# 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/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_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_IDMMPMM_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_rc_shift1 (Kr_rc) |  | 0.969 | 0.711 | 2.138 | 0.095 | 0.953 | 0.544 | 0.975 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; positions_6nt_m1 versus Kr_rc; m=1/1; ncol2=11; w=11; offset=1; strand=R; shift=1; score=      1; -yrAAaGGGTta---
    ; cor=0.969; Ncor=0.711; logoDP=2.138; NIcor=0.095; NsEucl=0.953; SSD=0.544; NSW=0.975; 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