# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/04/peak-motifs.2026-01-04.175405_2026-01-04.175405_YulKOI/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_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/2026/01/04/peak-motifs.2026-01-04.175405_2026-01-04.175405_YulKOI/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; wtTTAAGAAGww
    ; Alignment reference
    a	1730	1487	221	298	5169	5716	548	5640	5714	557	1905	2146
    c	1214	1224	232	256	421	38	196	188	47	192	1270	1166
    g	1196	1148	222	347	307	190	5258	172	187	5147	1373	1237
    t	2030	2311	5495	5269	273	226	168	170	222	274	1622	1621
MA0601.2_rc_shift1 (Arid3b_rc) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m1 versus MA0601.2_rc (Arid3b_rc); m=1/1; ncol2=7; w=0; offset=1; strand=R; shift=1; score=0.432418; -ATTAAtw----
    ; cor=; Ncor=
    a	0	911.0	89.0	0.0	1000.0	895.0	238.0	566.0	0	0	0	0
    c	0	0.0	0.0	0.0	0.0	0.0	34.0	80.0	0	0	0	0
    g	0	0.0	0.0	0.0	0.0	0.0	119.0	80.0	0	0	0	0
    t	0	89.0	911.0	1000.0	0.0	104.0	609.0	273.0	0	0	0	0