One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.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.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_footprintDB

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 3 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
dyads_m5_shift0 (dyads_m5)                                
; dyads_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; rkrCGCTGGAwr
; Alignment reference
a	18	10	25	4	0	1	1	0	0	49	18	13
c	10	10	9	43	1	49	0	0	0	0	7	12
g	14	18	14	3	46	1	0	51	51	1	12	18
t	9	13	3	1	4	0	50	0	0	1	14	8
2742_PF0055.1_JASPAR_CORE_2009__shift6 (2742_PF0055.1_JASPAR_CORE_2009_) 0.840 0.420 7.225 0.398 0.864 1.331 0.889 1 2 1 1 1 1 1 1.143 1
; dyads_m5 versus 2742_PF0055.1_JASPAR_CORE_2009_; m=1/2; ncol2=6; w=6; offset=6; strand=D; shift=6; score= 1.1429; ------TGGAAA
; cor=0.840; Ncor=0.420; logoDP=7.225; NIcor=0.398; NsEucl=0.864; SSD=1.331; NSW=0.889; rcor=1; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.143; match_rank=1
a	0	0	0	0	0	0	0	0	0	6612	6612	6612
c	0	0	0	0	0	0	0	0	0	0	0	0
g	0	0	0	0	0	0	0	6612	6612	0	0	0
t	0	0	0	0	0	0	6612	0	0	0	0	0
2533_MA0267.1_JASPAR_CORE_2009__rc_shift3 (2533_MA0267.1_JASPAR_CORE_2009__rc) 0.777 0.453 3.736 0.146 0.862 1.876 0.866 2 1 2 2 2 2 2 1.857 2
; dyads_m5 versus 2533_MA0267.1_JASPAR_CORE_2009__rc; m=2/2; ncol2=7; w=7; offset=3; strand=R; shift=3; score= 1.8571; ---tGCTGGk--
; cor=0.777; Ncor=0.453; logoDP=3.736; NIcor=0.146; NsEucl=0.862; SSD=1.876; NSW=0.866; rcor=2; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.857; match_rank=2
a	0	0	0	14	0	0	0	0	1	5	0	0
c	0	0	0	17	0	100	0	0	6	21	0	0
g	0	0	0	20	100	0	10	100	92	28	0	0
t	0	0	0	49	0	0	90	0	1	45	0	0