# 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_m3/peak-motifs_positions_6nt_m3.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_m3/peak-motifs_positions_6nt_m3_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_6nt_m3_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_m3_shift0 (positions_6nt_m3) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
    ; positions_6nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wrCAGGTAra
    ; Alignment reference
    a	|	1036	986	0	3557	0	0	0	3557	1228	1214
    c	|	764	745	3557	0	0	0	0	0	538	770
    g	|	860	1059	0	0	3557	3557	0	0	1249	762
    t	|	897	767	0	0	0	0	3557	0	542	811
sna_shift0 (sna) |  | 0.788 | 0.709 | 6.730 | 0.685 | 0.896 | 1.767 | 0.902 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; positions_6nt_m3 versus sna; m=1/1; ncol2=9; w=9; offset=0; strand=D; shift=0; score=      1; AdCArGTdr-
    ; cor=0.788; Ncor=0.709; logoDP=6.730; NIcor=0.685; NsEucl=0.896; SSD=1.767; NSW=0.902; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
    a	|	9	4	0	10	4	0	0	3	3	0
    c	|	2	0	11	0	0	0	0	0	2	0
    g	|	0	4	0	1	6	11	2	5	6	0
    t	|	0	3	0	0	1	0	9	3	0	0