One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.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/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift2 ; 6 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
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)                                
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=2; ncol=18; --mdGGGTCAGrr-----
; Alignment reference
a	0	0	425	502	0	0	0	0	0	1513	0	452	396	0	0	0	0	0
c	0	0	446	86	0	0	0	0	1513	0	0	285	256	0	0	0	0	0
g	0	0	284	466	1513	1513	1513	0	0	0	1513	477	526	0	0	0	0	0
t	0	0	358	459	0	0	0	1513	0	0	0	299	335	0	0	0	0	0
MA0258.1_shift2 (ESR2) 0.848 0.518 6.561 0.507 0.920 1.531 0.930 1 2 4 2 1 2 1 1.857 1
; oligos_6nt_test_vs_ctrl_m3 versus MA0258.1 (ESR2); m=1/5; ncol2=18; w=11; offset=0; strand=D; shift=2; score= 1.8571; --cwrGGTCAsgkTGmCC
; cor=0.848; Ncor=0.518; logoDP=6.561; NIcor=0.507; NsEucl=0.920; SSD=1.531; NSW=0.930; rcor=1; rNcor=2; rlogoDP=4; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.857; match_rank=1
a	0	0	78	158	186	27	18	13	0	337	49	64	52	21	63	178	34	46
c	0	0	161	51	15	0	20	19	357	1	123	63	61	33	25	99	268	289
g	0	0	63	41	154	275	319	33	0	0	113	149	147	24	265	19	2	0
t	0	0	55	107	2	55	0	292	0	19	72	81	97	279	4	61	53	22
MA0071.1_shift0 (RORA_1) 0.834 0.513 9.825 0.504 0.892 1.486 0.907 2 3 1 3 4 1 2 2.286 2
; oligos_6nt_test_vs_ctrl_m3 versus MA0071.1 (RORA_1); m=2/5; ncol2=10; w=8; offset=-2; strand=D; shift=0; score= 2.2857; wwcwAGGTCA--------
; cor=0.834; Ncor=0.513; logoDP=9.825; NIcor=0.504; NsEucl=0.892; SSD=1.486; NSW=0.907; rcor=2; rNcor=3; rlogoDP=1; rNIcor=3; rNsEucl=4; rSSD=1; rNSW=2; rank_mean=2.286; match_rank=2
a	15	9	6	11	21	0	0	0	0	25	0	0	0	0	0	0	0	0
c	1	1	12	2	0	0	0	0	25	0	0	0	0	0	0	0	0	0
g	2	0	4	5	4	25	25	0	0	0	0	0	0	0	0	0	0	0
t	7	15	3	7	0	0	0	25	0	0	0	0	0	0	0	0	0	0
MA0504.1_shift2 (NR2C2) 0.775 0.568 6.381 0.530 0.904 2.216 0.899 5 1 5 1 2 5 4 3.286 3
; oligos_6nt_test_vs_ctrl_m3 versus MA0504.1 (NR2C2); m=3/5; ncol2=15; w=11; offset=0; strand=D; shift=2; score= 3.2857; --mgrGGTCArAGGTCA-
; cor=0.775; Ncor=0.568; logoDP=6.381; NIcor=0.530; NsEucl=0.904; SSD=2.216; NSW=0.899; rcor=5; rNcor=1; rlogoDP=5; rNIcor=1; rNsEucl=2; rSSD=5; rNSW=4; rank_mean=3.286; match_rank=3
a	0	0	129	82	193	0	10	3	6	343	187	324	10	11	0	9	290	0
c	0	0	126	70	6	8	3	0	309	0	0	0	0	0	27	315	0	0
g	0	0	90	221	195	366	355	79	54	48	208	71	385	336	89	35	92	0
t	0	0	50	22	1	21	27	313	26	4	0	0	0	48	279	36	13	0
MA0258.2_shift4 (ESR2) 0.814 0.431 7.479 0.420 0.895 1.783 0.901 3 4 3 5 3 3 3 3.429 4
; oligos_6nt_test_vs_ctrl_m3 versus MA0258.2 (ESR2); m=4/5; ncol2=15; w=9; offset=2; strand=D; shift=4; score= 3.4286; ----rGGTCAsmstGaCC
; cor=0.814; Ncor=0.431; logoDP=7.479; NIcor=0.420; NsEucl=0.895; SSD=1.783; NSW=0.901; rcor=3; rNcor=4; rlogoDP=3; rNIcor=5; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.429; match_rank=4
a	0	0	0	0	5410	429	59	74	0	8098	502	2092	1808	1602	1121	3278	434	1111
c	0	0	0	0	96	0	0	147	7621	1	4202	3235	2510	975	398	2056	6469	5854
g	0	0	0	0	2563	7170	8143	989	533	57	2738	1688	2173	533	6658	1391	363	0
t	0	0	0	0	174	644	41	7033	89	87	801	1228	1752	5133	66	1518	977	1278
MA0074.1_shift4 (RXRA::VDR) 0.798 0.423 8.578 0.442 0.890 1.954 0.891 4 5 2 4 5 4 5 4.143 5
; oligos_6nt_test_vs_ctrl_m3 versus MA0074.1 (RXRA::VDR); m=5/5; ncol2=15; w=9; offset=2; strand=D; shift=4; score= 4.1429; ----RGGTCAwcGrGTTC
; cor=0.798; Ncor=0.423; logoDP=8.578; NIcor=0.442; NsEucl=0.890; SSD=1.954; NSW=0.891; rcor=4; rNcor=5; rlogoDP=2; rNIcor=4; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.143; match_rank=5
a	0	0	0	0	3	0	0	0	0	9	4	2	2	5	0	0	1	0
c	0	0	0	0	0	0	0	0	9	0	2	4	0	0	0	0	0	9
g	0	0	0	0	7	10	9	0	0	1	0	2	8	5	10	0	0	0
t	0	0	0	0	0	0	1	10	1	0	4	2	0	0	0	10	9	1