# 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/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/cisBP2/cisBP_Caenorhabditis_elegans_2019.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/2026/04/21/peak-motifs.2026-04-21.022353_2026-04-21.022353_CcghX5/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_vs_db_cisBP_Caenorhabditis_elegans

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -bmGCAAGACdr
    ; Alignment reference
    a	0	2	43	0	19	115	116	0	132	3	51	64
    c	0	38	48	0	113	0	0	16	0	113	2	20
    g	0	56	17	116	0	1	16	111	0	16	41	48
    t	0	36	24	16	0	16	0	5	0	0	38	0
M00591_2.00_shift0 (Y48G1C.6) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus M00591_2.00 (Y48G1C.6); m=1/1; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.55986; svyGCAAkwt--
    ; cor=; Ncor=
    a	24.1923	28.552	12.639	9.25583	6.43456	83.0881	78.5091	14.4739	31.88	24.2259	0	0
    c	26.7367	31.872	28.1286	2.11315e-05	84.0728	12.1813	6.84292	13.6311	16.6428	23.7462	0	0
    g	27.8278	31.872	7.97879	88.6994	1.06362	0.158802	5.94895	45.2567	18.9533	22.1408	0	0
    t	21.2432	7.70391	51.2536	2.04471	8.42904	4.57178	8.69905	26.6383	32.524	29.887	0	0