# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.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/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift2 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m4_shift2 (oligos_6-8nt_m4) |  |  |  |
    ; oligos_6-8nt_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --wrTAcATAya
    ; Alignment reference
    a	0	0	179	218	6	668	62	480	0	663	136	218
    c	0	0	172	150	4	24	473	77	2	22	198	166
    g	0	0	161	193	16	0	67	95	19	3	151	155
    t	0	0	186	137	672	6	96	46	677	10	213	159

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift8 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m3_shift8 (oligos_6-8nt_m3) |  |  |  |
    ; oligos_6-8nt_m3; m=0 (reference); ncol1=12; shift=8; ncol=20; --------ssCCCATGCAss
    ; Alignment reference
    a	0	0	0	0	0	0	0	0	119	90	15	33	18	556	32	8	12	546	135	138
    c	0	0	0	0	0	0	0	0	180	187	544	521	568	24	16	15	599	26	167	198
    g	0	0	0	0	0	0	0	0	199	230	39	45	27	19	18	591	12	29	198	180
    t	0	0	0	0	0	0	0	0	130	121	30	29	15	29	562	14	5	27	128	112

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift0 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |  |  |  |
    ; oligos_6-8nt_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; yrTACAGTAtyw
    ; Alignment reference
    a	74	95	8	311	15	253	14	4	303	46	77	86
    c	87	75	10	5	292	25	13	14	16	49	85	72
    g	82	90	12	15	13	25	294	5	10	46	78	81
    t	92	75	305	4	15	32	14	312	6	194	95	96

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift1 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m5_shift1 (oligos_6-8nt_m5) |  |  |  |
    ; oligos_6-8nt_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -gcCAAAATGgm
    ; Alignment reference
    a	0	161	157	46	553	573	579	583	8	32	160	162
    c	0	159	189	521	27	12	21	23	24	35	157	171
    g	0	188	151	51	39	33	23	24	20	556	182	153
    t	0	137	148	27	26	27	22	15	593	22	146	159

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift1 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m1_shift1 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -ccCCCtCCCCycc
    ; Alignment reference
    a	0	180	140	33	14	25	49	17	11	25	84	127	130	152
    c	0	412	461	868	940	902	227	895	916	900	709	379	428	426
    g	0	222	218	54	20	27	77	39	46	37	105	148	238	246
    t	0	175	170	34	15	35	636	38	16	27	91	335	193	165