One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.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.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_6nt_m4_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_6nt_m4_shift0 (positions_6nt_m4)                                
; positions_6nt_m4; m=0 (reference); ncol1=18; shift=0; ncol=18; wsATGTTGCACAACAGtr
; Alignment reference
a	39	29	88	5	6	0	1	4	2	115	3	118	117	2	106	5	21	32
c	22	32	16	1	4	0	0	0	114	0	110	0	0	110	2	8	25	29
g	27	31	7	0	106	0	0	110	1	0	1	0	0	3	2	99	25	33
t	30	26	7	112	2	118	117	4	1	3	4	0	1	3	8	6	47	24
MA0102.3_shift4 (CEBPA) 0.830 0.507 9.852 0.484 0.903 2.285 0.896 1 1 1 1 1 1 1 1.000 1
; positions_6nt_m4 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score=      1; ----aTTGCAyAAym---
; cor=0.830; Ncor=0.507; logoDP=9.852; NIcor=0.484; NsEucl=0.903; SSD=2.285; NSW=0.896; 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	0
c	0	0	0	0	1332	0	0	0	15318	1274	7654	3092	0	5688	4963	0	0	0
g	0	0	0	0	3635	0	0	11304	0	1066	0	0	0	1804	890	0	0	0
t	0	0	0	0	0	15318	15318	3309	0	1022	5004	0	0	7826	3661	0	0	0
MA0466.1_shift3 (CEBPB) 0.788 0.482 9.597 0.452 0.892 2.819 0.872 2 3 2 2 3 2 2 2.286 2
; positions_6nt_m4 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 2.2857; ---kATTGCAymAy----
; cor=0.788; Ncor=0.482; logoDP=9.597; NIcor=0.452; NsEucl=0.892; SSD=2.819; NSW=0.872; rcor=2; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=2.286; match_rank=2
a	0	0	0	13006	75198	0	0	4556	0	74715	8654	60151	99494	0	0	0	0	0
c	0	0	0	10026	5868	0	0	0	99494	5478	51954	39343	0	36038	0	0	0	0
g	0	0	0	33617	18428	0	0	75531	0	10015	0	0	0	2043	0	0	0	0
t	0	0	0	42845	0	99494	99494	19407	0	9286	38886	0	0	61413	0	0	0	0
MA0102.1_rc_shift1 (Cebpa_rc) 0.751 0.500 0.359 -0.161 0.895 3.152 0.869 3 2 3 3 2 3 3 2.714 3
; positions_6nt_m4 versus MA0102.1_rc (Cebpa_rc); m=3/3; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 2.7143; -vrbrTTGcrmaA-----
; cor=0.751; Ncor=0.500; logoDP=0.359; NIcor=-0.161; NsEucl=0.895; SSD=3.152; NSW=0.869; rcor=3; rNcor=2; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.714; match_rank=3
a	0	6	8	2	10	0	0	1	2	5	7	12	15	0	0	0	0	0
c	0	5	3	5	2	0	0	0	10	2	6	4	0	0	0	0	0	0
g	0	6	5	6	6	0	0	15	2	9	1	1	0	0	0	0	0	0
t	0	1	2	5	0	18	18	2	4	2	4	1	3	0	0	0	0	0