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.2026-04-21.022353_2026-04-21.022353_CcghX5/results/discovered_motifs/peak-motifs_motifs_discovered.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.2026-04-21.022353_2026-04-21.022353_CcghX5/results/discovered_vs_db/peak-motifs_motifs_vs_db_JASPAR2024_CORE_nematodes_non-redundant.tab
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |
 |
|
|
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; bmGCAAGACdr
; Alignment reference
a 2 43 0 19 115 116 0 132 3 51 64
c 38 48 0 113 0 0 16 0 113 2 20
g 56 17 116 0 1 16 111 0 16 41 48
t 36 24 16 0 16 0 5 0 0 38 0
|
| MA0925.2_rc_shift3 (sma-4_rc) |
 |
|
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; oligos_7nt_mkv2_m1 versus MA0925.2_rc (sma-4_rc); m=1/1; ncol2=7; w=0; offset=3; strand=R; shift=3; score=0.477602; ---CCAGACA-
; cor=; Ncor=
a 0 0 0 110.0 0.0 1000.0 0.0 917.0 83.0 901.0 0
c 0 0 0 836.0 785.0 0.0 0.0 0.0 917.0 33.0 0
g 0 0 0 27.0 0.0 0.0 1000.0 0.0 0.0 33.0 0
t 0 0 0 27.0 215.0 0.0 0.0 83.0 0.0 33.0 0
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |
 |
|
|
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; TCTGGCTTCAym
; Alignment reference
a 11 1 0 0 0 0 0 0 0 48 0 28
c 0 44 0 0 0 57 11 0 59 9 31 19
g 0 13 0 59 59 0 0 0 0 0 1 0
t 48 1 59 0 0 2 48 59 0 2 27 12
|
| MA0260.1_rc_shift3 (che-1_rc) |
 |
|
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; oligos_7nt_mkv2_m4 versus MA0260.1_rc (che-1_rc); m=1/1; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.455367; ---SGyTTC---
; cor=; Ncor=
a 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0 0 0
c 0 0 0 11.0 0.0 18.0 0.0 0.0 37.0 0 0 0
g 0 0 0 26.0 37.0 0.0 0.0 0.0 0.0 0 0 0
t 0 0 0 0.0 0.0 19.0 37.0 37.0 0.0 0 0 0
|