# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.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/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5) |  |  |  |
    ; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=16; shift=0; ncol=16; gtsTGTGyGTGTsTgt
    ; Alignment reference
    a	214	180	62	30	40	21	22	21	20	16	41	12	98	13	202	129
    c	294	260	792	62	50	39	43	1077	48	32	62	38	611	57	217	297
    g	895	280	760	38	1580	14	1604	24	1593	23	1556	28	898	67	1041	211
    t	294	977	83	1567	27	1623	28	575	36	1626	38	1619	90	1560	237	1060
klu_SANGER_10_FBgn0013469_shift5 (klu_SANGER_10_FBgn0013469) |  |  |  |
    ; oligos_6nt_mkv4_m5 versus klu_SANGER_10_FBgn0013469; m=1/1; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.491536; -----tGyGkGGGTGk
    ; cor=; Ncor=
    a	0	0	0	0	0	2	3	1	0	0	1	0	0	2	0	0
    c	0	0	0	0	0	2	0	10	0	0	0	0	0	0	0	2
    g	0	0	0	0	0	2	16	0	20	7	19	20	20	0	20	11
    t	0	0	0	0	0	12	0	9	0	13	0	0	0	18	0	7