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_m1/peak-motifs_local_words_7nt_m1.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_m1/peak-motifs_local_words_7nt_m1_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: local_words_7nt_m1_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
local_words_7nt_m1_shift0 (local_words_7nt_m1)                                
; local_words_7nt_m1; m=0 (reference); ncol1=21; shift=0; ncol=21; wbwCATTTcchgkAAATGtat
; Alignment reference
a	53	36	70	5	143	5	3	14	23	15	40	20	22	116	154	129	8	6	39	46	38
c	28	40	24	139	4	1	1	11	97	108	41	10	8	9	1	1	4	10	24	39	39
g	35	40	22	8	8	2	1	11	7	0	29	100	84	20	1	25	4	137	24	36	33
t	43	43	43	7	4	151	154	123	32	36	49	29	45	14	3	4	143	6	72	38	49
MA0137.2_shift3 (STAT1) 0.778 0.556 4.892 0.505 0.925 2.501 0.917 2 1 1 1 1 2 2 1.429 1
; local_words_7nt_m1 versus MA0137.2 (STAT1); m=1/2; ncol2=15; w=15; offset=3; strand=D; shift=3; score= 1.4286; ---cayTTCChrGAAryc---
; cor=0.778; Ncor=0.556; logoDP=4.892; NIcor=0.505; NsEucl=0.925; SSD=2.501; NSW=0.917; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.429; 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
MA0144.1_shift6 (Stat3) 0.860 0.410 4.350 0.385 0.917 1.374 0.931 1 2 2 2 2 1 1 1.571 2
; local_words_7nt_m1 versus MA0144.1 (Stat3); m=2/2; ncol2=10; w=10; offset=6; strand=D; shift=6; score= 1.5714; ------TTCCaGGAAr-----
; cor=0.860; Ncor=0.410; logoDP=4.350; NIcor=0.385; NsEucl=0.917; SSD=1.374; NSW=0.931; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.571; match_rank=2
a	0	0	0	0	0	0	20	13	38	6	321	8	6	585	606	191	0	0	0	0	0
c	0	0	0	0	0	0	19	10	552	541	21	0	2	21	1	15	0	0	0	0	0
g	0	0	0	0	0	0	25	129	9	1	148	605	592	7	5	393	0	0	0	0	0
t	0	0	0	0	0	0	549	461	14	65	123	0	13	0	1	14	0	0	0	0	0