# 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_m9/peak-motifs_dyads_m9.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_m9/peak-motifs_dyads_m9_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m9_shift0 (dyads_m9) |  |  |  |
    ; dyads_m9; m=0 (reference); ncol1=14; shift=0; ncol=14; caAACACACACmca
    ; Alignment reference
    a	665	1337	1976	2446	92	2530	67	2498	59	2477	62	891	527	1266
    c	1305	637	478	94	2450	56	2487	87	2538	99	2482	1505	1329	555
    g	367	345	63	67	43	57	48	47	32	30	70	152	464	441
    t	356	374	176	86	108	50	91	61	64	87	79	145	373	431
CG5953_SANGER_5_FBgn0032587_shift3 (CG5953_SANGER_5_FBgn0032587) |  |  |  |
    ; dyads_m9 versus CG5953_SANGER_5_FBgn0032587; m=1/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.414153; ---aCAAACAy---
    ; cor=; Ncor=
    a	0	0	0	10	0	16	16	16	0	16	1	0	0	0
    c	0	0	0	3	16	0	0	0	16	0	5	0	0	0
    g	0	0	0	0	0	0	0	0	0	0	0	0	0	0
    t	0	0	0	3	0	0	0	0	0	0	10	0	0	0
CG16778_SANGER_5_FBgn0003715_shift4 (CG16778_SANGER_5_FBgn0003715) |  |  |  |
    ; dyads_m9 versus CG16778_SANGER_5_FBgn0003715; m=2/3; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.407586; ----CACAyAYG--
    ; cor=; Ncor=
    a	0	0	0	0	0	18	0	20	0	17	0	0	0	0
    c	0	0	0	0	15	1	20	0	9	0	6	1	0	0
    g	0	0	0	0	2	0	0	0	0	3	0	18	0	0
    t	0	0	0	0	1	0	0	0	11	0	14	1	0	0
Ara_Cell_FBgn0015904_shift0 (Ara_Cell_FBgn0015904) |  |  |  |
    ; dyads_m9 versus Ara_Cell_FBgn0015904; m=3/3; ncol2=8; w=0; offset=0; strand=D; shift=0; score=0.40058; raAwwACA------
    ; cor=; Ncor=
    a	12	16	24	14	23	34	0	34	0	0	0	0	0	0
    c	5	7	1	0	0	0	34	0	0	0	0	0	0	0
    g	10	6	1	5	0	0	0	0	0	0	0	0	0	0
    t	7	5	8	15	11	0	0	0	0	0	0	0	0	0