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/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_motifs/oligos_6nt_mkv4_m6/peak-motifs_oligos_6nt_mkv4_m6_vs_db_IDMMPMM_drosophila
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
|