# 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.2025-11-26.205219_2025-11-26.205219_vuDZlG/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.2025-11-26.205219_2025-11-26.205219_vuDZlG/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=13; shift=0; ncol=13; acATACACACmca
    ; Alignment reference
    a	1425	347	2251	103	2337	38	2277	26	2263	37	767	520	1082
    c	426	1452	85	532	46	2255	72	2298	85	2267	1376	1114	522
    g	318	252	52	45	26	51	36	34	26	65	149	430	440
    t	266	384	47	1755	26	91	50	77	61	66	143	371	391
CG5953_SANGER_5_FBgn0032587_shift0 (CG5953_SANGER_5_FBgn0032587) |  |  |  |
    ; dyads_m9 versus CG5953_SANGER_5_FBgn0032587; m=1/3; ncol2=8; w=0; offset=0; strand=D; shift=0; score=0.44298; aCAAACAy-----
    ; cor=; Ncor=
    a	10	0	16	16	16	0	16	1	0	0	0	0	0
    c	3	16	0	0	0	16	0	5	0	0	0	0	0
    g	0	0	0	0	0	0	0	0	0	0	0	0	0
    t	3	0	0	0	0	0	0	10	0	0	0	0	0
Cf2-II_FlyReg_FBgn0000286_rc_shift0 (Cf2-II_FlyReg_FBgn0000286_rc) |  |  |  |
    ; dyads_m9 versus Cf2-II_FlyReg_FBgn0000286_rc; m=2/3; ncol2=8; w=0; offset=0; strand=R; shift=0; score=0.437862; wTATACdy-----
    ; cor=; Ncor=
    a	1	0	3	0	3	0	1	0	0	0	0	0	0
    c	0	0	0	0	0	3	0	2	0	0	0	0	0
    g	0	0	0	0	0	0	1	0	0	0	0	0	0
    t	2	3	0	3	0	0	1	1	0	0	0	0	0
CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715) |  |  |  |
    ; dyads_m9 versus CG16778_SANGER_5_FBgn0003715; m=3/3; ncol2=8; w=0; offset=5; strand=D; shift=5; score=0.43251; -----CACAyAYG
    ; cor=; Ncor=
    a	0	0	0	0	0	0	18	0	20	0	17	0	0
    c	0	0	0	0	0	15	1	20	0	9	0	6	1
    g	0	0	0	0	0	2	0	0	0	0	3	0	18
    t	0	0	0	0	0	1	0	0	0	11	0	14	1