# 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/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.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/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 2 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
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
positions_7nt_m1_shift0 (positions_7nt_m1) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
    ; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd
    ; Alignment reference
    a	|	325	287	388	918	991	801	0	0	0	1	1	821	814	317	252
    c	|	201	244	235	0	1	5	0	0	0	0	0	0	49	162	228
    g	|	288	256	319	72	12	200	1008	1008	1008	10	0	187	73	370	271
    t	|	194	221	66	18	4	2	0	0	0	997	1007	0	72	159	257
Kr_shift2 (Kr) |  | 0.966 | 0.644 | 5.908 | 0.641 | 0.943 | 0.659 | 0.967 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; positions_7nt_m1 versus Kr; m=1/1; ncol2=10; w=10; offset=2; strand=D; shift=2; score=      1; --aAAaGGGTta---
    ; cor=0.966; Ncor=0.644; logoDP=5.908; NIcor=0.641; NsEucl=0.943; SSD=0.659; NSW=0.967; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
    a	|	0	0	24	38	33	23	2	5	6	3	6	27	0	0	0
    c	|	0	0	7	3	8	10	0	0	4	0	5	6	0	0	0
    g	|	0	0	9	3	2	7	41	39	34	2	4	7	0	0	0
    t	|	0	0	5	1	2	5	2	1	1	40	30	5	0	0	0