# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: positions_6nt_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_6nt_m1_shift0 (positions_6nt_m1) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
    ; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd
    ; Alignment reference
    a	|	338	299	421	1039	1054	828	0	0	0	3	8	840	779	305	274
    c	|	216	265	122	1	2	15	1	0	0	0	4	1	89	195	240
    g	|	316	275	453	11	13	223	1073	1071	1074	27	1	232	103	393	287
    t	|	204	235	78	23	5	8	0	3	0	1044	1061	1	103	181	273
positions_7nt_m1_shift0 (positions_7nt_m1) |  | 0.996 | 0.996 | 12.961 | 0.997 | 0.990 | 0.047 | 0.998 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; positions_6nt_m1 versus positions_7nt_m1; m=1/1; ncol2=15; w=15; offset=0; strand=D; shift=0; score=      1; rrrAAAGGGTTAArd
    ; cor=0.996; Ncor=0.996; logoDP=12.961; NIcor=0.997; NsEucl=0.990; SSD=0.047; NSW=0.998; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
    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