# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181000_2026-01-25.181000_CpuIe4/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.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/2026/01/25/peak-motifs.2026-01-25.181000_2026-01-25.181000_CpuIe4/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m5_shift0 (dyads_m5) |  |  |  |
    ; dyads_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ycGCCGCCGcc
    ; Alignment reference
    a	1024	909	274	229	115	379	237	117	206	1236	982
    c	1634	1767	191	4280	4573	104	4199	4626	242	1428	1816
    g	1052	1179	4138	182	149	4234	287	93	4299	1198	983
    t	1251	1106	358	270	124	244	238	125	214	1099	1180
Med_shift2 (Med) |  |  |  |
    ; dyads_m5 versus Med; m=1/2; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.487707; --sCmssCsmm
    ; cor=; Ncor=
    a	0	0	1	0	5	0	0	0	0	3	4
    c	0	0	2	8	3	3	4	7	3	5	4
    g	0	0	5	0	0	4	4	1	5	0	0
    t	0	0	0	0	0	1	0	0	0	0	0
brk_shift2 (brk) |  |  |  |
    ; dyads_m5 versus brk; m=2/2; ncol2=7; w=0; offset=2; strand=D; shift=2; score=0.465891; --rGCGCCr--
    ; cor=; Ncor=
    a	0	0	4.4	2.2	0	0	0	0	5.5	0	0
    c	0	0	0	0	9.9	0	11	11	0	0	0
    g	0	0	6.6	8.8	0	9.9	0	0	5.5	0	0
    t	0	0	0	0	1.1	1.1	0	0	0	0	0