One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.180905_2026-01-25.180905_kvVFaU/results/discovered_motifs/oligos_6-8nt_m4/peak-motifs_oligos_6-8nt_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_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/2026/01/25/peak-motifs.2026-01-25.180905_2026-01-25.180905_kvVFaU/results/discovered_motifs/oligos_6-8nt_m4/peak-motifs_oligos_6-8nt_m4_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |
 |
|
|
; oligos_6-8nt_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; acgCACTCACctay
; Alignment reference
a 336 229 199 113 1001 22 76 27 984 29 222 165 328 216
c 276 407 193 832 26 1046 54 1004 36 1030 616 238 274 376
g 243 206 572 77 45 26 33 31 43 36 106 132 242 243
t 264 277 155 97 47 25 956 57 56 24 175 584 275 284
|
| z_rc_shift3 (z_rc) |
 |
|
|
; oligos_6-8nt_m4 versus z_rc; m=1/1; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.410393; ---CaCTCA-----
; cor=; Ncor=
a 0 0 0 5.12195 24.5854 0 0 0 29.7073 0 0 0 0 0
c 0 0 0 30.7317 0 42 0 42 3.07317 0 0 0 0 0
g 0 0 0 5.12195 10.2439 0 0 0 7.17073 0 0 0 0 0
t 0 0 0 1.02439 7.17073 0 42 0 2.04878 0 0 0 0 0
|