# 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_6nt_m1/peak-motifs_positions_6nt_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_6nt_m1/peak-motifs_positions_6nt_m1_vs_ref

## One-to-n matrix alignment; reference matrix: positions_6nt_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_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
MA0452.1_shift1 (Kr_JASPAR) |  | 0.953 | 0.699 | 8.659 | 0.701 | 0.950 | 0.608 | 0.972 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1.143 | 1 |
    ; positions_6nt_m1 versus MA0452.1 (Kr_JASPAR); m=1/2; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 1.1429; -crAAaGGGTTa---
    ; cor=0.953; Ncor=0.699; logoDP=8.659; NIcor=0.701; NsEucl=0.950; SSD=0.608; NSW=0.972; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.143; 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) |  | 0.958 | 0.639 | 5.639 | 0.639 | 0.935 | 0.845 | 0.958 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 1.857 | 2 |
    ; positions_6nt_m1 versus Kr_FlyReg_FBgn0001325 (Kr); m=2/2; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 1.8571; ---AAmGGGTtaw--
    ; cor=0.958; Ncor=0.639; logoDP=5.639; NIcor=0.639; NsEucl=0.935; SSD=0.845; NSW=0.958; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.857; 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