# 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_m8/peak-motifs_oligos_7nt_mkv5_m8.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_m8/peak-motifs_oligos_7nt_mkv5_m8_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m8_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv5_m8_shift1 (oligos_7nt_mkv5_m8) |  |  |  |
    ; oligos_7nt_mkv5_m8; m=0 (reference); ncol1=16; shift=1; ncol=17; -ACACACACACACACAC
    ; Alignment reference
    a	0	8417	950	10951	81	10965	77	11008	365	10967	66	10969	97	10629	540	7871	1079
    c	0	930	9006	72	10941	81	10953	55	8641	61	10901	68	10841	199	8182	1031	7805
    g	0	1252	434	157	68	126	82	127	261	144	98	141	131	216	1684	1414	1137
    t	0	646	855	65	155	73	133	55	1978	73	180	67	176	201	839	929	1224
klu_SANGER_10_FBgn0013469_rc_shift1 (klu_SANGER_10_FBgn0013469_rc) |  |  |  |
    ; oligos_7nt_mkv5_m8 versus klu_SANGER_10_FBgn0013469_rc; m=1/2; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.500964; -mCACCCmCrCa-----
    ; cor=; Ncor=
    a	0	7	0	18	0	0	0	13	0	9	0	12	0	0	0	0	0
    c	0	11	20	0	20	20	19	7	20	0	16	2	0	0	0	0	0
    g	0	2	0	0	0	0	0	0	0	10	0	2	0	0	0	0	0
    t	0	0	0	2	0	0	1	0	0	1	3	2	0	0	0	0	0
CG12029_SANGER_10_FBgn0035454_rc_shift0 (CG12029_SANGER_10_FBgn0035454_rc) |  |  |  |
    ; oligos_7nt_mkv5_m8 versus CG12029_SANGER_10_FBgn0035454_rc; m=2/2; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.419445; RCCACACCCac------
    ; cor=; Ncor=
    a	5	4	0	16	0	17	0	0	0	13	4	0	0	0	0	0	0
    c	0	14	20	2	20	0	20	20	20	3	11	0	0	0	0	0	0
    g	15	2	0	2	0	2	0	0	0	0	1	0	0	0	0	0	0
    t	0	0	0	0	0	1	0	0	0	4	4	0	0	0	0	0	0