One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.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/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift2 ; 2 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_m1_shift2 (positions_7nt_m1)                                
; positions_7nt_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --vsAGGGGCCgg
; Alignment reference
a	0	0	2	1	6	0	0	0	0	0	0	1	1
c	0	0	2	3	0	0	0	0	0	6	6	1	1
g	0	0	2	2	0	6	6	6	6	0	0	4	4
t	0	0	0	0	0	0	0	0	0	0	0	0	0
MA0155.1_shift0 (INSM1) 0.762 0.586 8.805 0.613 0.889 2.465 0.877 1 1 1 1 1 1 1 1.000 1
; positions_7nt_m1 versus MA0155.1 (INSM1); m=1/1; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=      1; TGymwGGGGkcr-
; cor=0.762; Ncor=0.586; logoDP=8.805; NIcor=0.613; NsEucl=0.889; SSD=2.465; NSW=0.877; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a	1	0	0	6	16	0	0	0	0	0	3	10	0
c	0	0	8	15	0	0	1	0	0	2	16	0	0
g	4	20	3	0	0	24	23	24	24	16	0	12	0
t	19	4	13	3	8	0	0	0	0	6	5	2	0