# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/local_words_7nt_m3/peak-motifs_local_words_7nt_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_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 $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/local_words_7nt_m3/peak-motifs_local_words_7nt_m3_vs_db_jaspar_core_vertebrates

## One-to-n matrix alignment; reference matrix: local_words_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
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
local_words_7nt_m3_shift0 (local_words_7nt_m3) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
    ; local_words_7nt_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; kdaCATTTyCmrgaAATGtmw
    ; Alignment reference
    a	38	43	81	8	142	9	3	13	24	22	40	68	25	103	157	154	13	10	36	48	40
    c	26	35	15	136	4	5	3	5	85	112	75	13	7	11	0	3	9	11	17	40	36
    g	43	41	27	6	6	8	0	10	8	0	10	65	96	34	2	1	9	127	21	37	32
    t	53	41	37	10	8	138	154	132	43	26	35	14	32	12	1	2	129	12	86	35	52
MA0137.2_shift3 (STAT1) |  | 0.783 | 0.559 | 4.929 | 0.508 | 0.927 | 2.382 | 0.921 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1.000 | 1 |
    ; local_words_7nt_m3 versus MA0137.2 (STAT1); m=1/1; ncol2=15; w=15; offset=3; strand=D; shift=3; score=      1; ---cayTTCChrGAAryc---
    ; cor=0.783; Ncor=0.559; logoDP=4.929; NIcor=0.508; NsEucl=0.927; SSD=2.382; NSW=0.921; 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	208	859	251	10	8	106	23	528	696	53	1900	2030	954	336	417	0	0	0
    c	0	0	0	1076	496	574	22	14	1921	1900	762	31	30	124	17	263	760	804	0	0	0
    g	0	0	0	415	279	144	11	38	14	7	115	1292	1700	29	23	552	270	425	0	0	0
    t	0	0	0	378	446	1112	2038	2023	44	155	680	66	302	32	15	315	714	431	0	0	0