# 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_m10/peak-motifs_dyads_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/dyads_m10/peak-motifs_dyads_m10_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m10_shift0 (dyads_m10) |  |  |  |
    ; dyads_m10; m=0 (reference); ncol1=18; shift=0; ncol=18; ACACACACACACACrCAC
    ; Alignment reference
    a	7238	1045	9369	539	9735	122	9879	128	9866	92	9777	133	9544	141	6688	222	6989	910
    c	1135	7513	282	7314	129	9753	75	9760	58	9807	42	9764	113	9671	320	9327	744	7303
    g	1101	600	342	286	208	86	171	64	179	69	269	87	355	180	2725	284	1578	877
    t	739	1055	220	2074	141	252	88	261	110	245	125	229	201	221	480	380	902	1123
klu_SANGER_10_FBgn0013469_rc_shift6 (klu_SANGER_10_FBgn0013469_rc) |  |  |  |
    ; dyads_m10 versus klu_SANGER_10_FBgn0013469_rc; m=1/1; ncol2=11; w=0; offset=6; strand=R; shift=6; score=0.463069; ------mCACCCmCrCa-
    ; cor=; Ncor=
    a	0	0	0	0	0	0	7	0	18	0	0	0	13	0	9	0	12	0
    c	0	0	0	0	0	0	11	20	0	20	20	19	7	20	0	16	2	0
    g	0	0	0	0	0	0	2	0	0	0	0	0	0	0	10	0	2	0
    t	0	0	0	0	0	0	0	0	2	0	0	1	0	0	1	3	2	0