One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.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/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 4 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
positions_7nt_m5_shift0 (positions_7nt_m5)                                
; positions_7nt_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; wyCTCTTGCACAACTbh
; Alignment reference
a	53	47	13	1	20	0	1	2	0	181	11	196	198	3	6	36	50
c	42	60	160	8	161	0	0	0	199	8	186	2	1	179	15	54	54
g	46	38	9	0	18	0	1	190	1	3	1	1	0	3	4	54	25
t	59	55	18	191	1	200	198	8	0	8	2	1	1	15	175	56	71
MA0102.3_shift4 (CEBPA) 0.811 0.525 9.745 0.510 0.900 2.402 0.891 1 1 1 1 1 1 1 1.000 1
; positions_7nt_m5 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score=      1; ----aTTGCAyAAym--
; cor=0.811; Ncor=0.525; logoDP=9.745; NIcor=0.510; NsEucl=0.900; SSD=2.402; NSW=0.891; 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	0	10351	0	0	705	0	11956	2660	12226	15318	0	5804	0	0
c	0	0	0	0	1332	0	0	0	15318	1274	7654	3092	0	5688	4963	0	0
g	0	0	0	0	3635	0	0	11304	0	1066	0	0	0	1804	890	0	0
t	0	0	0	0	0	15318	15318	3309	0	1022	5004	0	0	7826	3661	0	0
MA0466.1_shift3 (CEBPB) 0.791 0.512 9.578 0.490 0.895 2.681 0.878 2 2 2 2 2 3 2 2.143 2
; positions_7nt_m5 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 2.1429; ---kATTGCAymAy---
; cor=0.791; Ncor=0.512; logoDP=9.578; NIcor=0.490; NsEucl=0.895; SSD=2.681; NSW=0.878; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.143; match_rank=2
a	0	0	0	13006	75198	0	0	4556	0	74715	8654	60151	99494	0	0	0	0
c	0	0	0	10026	5868	0	0	0	99494	5478	51954	39343	0	36038	0	0	0
g	0	0	0	33617	18428	0	0	75531	0	10015	0	0	0	2043	0	0	0
t	0	0	0	42845	0	99494	99494	19407	0	9286	38886	0	0	61413	0	0	0
MA0102.2_shift5 (CEBPA) 0.774 0.410 6.119 0.384 0.877 2.449 0.864 3 3 3 3 3 2 3 2.857 3
; positions_7nt_m5 versus MA0102.2 (CEBPA); m=3/3; ncol2=9; w=9; offset=5; strand=D; shift=5; score= 2.8571; -----TtkygCAAy---
; cor=0.774; Ncor=0.410; logoDP=6.119; NIcor=0.384; NsEucl=0.877; SSD=2.449; NSW=0.864; rcor=3; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=2.857; match_rank=3
a	0	0	0	0	0	3	1	4	2	4	2	18	18	0	0	0	0
c	0	0	0	0	0	0	1	1	9	2	15	0	0	6	0	0	0
g	0	0	0	0	0	0	4	6	2	10	0	0	0	2	0	0	0
t	0	0	0	0	0	15	12	7	5	2	1	0	0	10	0	0	0