# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.motif.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/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift8 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m1_shift8 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=10; shift=8; ncol=18; --------daAAAGAArw
    ; Alignment reference
    a	0	0	0	0	0	0	0	0	11	15	36	36	36	0	36	36	15	14
    c	0	0	0	0	0	0	0	0	4	7	0	0	0	0	0	0	5	6
    g	0	0	0	0	0	0	0	0	10	7	0	0	0	36	0	0	9	5
    t	0	0	0	0	0	0	0	0	11	7	0	0	0	0	0	0	7	11

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift5 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=5; ncol=16; -----kyCGGCAACbt
    ; Alignment reference
    a	0	0	0	0	0	3	8	0	4	3	0	39	39	3	5	8
    c	0	0	0	0	0	3	11	41	6	3	39	0	0	39	11	9
    g	0	0	0	0	0	11	9	0	29	36	3	0	2	0	12	9
    t	0	0	0	0	0	25	14	1	3	0	0	3	1	0	14	16

## One-to-n matrix alignment; reference matrix: dyads_m1_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m1_shift5 (dyads_m1) |  |  |  |
    ; dyads_m1; m=0 (reference); ncol1=13; shift=5; ncol=18; -----mrGCArvwGGAyw
    ; Alignment reference
    a	0	0	0	0	0	8	16	1	0	25	17	10	10	0	3	28	5	11
    c	0	0	0	0	0	12	2	1	27	0	2	8	2	1	0	0	13	6
    g	0	0	0	0	0	3	7	26	1	0	8	8	4	27	24	0	3	3
    t	0	0	0	0	0	5	3	0	0	3	1	2	12	0	1	0	7	8

## One-to-n matrix alignment; reference matrix: dyads_m2_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m2_shift5 (dyads_m2) |  |  |  |
    ; dyads_m2; m=0 (reference); ncol1=20; shift=5; ncol=25; -----mmGGAmdywabrwymCGAmr
    ; Alignment reference
    a	0	0	0	0	0	13	15	0	1	26	9	9	4	10	15	4	13	9	5	13	0	0	29	11	10
    c	0	0	0	0	0	11	9	3	0	5	11	4	16	6	4	9	4	7	10	8	31	0	1	8	6
    g	0	0	0	0	0	6	5	24	30	0	4	8	2	6	5	10	10	3	7	7	0	31	1	5	11
    t	0	0	0	0	0	1	2	4	0	0	7	10	9	9	7	8	4	12	9	3	0	0	0	7	4

## One-to-n matrix alignment; reference matrix: dyads_m3_shift2 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m3_shift2 (dyads_m3) |  |  |  |
    ; dyads_m3; m=0 (reference); ncol1=30; shift=2; ncol=32; --thACCttsctyysmbwyrycrtrkyCAGtr
    ; Alignment reference
    a	0	0	5	12	30	0	0	9	9	5	5	8	9	8	6	15	1	13	5	17	2	6	16	6	15	7	7	0	29	1	6	12
    c	0	0	7	13	6	37	35	6	7	12	18	6	11	12	13	11	11	4	15	2	14	13	6	8	5	7	12	34	0	1	5	3
    g	0	0	9	1	0	0	1	7	9	13	5	4	4	4	10	6	12	9	1	12	7	9	12	9	15	13	8	0	7	35	8	14
    t	0	0	16	11	1	0	1	15	12	7	9	19	13	13	8	5	13	11	16	6	14	9	3	14	2	10	10	3	1	0	18	8