61 58 114 51 39 350 326 t 0 0 0 329 421 49 57 114 35 99 92 54 457 315
slp1_rc_shift0 (slp1_rc)				; oligos_7nt_mkv5_m1 versus slp1_rc; m=1/1; ncol2=13; w=-3; offset=-3; strand=R; shift=0; score=0.539029; ATGTmAACAmacc- ; cor=; Ncor= a 98.0004 3.80198 21.3479 26.4096 79.3423 138.449 138.733 6.4804 140.242 44.364 96.3207 23.9241 26.6933 0 c 5.11849 21.8926 7.865 8.63675 62.6136 3.5069 2.65571 126.827 0.28373 79.7509 8.81833 84.8921 76.8114 0 g 23.141 13.4715 110.938 0.28373 0.760397 0.760397 1.04413 0.760397 1.23706 4.64183 17.1033 21.8359 28.4865 0 t 16.7401 103.834 2.84865 107.67 0.28373 0.28373 0.56746 8.93183 1.23706 14.2433 20.7577 12.3479 11.0087 0