# 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/FlyFactorSurvey/PWM_FlyFactorSurvey.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_FlyFactorSurvey

## 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=12; yckCTCkCKCtc
    ; Alignment reference
    a	|	576	599	23	0	0	0	0	0	0	0	798	520
    c	|	1281	2822	4	5043	0	5043	0	5043	0	5043	816	2766
    g	|	950	581	1788	0	0	0	1653	0	1290	0	972	752
    t	|	2236	1041	3228	0	5043	0	3390	0	3753	0	2457	1005
Trl_FlyReg_FBgn0013263_shift0 (Trl_FlyReg_FBgn0013263) |  | 0.893 | 0.744 | 4.967 | 0.731 | 0.927 | 1.071 | 0.946 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; positions_7nt_m3 versus Trl_FlyReg_FBgn0013263; m=1/1; ncol2=10; w=10; offset=0; strand=D; shift=0; score=      1; yykCTCTCty--
    ; cor=0.893; Ncor=0.744; logoDP=4.967; NIcor=0.731; NsEucl=0.927; SSD=1.071; NSW=0.946; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
    a	|	4	6	12	0	3	1	13	5	7	9	0	0
    c	|	22	23	6	64	0	70	0	54	13	33	0	0
    g	|	9	11	30	3	14	0	2	7	11	10	0	0
    t	|	36	31	23	4	54	0	56	5	40	19	0	0