One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.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/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_footprintDB

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_shift0 ; 8 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv2_shift0 (oligos_7nt_mkv2)
; oligos_7nt_mkv2; m=0 (reference); ncol1=11; shift=0; ncol=11; TsAGGAGTAhw ; Alignment reference a 1 1 7 0 0 7 0 0 7 2 3 c 0 2 0 0 0 0 0 0 0 2 0 g 0 3 0 7 7 0 7 0 0 0 1 t 6 1 0 0 0 0 0 7 0 3 3

5131_YufM_DBTBS_1.0__shift2 (5131_YufM_DBTBS_1.0_) 0.786 0.572 7.999 0.589 0.874 2.045 0.872 3 2 2 1 3 6 3 2.857 1
; oligos_7nt_mkv2 versus 5131_YufM_DBTBS_1.0_; m=1/7; ncol2=8; w=8; offset=2; strand=D; shift=2; score= 2.8571; --ArGrGdws- ; cor=0.786; Ncor=0.572; logoDP=7.999; NIcor=0.589; NsEucl=0.874; SSD=2.045; NSW=0.872; rcor=3; rNcor=2; rlogoDP=2; rNIcor=1; rNsEucl=3; rSSD=6; rNSW=3; rank_mean=2.857; match_rank=1 a 0 0 3 1 0 2 0 1 2 0 0 c 0 0 0 0 0 0 0 0 0 1 0 g 0 0 0 2 3 1 3 1 0 2 0 t 0 0 0 0 0 0 0 1 1 0 0

5047_ZmHOX2a_1__Athamap_20091028__rc_shift0 (5047_ZmHOX2a_1__Athamap_20091028__rc) 0.825 0.525 0.129 -0.139 0.881 1.382 0.901 1 4 7 6 1 1 1 3.000 2
; oligos_7nt_mkv2 versus 5047_ZmHOX2a_1__Athamap_20091028__rc; m=2/7; ncol2=7; w=7; offset=0; strand=R; shift=0; score= 3; ttAGGAy---- ; cor=0.825; Ncor=0.525; logoDP=0.129; NIcor=-0.139; NsEucl=0.881; SSD=1.382; NSW=0.901; rcor=1; rNcor=4; rlogoDP=7; rNIcor=6; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=3.000; match_rank=2 a 8 6 38 0 0 38 7 0 0 0 0 c 3 8 0 0 0 0 16 0 0 0 0 g 6 7 0 38 38 0 4 0 0 0 0 t 21 17 0 0 0 0 11 0 0 0 0

2780_PF0093.1_JASPAR_CORE_2009__shift3 (2780_PF0093.1_JASPAR_CORE_2009_) 0.778 0.424 9.609 0.424 0.833 2.000 0.833 4 5 1 3 5 2 5 3.571 3
; oligos_7nt_mkv2 versus 2780_PF0093.1_JASPAR_CORE_2009_; m=3/7; ncol2=6; w=6; offset=3; strand=D; shift=3; score= 3.5714; ---GGATTA-- ; cor=0.778; Ncor=0.424; logoDP=9.609; NIcor=0.424; NsEucl=0.833; SSD=2.000; NSW=0.833; rcor=4; rNcor=5; rlogoDP=1; rNIcor=3; rNsEucl=5; rSSD=2; rNSW=5; rank_mean=3.571; match_rank=3 a 0 0 0 0 0 1992 0 0 1992 0 0 c 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 1992 1992 0 0 0 0 0 0 t 0 0 0 0 0 0 1992 1992 0 0 0

3095_NarP_RegulonDB_7.5__rc_shift2 (3095_NarP_RegulonDB_7.5__rc) 0.789 0.574 0.939 -0.161 0.874 2.044 0.872 2 1 6 7 2 5 2 3.571 4
; oligos_7nt_mkv2 versus 3095_NarP_RegulonDB_7.5__rc; m=4/7; ncol2=8; w=8; offset=2; strand=R; shift=2; score= 3.5714; --AgrrGTAk- ; cor=0.789; Ncor=0.574; logoDP=0.939; NIcor=-0.161; NsEucl=0.874; SSD=2.044; NSW=0.872; rcor=2; rNcor=1; rlogoDP=6; rNIcor=7; rNsEucl=2; rSSD=5; rNSW=2; rank_mean=3.571; match_rank=4 a 0 0 14 4 5 6 0 0 20 2 0 c 0 0 3 0 2 1 0 2 0 0 0 g 0 0 2 12 10 13 16 0 0 9 0 t 0 0 1 4 3 0 4 18 0 9 0

3094_NarL_RegulonDB_7.5__shift1 (3094_NarL_RegulonDB_7.5_) 0.764 0.555 4.299 0.537 0.866 2.289 0.857 7 3 3 2 4 7 4 4.286 5
; oligos_7nt_mkv2 versus 3094_NarL_RegulonDB_7.5_; m=5/7; ncol2=8; w=8; offset=1; strand=D; shift=1; score= 4.2857; -wakrrkTA-- ; cor=0.764; Ncor=0.555; logoDP=4.299; NIcor=0.537; NsEucl=0.866; SSD=2.289; NSW=0.857; rcor=7; rNcor=3; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=7; rNSW=4; rank_mean=4.286; match_rank=5 a 0 38 54 8 25 41 9 0 86 0 0 c 0 4 9 0 12 5 0 4 0 0 0 g 0 17 15 36 45 45 54 2 0 0 0 t 0 32 13 47 9 0 28 85 5 0 0

1771_MA0212.1_JASPAR_CORE_2009__rc_shift3 (1771_MA0212.1_JASPAR_CORE_2009__rc) 0.767 0.418 1.998 -0.055 0.832 2.025 0.831 5 6 5 5 6 3 6 5.143 6
; oligos_7nt_mkv2 versus 1771_MA0212.1_JASPAR_CORE_2009__rc; m=6/7; ncol2=6; w=6; offset=3; strand=R; shift=3; score= 5.1429; ---GGATTA-- ; cor=0.767; Ncor=0.418; logoDP=1.998; NIcor=-0.055; NsEucl=0.832; SSD=2.025; NSW=0.831; rcor=5; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=3; rNSW=6; rank_mean=5.143; match_rank=6 a 0 0 0 1 0 21 0 2 22 0 0 c 0 0 0 0 0 1 0 0 0 0 0 g 0 0 0 21 22 0 0 0 0 0 0 t 0 0 0 0 0 0 22 20 0 0 0

1792_MA0234.1_JASPAR_CORE_2009__rc_shift3 (1792_MA0234.1_JASPAR_CORE_2009__rc) 0.764 0.417 2.075 -0.055 0.832 2.039 0.830 6 7 4 4 7 4 7 5.571 7
; oligos_7nt_mkv2 versus 1792_MA0234.1_JASPAR_CORE_2009__rc; m=7/7; ncol2=6; w=6; offset=3; strand=R; shift=3; score= 5.5714; ---GGATTA-- ; cor=0.764; Ncor=0.417; logoDP=2.075; NIcor=-0.055; NsEucl=0.832; SSD=2.039; NSW=0.830; rcor=6; rNcor=7; rlogoDP=4; rNIcor=4; rNsEucl=7; rSSD=4; rNSW=7; rank_mean=5.571; match_rank=7 a 0 0 0 1 0 17 0 0 19 0 0 c 0 0 0 1 0 2 0 0 0 0 0 g 0 0 0 17 19 0 0 0 0 0 0 t 0 0 0 0 0 0 19 19 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv2_shift0 (oligos_7nt_mkv2)																	; oligos_7nt_mkv2; m=0 (reference); ncol1=11; shift=0; ncol=11; TsAGGAGTAhw ; Alignment reference a 1 1 7 0 0 7 0 0 7 2 3 c 0 2 0 0 0 0 0 0 0 2 0 g 0 3 0 7 7 0 7 0 0 0 1 t 6 1 0 0 0 0 0 7 0 3 3
5131_YufM_DBTBS_1.0__shift2 (5131_YufM_DBTBS_1.0_)	0.786	0.572	7.999	0.589	0.874	2.045	0.872	3	2	2	1	3	6	3	2.857	1	; oligos_7nt_mkv2 versus 5131_YufM_DBTBS_1.0_; m=1/7; ncol2=8; w=8; offset=2; strand=D; shift=2; score= 2.8571; --ArGrGdws- ; cor=0.786; Ncor=0.572; logoDP=7.999; NIcor=0.589; NsEucl=0.874; SSD=2.045; NSW=0.872; rcor=3; rNcor=2; rlogoDP=2; rNIcor=1; rNsEucl=3; rSSD=6; rNSW=3; rank_mean=2.857; match_rank=1 a 0 0 3 1 0 2 0 1 2 0 0 c 0 0 0 0 0 0 0 0 0 1 0 g 0 0 0 2 3 1 3 1 0 2 0 t 0 0 0 0 0 0 0 1 1 0 0
5047_ZmHOX2a_1__Athamap_20091028__rc_shift0 (5047_ZmHOX2a_1__Athamap_20091028__rc)	0.825	0.525	0.129	-0.139	0.881	1.382	0.901	1	4	7	6	1	1	1	3.000	2	; oligos_7nt_mkv2 versus 5047_ZmHOX2a_1__Athamap_20091028__rc; m=2/7; ncol2=7; w=7; offset=0; strand=R; shift=0; score= 3; ttAGGAy---- ; cor=0.825; Ncor=0.525; logoDP=0.129; NIcor=-0.139; NsEucl=0.881; SSD=1.382; NSW=0.901; rcor=1; rNcor=4; rlogoDP=7; rNIcor=6; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=3.000; match_rank=2 a 8 6 38 0 0 38 7 0 0 0 0 c 3 8 0 0 0 0 16 0 0 0 0 g 6 7 0 38 38 0 4 0 0 0 0 t 21 17 0 0 0 0 11 0 0 0 0
2780_PF0093.1_JASPAR_CORE_2009__shift3 (2780_PF0093.1_JASPAR_CORE_2009_)	0.778	0.424	9.609	0.424	0.833	2.000	0.833	4	5	1	3	5	2	5	3.571	3	; oligos_7nt_mkv2 versus 2780_PF0093.1_JASPAR_CORE_2009_; m=3/7; ncol2=6; w=6; offset=3; strand=D; shift=3; score= 3.5714; ---GGATTA-- ; cor=0.778; Ncor=0.424; logoDP=9.609; NIcor=0.424; NsEucl=0.833; SSD=2.000; NSW=0.833; rcor=4; rNcor=5; rlogoDP=1; rNIcor=3; rNsEucl=5; rSSD=2; rNSW=5; rank_mean=3.571; match_rank=3 a 0 0 0 0 0 1992 0 0 1992 0 0 c 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 1992 1992 0 0 0 0 0 0 t 0 0 0 0 0 0 1992 1992 0 0 0
3095_NarP_RegulonDB_7.5__rc_shift2 (3095_NarP_RegulonDB_7.5__rc)	0.789	0.574	0.939	-0.161	0.874	2.044	0.872	2	1	6	7	2	5	2	3.571	4	; oligos_7nt_mkv2 versus 3095_NarP_RegulonDB_7.5__rc; m=4/7; ncol2=8; w=8; offset=2; strand=R; shift=2; score= 3.5714; --AgrrGTAk- ; cor=0.789; Ncor=0.574; logoDP=0.939; NIcor=-0.161; NsEucl=0.874; SSD=2.044; NSW=0.872; rcor=2; rNcor=1; rlogoDP=6; rNIcor=7; rNsEucl=2; rSSD=5; rNSW=2; rank_mean=3.571; match_rank=4 a 0 0 14 4 5 6 0 0 20 2 0 c 0 0 3 0 2 1 0 2 0 0 0 g 0 0 2 12 10 13 16 0 0 9 0 t 0 0 1 4 3 0 4 18 0 9 0
3094_NarL_RegulonDB_7.5__shift1 (3094_NarL_RegulonDB_7.5_)	0.764	0.555	4.299	0.537	0.866	2.289	0.857	7	3	3	2	4	7	4	4.286	5	; oligos_7nt_mkv2 versus 3094_NarL_RegulonDB_7.5_; m=5/7; ncol2=8; w=8; offset=1; strand=D; shift=1; score= 4.2857; -wakrrkTA-- ; cor=0.764; Ncor=0.555; logoDP=4.299; NIcor=0.537; NsEucl=0.866; SSD=2.289; NSW=0.857; rcor=7; rNcor=3; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=7; rNSW=4; rank_mean=4.286; match_rank=5 a 0 38 54 8 25 41 9 0 86 0 0 c 0 4 9 0 12 5 0 4 0 0 0 g 0 17 15 36 45 45 54 2 0 0 0 t 0 32 13 47 9 0 28 85 5 0 0
1771_MA0212.1_JASPAR_CORE_2009__rc_shift3 (1771_MA0212.1_JASPAR_CORE_2009__rc)	0.767	0.418	1.998	-0.055	0.832	2.025	0.831	5	6	5	5	6	3	6	5.143	6	; oligos_7nt_mkv2 versus 1771_MA0212.1_JASPAR_CORE_2009__rc; m=6/7; ncol2=6; w=6; offset=3; strand=R; shift=3; score= 5.1429; ---GGATTA-- ; cor=0.767; Ncor=0.418; logoDP=1.998; NIcor=-0.055; NsEucl=0.832; SSD=2.025; NSW=0.831; rcor=5; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=3; rNSW=6; rank_mean=5.143; match_rank=6 a 0 0 0 1 0 21 0 2 22 0 0 c 0 0 0 0 0 1 0 0 0 0 0 g 0 0 0 21 22 0 0 0 0 0 0 t 0 0 0 0 0 0 22 20 0 0 0
1792_MA0234.1_JASPAR_CORE_2009__rc_shift3 (1792_MA0234.1_JASPAR_CORE_2009__rc)	0.764	0.417	2.075	-0.055	0.832	2.039	0.830	6	7	4	4	7	4	7	5.571	7	; oligos_7nt_mkv2 versus 1792_MA0234.1_JASPAR_CORE_2009__rc; m=7/7; ncol2=6; w=6; offset=3; strand=R; shift=3; score= 5.5714; ---GGATTA-- ; cor=0.764; Ncor=0.417; logoDP=2.075; NIcor=-0.055; NsEucl=0.832; SSD=2.039; NSW=0.830; rcor=6; rNcor=7; rlogoDP=4; rNIcor=4; rNsEucl=7; rSSD=4; rNSW=7; rank_mean=5.571; match_rank=7 a 0 0 0 1 0 17 0 0 19 0 0 c 0 0 0 1 0 2 0 0 0 0 0 g 0 0 0 17 19 0 0 0 0 0 0 t 0 0 0 0 0 0 19 19 0 0 0