# 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 transfac -file2 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.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_ref

## One-to-n matrix alignment; reference matrix: positions_7nt_m1_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
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
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
MA0452.1_shift1 (Kr_JASPAR) |  | 0.953 | 0.699 | 8.685 | 0.699 | 0.950 | 0.614 | 0.972 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; positions_7nt_m1 versus MA0452.1 (Kr_JASPAR); m=1/2; ncol2=11; w=11; offset=1; strand=D; shift=1; score=      1; -crAAaGGGTTa---
    ; cor=0.953; Ncor=0.699; logoDP=8.685; NIcor=0.699; NsEucl=0.950; SSD=0.614; NSW=0.972; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
    a	|	0	3	11	24	30	18	0	2	2	0	4	20	0	0	0
    c	|	0	17	4	0	0	6	0	0	0	1	0	4	0	0	0
    g	|	0	5	10	7	0	7	31	29	29	7	5	3	0	0	0
    t	|	0	6	6	0	1	0	0	0	0	23	22	4	0	0	0
Kr_FlyReg_FBgn0001325_shift3 (Kr) |  | 0.950 | 0.634 | 5.608 | 0.630 | 0.931 | 0.965 | 0.952 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2.000 | 2 |
    ; positions_7nt_m1 versus Kr_FlyReg_FBgn0001325 (Kr); m=2/2; ncol2=10; w=10; offset=3; strand=D; shift=3; score=      2; ---AAmGGGTtaw--
    ; cor=0.950; Ncor=0.634; logoDP=5.608; NIcor=0.630; NsEucl=0.931; SSD=0.965; NSW=0.952; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
    a	|	0	0	0	37	33	20	2	4	6	1	8	28	16	0	0
    c	|	0	0	0	0	6	11	0	1	3	3	4	6	8	0	0
    g	|	0	0	0	4	1	9	40	37	35	4	4	5	5	0	0
    t	|	0	0	0	3	4	4	2	2	0	36	28	5	15	0	0