# 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/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/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_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_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
    ; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; wwTATYTkKAww
    ; Alignment reference
    a	|	1274	1387	0	4484	0	0	0	0	0	4484	1227	1330
    c	|	685	584	0	0	0	1204	0	0	0	0	707	1019
    g	|	685	1071	0	0	0	0	0	1682	1241	0	715	758
    t	|	1840	1442	4484	0	4484	3280	4484	2802	3243	0	1835	1377
Antp_rc_shift0 (Antp_rc) |  | 0.858 | 0.429 | 3.592 | 0.239 | 0.890 | 0.875 | 0.927 | 1 | 2 | 1 | 1 | 2 | 1 | 1 | 1.286 | 1 |
    ; oligos_7nt_mkv5_m1 versus Antp_rc; m=1/2; ncol2=6; w=6; offset=0; strand=R; shift=0; score= 1.2857; wTTATk------
    ; cor=0.858; Ncor=0.429; logoDP=3.592; NIcor=0.239; NsEucl=0.890; SSD=0.875; NSW=0.927; rcor=1; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
    a	|	10.5	0	0	18	0	0	0	0	0	0	0	0
    c	|	0	0	1.5	0	0	3	0	0	0	0	0	0
    g	|	0	0	0	0	0	4.5	0	0	0	0	0	0
    t	|	7.5	18	16.5	0	18	10.5	0	0	0	0	0	0
br-Z1_rc_shift4 (br-Z1_rc) |  | 0.802 | 0.535 | 1.425 | 0.089 | 0.901 | 1.244 | 0.922 | 2 | 1 | 2 | 2 | 1 | 2 | 2 | 1.714 | 2 |
    ; oligos_7nt_mkv5_m1 versus br-Z1_rc; m=2/2; ncol2=8; w=8; offset=4; strand=R; shift=4; score= 1.7143; ----TTwGtAty
    ; cor=0.802; Ncor=0.535; logoDP=1.425; NIcor=0.089; NsEucl=0.901; SSD=1.244; NSW=0.922; rcor=2; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.714; match_rank=2
    a	|	0	0	0	0	0	0	7.41176	0	0	14.8235	3.17647	0
    c	|	0	0	0	0	0	0	0	2.11765	3.17647	1.05882	3.17647	7.41176
    g	|	0	0	0	0	0	2.11765	1.05882	12.7059	3.17647	0	0	0
    t	|	0	0	0	0	18	15.8824	9.52941	3.17647	11.6471	2.11765	11.6471	10.5882