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.2026-04-21.015247_2026-04-21.015247_DTyOML/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.2026-04-21.015247_2026-04-21.015247_DTyOML/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_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m2_shift0 (positions_6nt_m2) |
 |
|
|
; positions_6nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; twAAAAAAww
; Alignment reference
a 115 130 507 507 507 507 507 507 130 182
c 104 118 0 0 0 0 0 0 60 108
g 119 105 0 0 0 0 0 0 56 46
t 169 154 0 0 0 0 0 0 261 171
|
| MA1440.1_shift1 (fkh-9) |
 |
|
|
; positions_6nt_m2 versus MA1440.1 (fkh-9); m=1/2; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.595686; -aAwAACAw-
; cor=; Ncor=
a 0 527.0 809.0 655.0 983.0 999.0 47.0 968.0 574.0 0
c 0 236.0 16.0 93.0 15.0 0.0 780.0 0.0 75.0 0
g 0 236.0 0.0 0.0 0.0 0.0 0.0 0.0 75.0 0
t 0 0.0 174.0 250.0 0.0 0.0 171.0 31.0 274.0 0
|
| MA2173.1_shift4 (mef-2) |
 |
|
|
; positions_6nt_m2 versus MA2173.1 (mef-2); m=2/2; ncol2=7; w=0; offset=4; strand=D; shift=4; score=0.475956; ----AAAATA
; cor=; Ncor=
a 0 0 0 0 422.0 517.0 501.0 516.0 9.0 514.0
c 0 0 0 0 26.0 9.0 15.0 11.0 7.0 12.0
g 0 0 0 0 80.0 27.0 26.0 8.0 12.0 19.0
t 0 0 0 0 30.0 5.0 16.0 23.0 530.0 13.0
|