# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_jaspar_core_insects

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name | Aligned logos | cor | Ncor | logoDP | NIcor | NsEucl | SSD | NSW | rcor | rNcor | rlogoDP | rNIcor | rNsEucl | rSSD | rNSW | rank_mean | match_rank | Aligned matrices
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
    ; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=0; ncol=11; yaTACATAta-
    ; Alignment reference
    a	|	1566	3368	0	7443	0	7443	0	7443	1588	3283	0
    c	|	1981	835	0	0	7443	0	0	0	1762	858	0
    g	|	900	1799	0	0	0	0	0	0	757	1698	0
    t	|	2996	1441	7443	0	0	0	7443	0	3336	1604	0
MA0015.1_rc_shift1 (Cf2_II_rc) |  | 0.825 | 0.675 | 6.525 | 0.570 | 0.902 | 1.544 | 0.914 | 2 | 1 | 1 | 1 | 1 | 2 | 1 | 1.286 | 1 |
    ; oligos_6nt_mkv4_m3 versus MA0015.1_rc (Cf2_II_rc); m=1/2; ncol2=10; w=9; offset=1; strand=R; shift=1; score= 1.2857; -ryAyATATAy
    ; cor=0.825; Ncor=0.675; logoDP=6.525; NIcor=0.570; NsEucl=0.902; SSD=1.544; NSW=0.914; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.286; match_rank=1
    a	|	0	24	4	68	1	74	0	67	0	76	2
    c	|	0	15	20	1	36	1	0	4	4	1	40
    g	|	0	29	3	9	2	4	2	9	2	2	13
    t	|	0	12	53	2	41	1	78	0	74	1	25
MA0210.1_shift1 (ara) |  | 0.828 | 0.414 | 6.119 | 0.401 | 0.859 | 1.000 | 0.900 | 1 | 2 | 2 | 2 | 2 | 1 | 2 | 1.714 | 2 |
    ; oligos_6nt_mkv4_m3 versus MA0210.1 (ara); m=2/2; ncol2=5; w=5; offset=1; strand=D; shift=1; score= 1.7143; -wwACA-----
    ; cor=0.828; Ncor=0.414; logoDP=6.119; NIcor=0.401; NsEucl=0.859; SSD=1.000; NSW=0.900; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=2; rank_mean=1.714; match_rank=2
    a	|	0	14	23	34	0	34	0	0	0	0	0
    c	|	0	0	0	0	34	0	0	0	0	0	0
    g	|	0	5	0	0	0	0	0	0	0	0	0
    t	|	0	15	11	0	0	0	0	0	0	0	0