# 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/dyads_m6/peak-motifs_dyads_m6.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/dyads_m6/peak-motifs_dyads_m6_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: dyads_m6_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m6_shift1 (dyads_m6) |  |  |  |
    ; dyads_m6; m=0 (reference); ncol1=13; shift=1; ncol=14; -camACACACAyac
    ; Alignment reference
    a	0	641	1787	1910	2920	40	2982	31	2973	30	2915	148	1847	393
    c	0	1706	619	936	41	2945	17	2942	28	2937	41	987	432	1939
    g	0	346	362	48	33	15	30	21	19	24	30	98	415	351
    t	0	345	270	144	44	38	9	44	18	47	52	1805	344	355
CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715) |  |  |  |
    ; dyads_m6 versus CG16778_SANGER_5_FBgn0003715; m=1/3; ncol2=8; w=0; offset=4; strand=D; shift=5; score=0.503517; -----CACAyAYG-
    ; cor=; Ncor=
    a	0	0	0	0	0	0	18	0	20	0	17	0	0	0
    c	0	0	0	0	0	15	1	20	0	9	0	6	1	0
    g	0	0	0	0	0	2	0	0	0	0	3	0	18	0
    t	0	0	0	0	0	1	0	0	0	11	0	14	1	0
CG5953_SANGER_5_FBgn0032587_shift4 (CG5953_SANGER_5_FBgn0032587) |  |  |  |
    ; dyads_m6 versus CG5953_SANGER_5_FBgn0032587; m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=4; score=0.486142; ----aCAAACAy--
    ; cor=; Ncor=
    a	0	0	0	0	10	0	16	16	16	0	16	1	0	0
    c	0	0	0	0	3	16	0	0	0	16	0	5	0	0
    g	0	0	0	0	0	0	0	0	0	0	0	0	0	0
    t	0	0	0	0	3	0	0	0	0	0	0	10	0	0
foxo_SANGER_10_FBgn0038197_rc_shift0 (foxo_SANGER_10_FBgn0038197_rc) |  |  |  |
    ; dyads_m6 versus foxo_SANGER_10_FBgn0038197_rc; m=3/3; ncol2=9; w=-1; offset=-1; strand=R; shift=0; score=0.421793; ycrwAAACA-----
    ; cor=; Ncor=
    a	0	3	8	8	16	16	20	0	20	0	0	0	0	0
    c	6	12	0	0	1	4	0	18	0	0	0	0	0	0
    g	3	3	11	0	0	0	0	0	0	0	0	0	0	0
    t	11	2	1	12	3	0	0	2	0	0	0	0	0	0