# 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_m1/peak-motifs_oligos_6nt_mkv4_m1.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_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_jaspar_core_insects

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 3 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_m1_shift0 (oligos_6nt_mkv4_m1) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
    ; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wkCTTATsArw
    ; Alignment reference
    a	|	474	394	0	0	0	1796	0	0	1796	611	473
    c	|	435	355	1796	0	0	0	0	1203	0	347	443
    g	|	342	496	0	0	0	0	0	593	0	458	295
    t	|	545	551	0	1796	1796	0	1796	0	0	380	585
MA0199.1_rc_shift4 (Optix_rc) |  | 0.957 | 0.435 | 2.664 | 0.084 | 0.924 | 0.289 | 0.971 | 1 | 1 | 2 | 2 | 1 | 1 | 1 | 1.286 | 1 |
    ; oligos_6nt_mkv4_m1 versus MA0199.1_rc (Optix_rc); m=1/2; ncol2=5; w=5; offset=4; strand=R; shift=4; score= 1.2857; ----TATCA--
    ; cor=0.957; Ncor=0.435; logoDP=2.664; NIcor=0.084; NsEucl=0.924; SSD=0.289; NSW=0.971; rcor=1; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
    a	|	0	0	0	0	0	27	0	0	22	0	0
    c	|	0	0	0	0	1	0	0	27	0	0	0
    g	|	0	0	0	0	0	0	0	0	5	0	0
    t	|	0	0	0	0	26	0	27	0	0	0	0
MA0246.1_rc_shift3 (so_rc) |  | 0.768 | 0.419 | 5.200 | 0.225 | 0.839 | 1.868 | 0.844 | 2 | 2 | 1 | 1 | 2 | 2 | 2 | 1.714 | 2 |
    ; oligos_6nt_mkv4_m1 versus MA0246.1_rc (so_rc); m=2/2; ncol2=6; w=6; offset=3; strand=R; shift=3; score= 1.7143; ---GTATCA--
    ; cor=0.768; Ncor=0.419; logoDP=5.200; NIcor=0.225; NsEucl=0.839; SSD=1.868; NSW=0.844; rcor=2; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.714; match_rank=2
    a	|	0	0	0	3	0	26	0	0	26	0	0
    c	|	0	0	0	0	0	1	0	27	1	0	0
    g	|	0	0	0	10	0	0	0	0	0	0	0
    t	|	0	0	0	0	27	0	27	0	0	0	0