# 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_m10/peak-motifs_oligos_6nt_mkv4_m10.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_m10/peak-motifs_oligos_6nt_mkv4_m10_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m10_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv4_m10_shift0 (oligos_6nt_mkv4_m10) |  |  |  |
    ; oligos_6nt_mkv4_m10; m=0 (reference); ncol1=12; shift=0; ncol=12; rrAAGCAAcgvr
    ; Alignment reference
    a	589	587	1758	1825	53	108	1816	1760	386	322	537	607
    c	425	404	74	41	44	1659	28	38	1074	268	486	435
    g	571	645	48	40	1811	132	55	87	288	1155	600	504
    t	354	303	59	33	31	40	40	54	191	194	316	393
CG3838_SANGER_5_FBgn0032130_shift2 (CG3838_SANGER_5_FBgn0032130) |  |  |  |
    ; oligos_6nt_mkv4_m10 versus CG3838_SANGER_5_FBgn0032130; m=1/2; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.529153; --AwrCRACAW-
    ; cor=; Ncor=
    a	0	0	18	8	5	3	15	20	0	19	5	0
    c	0	0	0	4	2	17	0	0	20	0	1	0
    g	0	0	2	1	13	0	5	0	0	0	0	0
    t	0	0	0	7	0	0	0	0	0	1	14	0
onecut_Cell_FBgn0028996_rc_shift1 (onecut_Cell_FBgn0028996_rc) |  |  |  |
    ; oligos_6nt_mkv4_m10 versus onecut_Cell_FBgn0028996_rc; m=2/2; ncol2=7; w=0; offset=1; strand=R; shift=1; score=0.430483; -hAATCAA----
    ; cor=; Ncor=
    a	0	6	15	15	0	0	15	12	0	0	0	0
    c	0	4	0	0	0	15	0	0	0	0	0	0
    g	0	0	0	0	0	0	0	2	0	0	0	0
    t	0	5	0	0	15	0	0	1	0	0	0	0