# 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/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_m3/peak-motifs_positions_6nt_m3_vs_db_IDMMPMM_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_rc_shift0 (sna_rc) |  | 0.796 | 0.717 | 0.166 | -0.225 | 0.897 | 1.717 | 0.905 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; positions_6nt_m3 versus sna_rc; m=1/1; ncol2=9; w=9; offset=0; strand=R; shift=0; score=      1; arCAGGTks-
    ; cor=0.796; Ncor=0.717; logoDP=0.166; NIcor=-0.225; NsEucl=0.897; SSD=1.717; NSW=0.905; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
    a	|	142.347	141.178	0.522917	241.825	51.8638	12.6261	0	30.6144	25.4898	0
    c	|	39.4755	1.56875	249.431	8.12898	0.522917	0	0	0	80.7859	0
    g	|	60.8105	90.2934	0.522917	0.522917	183.791	238.374	7.60606	156.419	95.8839	0
    t	|	8.36667	17.9598	0.522917	0.522917	14.8223	0	243.394	63.967	48.8404	0