# 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 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_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_DMMPMM_drosophila

## 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
Kr_shift2 (Kr) |  | 0.967 | 0.645 | 5.916 | 0.643 | 0.943 | 0.658 | 0.967 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; positions_6nt_m1 versus Kr; m=1/1; ncol2=10; w=10; offset=2; strand=D; shift=2; score=      1; --aAAaGGGTta---
    ; cor=0.967; Ncor=0.645; logoDP=5.916; NIcor=0.643; NsEucl=0.943; SSD=0.658; 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