# 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/idmmpmm_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_IDMMPMM_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_rc_shift1 (Kr_rc) |  | 0.966 | 0.708 | 2.082 | 0.090 | 0.951 | 0.571 | 0.974 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; positions_7nt_m1 versus Kr_rc; m=1/1; ncol2=11; w=11; offset=1; strand=R; shift=1; score=      1; -yrAAaGGGTta---
    ; cor=0.966; Ncor=0.708; logoDP=2.082; NIcor=0.090; NsEucl=0.951; SSD=0.571; NSW=0.974; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
    a	|	0	41.2239	122.207	250.55	255.546	173.904	0	41.8348	42.4092	16.3753	47.7674	157.647	0	0	0
    c	|	0	105.041	41.2178	0	10.3333	45.6551	0	0	8.06	5.93559	17.977	28.7388	0	0	0
    g	|	0	52.2137	85.1102	28.4501	2.06667	35.0057	266.548	226.987	225.999	30.0548	29.6445	40.4672	0	0	0
    t	|	0	80.521	30.4651	0	11.0536	24.4353	12.4517	10.1783	2.53167	226.634	183.611	52.1469	0	0	0