# 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_7nt_m3/peak-motifs_positions_7nt_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_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_7nt_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_7nt_m3_shift0 (positions_7nt_m3) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
    ; positions_7nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=13; yckCTCkCKCtc-
    ; Alignment reference
    a	|	576	599	23	0	0	0	0	0	0	0	798	520	0
    c	|	1281	2822	4	5043	0	5043	0	5043	0	5043	816	2766	0
    g	|	950	581	1788	0	0	0	1653	0	1290	0	972	752	0
    t	|	2236	1041	3228	0	5043	0	3390	0	3753	0	2457	1005	0
Trl_shift0 (Trl) |  | 0.821 | 0.757 | 3.792 | 0.727 | 0.924 | 1.679 | 0.930 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; positions_7nt_m3 versus Trl; m=1/1; ncol2=13; w=12; offset=0; strand=D; shift=0; score=      1; TtkykCTCtCtct
    ; cor=0.821; Ncor=0.757; logoDP=3.792; NIcor=0.727; NsEucl=0.924; SSD=1.679; NSW=0.930; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
    a	|	10	15	4	0	7	0	4	2	6	13	9	4	18
    c	|	10	8	19	41	3	72	0	56	12	56	16	47	3
    g	|	0	13	24	10	27	5	11	8	9	1	6	9	14
    t	|	57	41	30	26	40	0	62	11	50	7	46	17	42