# 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/oligos_6nt_mkv4_m6/peak-motifs_oligos_6nt_mkv4_m6.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DrosophilaTFs/DrosophilaTFs_2015-11-06.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/oligos_6nt_mkv4_m6/peak-motifs_oligos_6nt_mkv4_m6_vs_db_DrosophilaTFs

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m6_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv4_m6_shift3 (oligos_6nt_mkv4_m6) |  |  |  |
    ; oligos_6nt_mkv4_m6; m=0 (reference); ncol1=12; shift=3; ncol=15; ---yyCTTATCagym
    ; Alignment reference
    a	0	0	0	258	185	81	30	34	1157	9	27	667	140	266	331
    c	0	0	0	411	359	1020	64	33	44	19	1173	127	207	383	328
    g	0	0	0	231	277	65	39	16	8	37	9	266	679	226	283
    t	0	0	0	339	418	73	1106	1156	30	1174	30	179	213	364	297
4988_srp_DrosophilaTF_1.1__rc_shift3 (4988_srp_DrosophilaTF_1.1__rc) |  |  |  |
    ; oligos_6nt_mkv4_m6 versus 4988_srp_DrosophilaTF_1.1__rc; m=1/3; ncol2=10; w=0; offset=0; strand=R; shift=3; score=0.760079; ---rysTTATCrm--
    ; cor=; Ncor=
    a	0	0	0	28	3	9	0	0	1	0	0	37	28	0	0
    c	0	0	0	19	41	56	3	0	0	0	1	0	50	0	0
    g	0	0	0	34	9	35	0	0	0	0	0	44	13	0	0
    t	0	0	0	19	47	0	97	1	0	1	0	19	9	0	0
4978_pnr_DrosophilaTF_1.1__rc_shift0 (4978_pnr_DrosophilaTF_1.1__rc) |  |  |  |
    ; oligos_6nt_mkv4_m6 versus 4978_pnr_DrosophilaTF_1.1__rc; m=2/3; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.625142; vbcyscTTATCdsmm
    ; cor=; Ncor=
    a	42	17	23	20	6	16	10	0	1	0	0	42	22	40	33
    c	25	33	31	40	50	63	10	0	0	0	1	0	34	27	34
    g	25	25	23	7	31	21	10	0	0	0	0	32	33	13	13
    t	8	25	23	33	13	0	70	1	0	1	0	26	11	20	20
4945_TFAM_DrosophilaTF_1.1__shift6 (4945_TFAM_DrosophilaTF_1.1_) |  |  |  |
    ; oligos_6nt_mkv4_m6 versus 4945_TFAM_DrosophilaTF_1.1_; m=3/3; ncol2=5; w=0; offset=3; strand=D; shift=6; score=0.412265; ------TTATC----
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
    c	0	0	0	0	0	0	0	0	0	0	82	0	0	0	0
    g	0	0	0	0	0	0	0	0	0	0	18	0	0	0	0
    t	0	0	0	0	0	0	1	1	0	1	0	0	0	0	0