One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_7nt_mkv1_m2/peak-motifs_oligos_7nt_mkv1_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_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/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_7nt_mkv1_m2/peak-motifs_oligos_7nt_mkv1_m2_vs_db_JASPAR2024_CORE_plants_non-redundant
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |
 |
|
|
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; bhATGGCYCww
; Alignment reference
a 1 2 8 0 0 0 1 0 0 3 2
c 2 2 0 0 1 0 7 2 7 1 1
g 3 1 0 0 7 7 0 0 1 1 0
t 2 3 0 8 0 1 0 6 0 3 5
|
| MA1794.2_shift3 (NLP7) |
 |
|
|
; oligos_7nt_mkv1_m2 versus MA1794.2 (NLP7); m=1/2; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.540025; ---TGrCyyTT
; cor=; Ncor=
a 0 0 0 10.0 66.0 329.0 0.0 0.0 18.0 10.0 39.0
c 0 0 0 182.0 0.0 175.0 1000.0 444.0 390.0 81.0 15.0
g 0 0 0 2.0 934.0 339.0 0.0 40.0 22.0 0.0 0.0
t 0 0 0 807.0 0.0 156.0 0.0 516.0 570.0 909.0 946.0
|
| MA1414.2_rc_shift3 (E2FA_rc) |
 |
|
|
; oligos_7nt_mkv1_m2 versus MA1414.2_rc (E2FA_rc); m=2/2; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.427624; ---TGGCGC--
; cor=; Ncor=
a 0 0 0 52.0 73.0 11.0 19.0 33.0 11.0 0 0
c 0 0 0 21.0 1.0 18.0 1391.0 22.0 1355.0 0 0
g 0 0 0 10.0 1376.0 1415.0 6.0 1375.0 62.0 0 0
t 0 0 0 1368.0 1.0 7.0 35.0 21.0 23.0 0 0
|