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_6nt_m2/peak-motifs_positions_6nt_m2.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_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift2 ; 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_m2_shift2 (positions_6nt_m2)                                
; positions_6nt_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --TCCCCTAGCGC
; Alignment reference
a	0	0	0	0	0	0	0	0	1	0	0	0	0
c	0	0	0	1	1	1	1	0	0	0	1	0	1
g	0	0	0	0	0	0	0	0	0	1	0	1	0
t	0	0	1	0	0	0	0	1	0	0	0	0	0
MA0056.1_rc_shift2 (MZF1_1-4_rc) 0.878 0.479 0.037 -0.132 0.880 1.035 0.914 1 1 3 2 1 1 1 1.429 1
; positions_6nt_m2 versus MA0056.1_rc (MZF1_1-4_rc); m=1/3; ncol2=6; w=6; offset=0; strand=R; shift=2; score= 1.4286; --TCCCCr-----
; cor=0.878; Ncor=0.479; logoDP=0.037; NIcor=-0.132; NsEucl=0.880; SSD=1.035; NSW=0.914; rcor=1; rNcor=1; rlogoDP=3; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.429; match_rank=1
a	0	0	0	0	1	0	1	8	0	0	0	0	0
c	0	0	2	20	19	18	19	4	0	0	0	0	0
g	0	0	0	0	0	0	0	5	0	0	0	0	0
t	0	0	18	0	0	2	0	3	0	0	0	0	0
MA0057.1_rc_shift0 (MZF1_5-13_rc) 0.755 0.465 0.728 -0.108 0.858 2.594 0.838 3 2 1 1 2 3 3 2.143 2
; positions_6nt_m2 versus MA0057.1_rc (MZF1_5-13_rc); m=2/3; ncol2=10; w=8; offset=-2; strand=R; shift=0; score= 2.1429; yymCCCMTmv---
; cor=0.755; Ncor=0.465; logoDP=0.728; NIcor=-0.108; NsEucl=0.858; SSD=2.594; NSW=0.838; rcor=3; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.143; match_rank=2
a	2	2	4	2	0	1	5	0	7	4	0	0	0
c	4	4	8	14	14	15	11	0	7	7	0	0	0
g	2	0	1	0	2	0	0	1	0	4	0	0	0
t	8	10	3	0	0	0	0	15	2	1	0	0	0
MA0081.1_rc_shift1 (SPIB_rc) 0.801 0.401 0.209 -0.140 0.850 1.616 0.865 2 3 2 3 3 2 2 2.429 3
; positions_6nt_m2 versus MA0081.1_rc (SPIB_rc); m=3/3; ncol2=7; w=6; offset=-1; strand=R; shift=1; score= 2.4286; -TTCCksw-----
; cor=0.801; Ncor=0.401; logoDP=0.209; NIcor=-0.140; NsEucl=0.850; SSD=1.616; NSW=0.865; rcor=2; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=2.429; match_rank=3
a	0	2	1	1	0	2	2	18	0	0	0	0	0
c	0	0	0	47	47	7	29	0	0	0	0	0	0
g	0	0	0	0	0	16	14	0	0	0	0	0	0
t	0	47	48	1	2	24	4	31	0	0	0	0	0