One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.024047_2026-04-21.024047_gRzMOf/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_nematodes_non-redundant_pfms_transfac.txt -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/2026/04/21/peak-motifs.2026-04-21.024047_2026-04-21.024047_gRzMOf/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_JASPAR2024_CORE_nematodes_non-redundant
One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift3 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m2_shift3 (positions_6nt_m2) |
 |
|
|
; positions_6nt_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---wrTTCAAAaw
; Alignment reference
a 0 0 0 44 46 0 0 0 142 142 142 94 58
c 0 0 0 30 24 0 0 142 0 0 0 15 13
g 0 0 0 8 40 0 0 0 0 0 0 7 23
t 0 0 0 60 32 142 142 0 0 0 0 26 48
|
| MA1450.2_shift0 (lin-54) |
 |
|
|
; positions_6nt_m2 versus MA1450.2 (lin-54); m=1/1; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.640499; ggaAATTCAAATw
; cor=; Ncor=
a 445.0 543.0 1740.0 2616.0 2709.0 23.0 14.0 66.0 2771.0 2901.0 2820.0 327.0 814.0
c 351.0 393.0 174.0 93.0 16.0 27.0 11.0 2612.0 51.0 14.0 13.0 158.0 159.0
g 1823.0 1744.0 554.0 109.0 98.0 5.0 23.0 19.0 109.0 11.0 17.0 29.0 338.0
t 328.0 267.0 479.0 129.0 124.0 2892.0 2899.0 250.0 16.0 21.0 97.0 2433.0 1636.0
|