# 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_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_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_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_jaspar_core_insects

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift1 ; 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_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
    ; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTATYTkKAww
    ; Alignment reference
    a	|	0	1274	1387	0	4484	0	0	0	0	0	4484	1227	1330
    c	|	0	685	584	0	0	0	1204	0	0	0	0	707	1019
    g	|	0	685	1071	0	0	0	0	0	1682	1241	0	715	758
    t	|	0	1840	1442	4484	0	4484	3280	4484	2802	3243	0	1835	1377
MA0011.1_shift0 (br_Z2) |  | 0.822 | 0.443 | 4.369 | 0.437 | 0.893 | 1.126 | 0.920 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; oligos_7nt_mkv5_m1 versus MA0011.1 (br_Z2); m=1/1; ncol2=8; w=7; offset=-1; strand=D; shift=0; score=      1; wwCTAtTt-----
    ; cor=0.822; Ncor=0.443; logoDP=4.369; NIcor=0.437; NsEucl=0.893; SSD=1.126; NSW=0.920; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
    a	|	3	5	0	0	12	1	2	1	0	0	0	0	0
    c	|	1	2	10	1	0	1	0	2	0	0	0	0	0
    g	|	1	1	0	0	0	2	1	1	0	0	0	0	0
    t	|	7	4	2	11	0	8	9	8	0	0	0	0	0