# 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_7nt_mkv5_m7/peak-motifs_oligos_7nt_mkv5_m7.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_7nt_mkv5_m7/peak-motifs_oligos_7nt_mkv5_m7_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m7_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv5_m7_shift0 (oligos_7nt_mkv5_m7) |  |  |  |
    ; oligos_7nt_mkv5_m7; m=0 (reference); ncol1=14; shift=0; ncol=14; ctCTCTyTCTCTCt
    ; Alignment reference
    a	503	585	161	215	120	150	166	109	121	141	154	241	435	595
    c	4268	736	5741	282	5809	301	4049	266	5870	243	5779	444	4387	960
    g	471	820	143	252	136	244	156	293	76	286	147	332	524	719
    t	1206	4307	403	5699	383	5753	2077	5780	381	5778	368	5431	1102	4174
Trl_FlyReg_FBgn0013263_shift3 (Trl_FlyReg_FBgn0013263) |  |  |  |
    ; oligos_7nt_mkv5_m7 versus Trl_FlyReg_FBgn0013263; m=1/2; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.582354; ---yykCTCTCty-
    ; cor=; Ncor=
    a	0	0	0	4	6	12	0	3	1	13	5	7	9	0
    c	0	0	0	22	23	6	64	0	70	0	54	13	33	0
    g	0	0	0	9	11	30	3	14	0	2	7	11	10	0
    t	0	0	0	36	31	23	4	54	0	56	5	40	19	0
ken_SANGER_10_FBgn0011236_rc_shift3 (ken_SANGER_10_FBgn0011236_rc) |  |  |  |
    ; oligos_7nt_mkv5_m7 versus ken_SANGER_10_FBgn0011236_rc; m=2/2; ncol2=9; w=0; offset=3; strand=R; shift=3; score=0.450205; ---ACTTTCwCy--
    ; cor=; Ncor=
    a	0	0	0	17	0	0	0	1	0	8	0	0	0	0
    c	0	0	0	3	24	0	0	0	24	1	22	14	0	0
    g	0	0	0	4	0	0	0	0	0	2	0	1	0	0
    t	0	0	0	0	0	24	24	23	0	13	2	9	0	0