# 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_6nt_mkv4_m7/peak-motifs_oligos_6nt_mkv4_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_6nt_mkv4_m7/peak-motifs_oligos_6nt_mkv4_m7_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m7_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv4_m7_shift0 (oligos_6nt_mkv4_m7) |  |  |  |
    ; oligos_6nt_mkv4_m7; m=0 (reference); ncol1=10; shift=0; ncol=10; mmACTGCAcm
    ; Alignment reference
    a	280	224	857	0	0	11	0	847	189	254
    c	248	345	0	857	0	7	838	3	344	244
    g	195	114	0	0	0	838	12	0	175	170
    t	134	174	0	0	857	1	7	7	149	189
lola-PW_SOLEXA_FBgn0005630_rc_shift0 (lola-PW_SOLEXA_FBgn0005630_rc) |  |  |  |
    ; oligos_6nt_mkv4_m7 versus lola-PW_SOLEXA_FBgn0005630_rc; m=1/2; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.803184; yskCTGCAmr
    ; cor=; Ncor=
    a	76	44	22	0	0	0	0	389	204	224
    c	137	102	59	392	0	0	364	0	125	31
    g	75	154	103	0	0	392	0	2	18	116
    t	103	90	204	0	392	0	27	0	43	19
lola-PW_SANGER_5_FBgn0005630_shift1 (lola-PW_SANGER_5_FBgn0005630) |  |  |  |
    ; oligos_6nt_mkv4_m7 versus lola-PW_SANGER_5_FBgn0005630; m=2/2; ncol2=7; w=0; offset=1; strand=D; shift=1; score=0.508896; -STCTGCA--
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	11	0	0
    c	0	3	0	10	0	0	11	0	0	0
    g	0	9	2	0	0	12	0	0	0	0
    t	0	0	10	2	12	0	1	1	0	0