# 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/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.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/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_db_jaspar_core_insects

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_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
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
    ; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; acAGATACaw
    ; Alignment reference
    a	|	1904	1156	4754	0	4754	0	4754	0	2319	1234
    c	|	841	1841	0	0	0	0	0	4754	563	1169
    g	|	931	929	0	4754	0	0	0	0	724	1054
    t	|	1078	828	0	0	0	4754	0	0	1148	1297
MA0246.1_shift2 (so) |  | 0.762 | 0.457 | 8.307 | 0.458 | 0.832 | 2.038 | 0.830 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; oligos_6nt_mkv4_m2 versus MA0246.1 (so); m=1/1; ncol2=6; w=6; offset=2; strand=D; shift=2; score=      1; --TGATAC--
    ; cor=0.762; Ncor=0.457; logoDP=8.307; NIcor=0.458; NsEucl=0.832; SSD=2.038; NSW=0.830; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
    a	|	0	0	0	0	27	0	27	0	0	0
    c	|	0	0	0	0	0	0	0	10	0	0
    g	|	0	0	1	27	0	1	0	0	0	0
    t	|	0	0	26	0	0	26	0	3	0	0