# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/Homer/Homer_motifs.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/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_vs_db_Homer

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1) |  |  |  |
    ; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -ccgCCTCCCmm
    ; Alignment reference
    a	0	62	100	37	6	5	11	12	8	4	131	107
    c	0	190	142	66	402	397	7	386	380	375	117	133
    g	0	76	90	261	2	8	32	11	15	21	83	101
    t	0	89	85	53	7	7	367	8	14	17	86	76
homer_317_Znf263_shift0 (homer_317_Znf263) |  |  |  |
    ; oligos_6nt_mkv3_m1 versus homer_317_Znf263; m=1/2; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score= 0.5594; crsTsCTCCc--
    ; cor=; Ncor=
    a	15.2	33.3	0.5	0.1	0.1	0.1	0.1	0.1	0.1	13.8	0	0
    c	41.3	24	33.4	0.1	51.2	99.7	0.1	99.7	99.7	65.8	0	0
    g	24.2	30.9	66	0.1	48.6	0.1	0.1	0.1	0.1	0.2	0	0
    t	19.3	11.8	0.1	99.7	0.1	0.1	99.7	0.1	0.1	20.3	0	0
homer_63_Egr2_rc_shift3 (homer_63_Egr2_rc) |  |  |  |
    ; oligos_6nt_mkv3_m1 versus homer_63_Egr2_rc; m=2/2; ncol2=12; w=0; offset=2; strand=R; shift=3; score=0.45297; ---cmCrCCCAC
    ; cor=; Ncor=
    a	0	0	0	20.4	32.9	1.4	25.3	0.1	0.1	0.1	86.1	0.1
    c	0	0	0	35.7	51.3	95.3	0.1	99.7	99.7	94.3	13.7	99.7
    g	0	0	0	19.2	6.6	0.1	58.7	0.1	0.1	0.1	0.1	0.1
    t	0	0	0	24.8	9.2	3.2	15.9	0.1	0.1	5.5	0.1	0.1