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/oligos_6nt_mkv3/peak-motifs_oligos_6nt_mkv3.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/oligos_6nt_mkv3/peak-motifs_oligos_6nt_mkv3_vs_db_footprintDB

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_shift2 ; 11 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_6nt_mkv3_shift2 (oligos_6nt_mkv3)
; oligos_6nt_mkv3; m=0 (reference); ncol1=12; shift=2; ncol=15; --hkGAAGAGATcd- ; Alignment reference a 0 0 3 2 0 12 12 0 12 0 12 0 2 4 0 c 0 0 4 2 0 0 0 0 0 0 0 0 8 1 0 g 0 0 2 4 12 0 0 12 0 12 0 1 2 4 0 t 0 0 3 4 0 0 0 0 0 0 0 11 0 3 0

2470_MA0080.1_JASPAR_CORE_2009__shift2 (2470_MA0080.1_JASPAR_CORE_2009_) 0.878 0.439 5.219 0.428 0.901 0.712 0.941 1 4 5 2 1 1 1 2.143 1
; oligos_6nt_mkv3 versus 2470_MA0080.1_JASPAR_CORE_2009_; m=1/10; ncol2=6; w=6; offset=0; strand=D; shift=2; score= 2.1429; --sGGAAs------- ; cor=0.878; Ncor=0.439; logoDP=5.219; NIcor=0.428; NsEucl=0.901; SSD=0.712; NSW=0.941; rcor=1; rNcor=4; rlogoDP=5; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.143; match_rank=1 a 0 0 14 4 3 56 56 3 0 0 0 0 0 0 0 c 0 0 21 2 0 1 0 18 0 0 0 0 0 0 0 g 0 0 19 48 52 0 0 34 0 0 0 0 0 0 0 t 0 0 3 3 2 0 1 2 0 0 0 0 0 0 0

5987_1awc_A_3D-footprint_20130124__shift2 (5987_1awc_A_3D-footprint_20130124_) 0.857 0.428 6.011 0.401 0.888 0.910 0.924 4 7 4 4 2 2 2 3.571 2
; oligos_6nt_mkv3 versus 5987_1awc_A_3D-footprint_20130124_; m=2/10; ncol2=6; w=6; offset=0; strand=D; shift=2; score= 3.5714; --cGGAAg------- ; cor=0.857; Ncor=0.428; logoDP=6.011; NIcor=0.401; NsEucl=0.888; SSD=0.910; NSW=0.924; rcor=4; rNcor=7; rlogoDP=4; rNIcor=4; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=3.571; match_rank=2 a 0 0 13 0 0 96 96 13 0 0 0 0 0 0 0 c 0 0 54 0 0 0 0 13 0 0 0 0 0 0 0 g 0 0 16 96 96 0 0 57 0 0 0 0 0 0 0 t 0 0 13 0 0 0 0 13 0 0 0 0 0 0 0

108_MA0062.1_JASPAR_CORE_2009__shift0 (108_MA0062.1_JASPAR_CORE_2009_) 0.809 0.462 8.128 0.420 0.884 1.722 0.892 6 1 1 3 3 7 5 3.714 3
; oligos_6nt_mkv3 versus 108_MA0062.1_JASPAR_CORE_2009_; m=3/10; ncol2=10; w=8; offset=-2; strand=D; shift=0; score= 3.7143; ACCGGAAGws----- ; cor=0.809; Ncor=0.462; logoDP=8.128; NIcor=0.420; NsEucl=0.884; SSD=1.722; NSW=0.892; rcor=6; rNcor=1; rlogoDP=1; rNIcor=3; rNsEucl=3; rSSD=7; rNSW=5; rank_mean=3.714; match_rank=3 a 5 1 1 0 0 7 7 0 3 0 0 0 0 0 0 c 1 5 6 0 0 0 0 0 1 2 0 0 0 0 0 g 1 1 0 7 7 0 0 7 1 4 0 0 0 0 0 t 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0

3027_POL008.1_JASPAR_CORE_2009__rc_shift3 (3027_POL008.1_JASPAR_CORE_2009__rc) 0.858 0.429 0.193 -0.128 0.874 1.135 0.905 3 6 8 8 5 3 3 5.143 4
; oligos_6nt_mkv3 versus 3027_POL008.1_JASPAR_CORE_2009__rc; m=4/10; ncol2=6; w=6; offset=1; strand=R; shift=3; score= 5.1429; ---sGaAGc------ ; cor=0.858; Ncor=0.429; logoDP=0.193; NIcor=-0.128; NsEucl=0.874; SSD=1.135; NSW=0.905; rcor=3; rNcor=6; rlogoDP=8; rNIcor=8; rNsEucl=5; rSSD=3; rNSW=3; rank_mean=5.143; match_rank=4 a 0 0 0 25 6 72 85 5 25 0 0 0 0 0 0 c 0 0 0 27 7 20 8 6 46 0 0 0 0 0 0 g 0 0 0 34 93 12 12 93 19 0 0 0 0 0 0 t 0 0 0 22 2 4 3 4 18 0 0 0 0 0 0

6730_4b06_A_3D-footprint_20130124__rc_shift2 (6730_4b06_A_3D-footprint_20130124__rc) 0.856 0.428 1.961 0.016 0.870 1.208 0.899 5 8 7 7 8 4 4 6.143 5
; oligos_6nt_mkv3 versus 6730_4b06_A_3D-footprint_20130124__rc; m=5/10; ncol2=6; w=6; offset=0; strand=R; shift=2; score= 6.1429; --CGGAAG------- ; cor=0.856; Ncor=0.428; logoDP=1.961; NIcor=0.016; NsEucl=0.870; SSD=1.208; NSW=0.899; rcor=5; rNcor=8; rlogoDP=7; rNIcor=7; rNsEucl=8; rSSD=4; rNSW=4; rank_mean=6.143; match_rank=5 a 0 0 0 0 0 96 96 0 0 0 0 0 0 0 0 c 0 0 96 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 96 96 0 0 96 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

6697_3rkq_B_3D-footprint_20130124__shift3 (6697_3rkq_B_3D-footprint_20130124_) 0.760 0.444 6.887 0.445 0.859 1.955 0.860 9 3 2 1 10 9 10 6.286 6
; oligos_6nt_mkv3 versus 6697_3rkq_B_3D-footprint_20130124_; m=6/10; ncol2=7; w=7; offset=1; strand=D; shift=3; score= 6.2857; ---TcaAGAG----- ; cor=0.760; Ncor=0.444; logoDP=6.887; NIcor=0.445; NsEucl=0.859; SSD=1.955; NSW=0.860; rcor=9; rNcor=3; rlogoDP=2; rNIcor=1; rNsEucl=10; rSSD=9; rNSW=10; rank_mean=6.286; match_rank=6 a 0 0 0 4 12 48 96 4 92 4 0 0 0 0 0 c 0 0 0 20 60 16 0 0 0 0 0 0 0 0 0 g 0 0 0 4 4 16 0 92 0 92 0 0 0 0 0 t 0 0 0 68 20 16 0 0 4 0 0 0 0 0 0

6749_4hn6_A_3D-footprint_20130124__rc_shift4 (6749_4hn6_A_3D-footprint_20130124__rc) 0.861 0.431 0.148 -0.136 0.863 1.342 0.888 2 5 9 9 9 5 6 6.429 7
; oligos_6nt_mkv3 versus 6749_4hn6_A_3D-footprint_20130124__rc; m=7/10; ncol2=6; w=6; offset=2; strand=R; shift=4; score= 6.4286; ----GnagAG----- ; cor=0.861; Ncor=0.431; logoDP=0.148; NIcor=-0.136; NsEucl=0.863; SSD=1.342; NSW=0.888; rcor=2; rNcor=5; rlogoDP=9; rNIcor=9; rNsEucl=9; rSSD=5; rNSW=6; rank_mean=6.429; match_rank=7 a 0 0 0 0 0 24 60 15 80 10 0 0 0 0 0 c 0 0 0 0 0 24 10 20 5 0 0 0 0 0 0 g 0 0 0 0 96 24 21 50 5 80 0 0 0 0 0 t 0 0 0 0 0 24 5 11 6 6 0 0 0 0 0

2554_MA0293.1_JASPAR_CORE_2009__shift6 (2554_MA0293.1_JASPAR_CORE_2009_) 0.774 0.413 4.982 0.387 0.879 1.865 0.883 8 9 6 5 4 8 8 6.857 8
; oligos_6nt_mkv3 versus 2554_MA0293.1_JASPAR_CORE_2009_; m=8/10; ncol2=11; w=8; offset=4; strand=D; shift=6; score= 6.8571; ------mmAGATCtw ; cor=0.774; Ncor=0.413; logoDP=4.982; NIcor=0.387; NsEucl=0.879; SSD=1.865; NSW=0.883; rcor=8; rNcor=9; rlogoDP=6; rNIcor=5; rNsEucl=4; rSSD=8; rNSW=8; rank_mean=6.857; match_rank=8 a 0 0 0 0 0 0 31 33 72 10 100 3 1 14 30 c 0 0 0 0 0 0 25 25 11 2 0 0 90 19 23 g 0 0 0 0 0 0 23 22 10 86 0 0 3 14 21 t 0 0 0 0 0 0 21 20 7 2 0 97 7 53 26

5048_ZmHOX2a_2__Athamap_20091028__rc_shift7 (5048_ZmHOX2a_2__Athamap_20091028__rc) 0.780 0.455 0.100 -0.141 0.871 1.623 0.884 7 2 10 10 7 6 7 7.000 9
; oligos_6nt_mkv3 versus 5048_ZmHOX2a_2__Athamap_20091028__rc; m=9/10; ncol2=7; w=7; offset=5; strand=R; shift=7; score= 7; -------cmGATCa- ; cor=0.780; Ncor=0.455; logoDP=0.100; NIcor=-0.141; NsEucl=0.871; SSD=1.623; NSW=0.884; rcor=7; rNcor=2; rlogoDP=10; rNIcor=10; rNsEucl=7; rSSD=6; rNSW=7; rank_mean=7.000; match_rank=9 a 0 0 0 0 0 0 0 6 16 0 27 0 0 15 0 c 0 0 0 0 0 0 0 14 7 0 0 0 27 5 0 g 0 0 0 0 0 0 0 4 4 27 0 0 0 2 0 t 0 0 0 0 0 0 0 3 0 0 0 27 0 5 0

2560_MA0302.1_JASPAR_CORE_2009__shift6 (2560_MA0302.1_JASPAR_CORE_2009_) 0.756 0.403 6.109 0.380 0.873 2.059 0.871 10 10 3 6 6 10 9 7.714 10
; oligos_6nt_mkv3 versus 2560_MA0302.1_JASPAR_CORE_2009_; m=10/10; ncol2=11; w=8; offset=4; strand=D; shift=6; score= 7.7143; ------ahAGATCya ; cor=0.756; Ncor=0.403; logoDP=6.109; NIcor=0.380; NsEucl=0.873; SSD=2.059; NSW=0.871; rcor=10; rNcor=10; rlogoDP=3; rNIcor=6; rNsEucl=6; rSSD=10; rNSW=9; rank_mean=7.714; match_rank=10 a 0 0 0 0 0 0 36 31 80 3 98 0 0 5 40 c 0 0 0 0 0 0 21 26 4 0 0 0 99 28 20 g 0 0 0 0 0 0 24 18 12 96 0 0 0 3 23 t 0 0 0 0 0 0 20 26 4 0 2 99 0 64 17

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv3_shift2 (oligos_6nt_mkv3)																	; oligos_6nt_mkv3; m=0 (reference); ncol1=12; shift=2; ncol=15; --hkGAAGAGATcd- ; Alignment reference a 0 0 3 2 0 12 12 0 12 0 12 0 2 4 0 c 0 0 4 2 0 0 0 0 0 0 0 0 8 1 0 g 0 0 2 4 12 0 0 12 0 12 0 1 2 4 0 t 0 0 3 4 0 0 0 0 0 0 0 11 0 3 0
2470_MA0080.1_JASPAR_CORE_2009__shift2 (2470_MA0080.1_JASPAR_CORE_2009_)	0.878	0.439	5.219	0.428	0.901	0.712	0.941	1	4	5	2	1	1	1	2.143	1	; oligos_6nt_mkv3 versus 2470_MA0080.1_JASPAR_CORE_2009_; m=1/10; ncol2=6; w=6; offset=0; strand=D; shift=2; score= 2.1429; --sGGAAs------- ; cor=0.878; Ncor=0.439; logoDP=5.219; NIcor=0.428; NsEucl=0.901; SSD=0.712; NSW=0.941; rcor=1; rNcor=4; rlogoDP=5; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.143; match_rank=1 a 0 0 14 4 3 56 56 3 0 0 0 0 0 0 0 c 0 0 21 2 0 1 0 18 0 0 0 0 0 0 0 g 0 0 19 48 52 0 0 34 0 0 0 0 0 0 0 t 0 0 3 3 2 0 1 2 0 0 0 0 0 0 0
5987_1awc_A_3D-footprint_20130124__shift2 (5987_1awc_A_3D-footprint_20130124_)	0.857	0.428	6.011	0.401	0.888	0.910	0.924	4	7	4	4	2	2	2	3.571	2	; oligos_6nt_mkv3 versus 5987_1awc_A_3D-footprint_20130124_; m=2/10; ncol2=6; w=6; offset=0; strand=D; shift=2; score= 3.5714; --cGGAAg------- ; cor=0.857; Ncor=0.428; logoDP=6.011; NIcor=0.401; NsEucl=0.888; SSD=0.910; NSW=0.924; rcor=4; rNcor=7; rlogoDP=4; rNIcor=4; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=3.571; match_rank=2 a 0 0 13 0 0 96 96 13 0 0 0 0 0 0 0 c 0 0 54 0 0 0 0 13 0 0 0 0 0 0 0 g 0 0 16 96 96 0 0 57 0 0 0 0 0 0 0 t 0 0 13 0 0 0 0 13 0 0 0 0 0 0 0
108_MA0062.1_JASPAR_CORE_2009__shift0 (108_MA0062.1_JASPAR_CORE_2009_)	0.809	0.462	8.128	0.420	0.884	1.722	0.892	6	1	1	3	3	7	5	3.714	3	; oligos_6nt_mkv3 versus 108_MA0062.1_JASPAR_CORE_2009_; m=3/10; ncol2=10; w=8; offset=-2; strand=D; shift=0; score= 3.7143; ACCGGAAGws----- ; cor=0.809; Ncor=0.462; logoDP=8.128; NIcor=0.420; NsEucl=0.884; SSD=1.722; NSW=0.892; rcor=6; rNcor=1; rlogoDP=1; rNIcor=3; rNsEucl=3; rSSD=7; rNSW=5; rank_mean=3.714; match_rank=3 a 5 1 1 0 0 7 7 0 3 0 0 0 0 0 0 c 1 5 6 0 0 0 0 0 1 2 0 0 0 0 0 g 1 1 0 7 7 0 0 7 1 4 0 0 0 0 0 t 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0
3027_POL008.1_JASPAR_CORE_2009__rc_shift3 (3027_POL008.1_JASPAR_CORE_2009__rc)	0.858	0.429	0.193	-0.128	0.874	1.135	0.905	3	6	8	8	5	3	3	5.143	4	; oligos_6nt_mkv3 versus 3027_POL008.1_JASPAR_CORE_2009__rc; m=4/10; ncol2=6; w=6; offset=1; strand=R; shift=3; score= 5.1429; ---sGaAGc------ ; cor=0.858; Ncor=0.429; logoDP=0.193; NIcor=-0.128; NsEucl=0.874; SSD=1.135; NSW=0.905; rcor=3; rNcor=6; rlogoDP=8; rNIcor=8; rNsEucl=5; rSSD=3; rNSW=3; rank_mean=5.143; match_rank=4 a 0 0 0 25 6 72 85 5 25 0 0 0 0 0 0 c 0 0 0 27 7 20 8 6 46 0 0 0 0 0 0 g 0 0 0 34 93 12 12 93 19 0 0 0 0 0 0 t 0 0 0 22 2 4 3 4 18 0 0 0 0 0 0
6730_4b06_A_3D-footprint_20130124__rc_shift2 (6730_4b06_A_3D-footprint_20130124__rc)	0.856	0.428	1.961	0.016	0.870	1.208	0.899	5	8	7	7	8	4	4	6.143	5	; oligos_6nt_mkv3 versus 6730_4b06_A_3D-footprint_20130124__rc; m=5/10; ncol2=6; w=6; offset=0; strand=R; shift=2; score= 6.1429; --CGGAAG------- ; cor=0.856; Ncor=0.428; logoDP=1.961; NIcor=0.016; NsEucl=0.870; SSD=1.208; NSW=0.899; rcor=5; rNcor=8; rlogoDP=7; rNIcor=7; rNsEucl=8; rSSD=4; rNSW=4; rank_mean=6.143; match_rank=5 a 0 0 0 0 0 96 96 0 0 0 0 0 0 0 0 c 0 0 96 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 96 96 0 0 96 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6697_3rkq_B_3D-footprint_20130124__shift3 (6697_3rkq_B_3D-footprint_20130124_)	0.760	0.444	6.887	0.445	0.859	1.955	0.860	9	3	2	1	10	9	10	6.286	6	; oligos_6nt_mkv3 versus 6697_3rkq_B_3D-footprint_20130124_; m=6/10; ncol2=7; w=7; offset=1; strand=D; shift=3; score= 6.2857; ---TcaAGAG----- ; cor=0.760; Ncor=0.444; logoDP=6.887; NIcor=0.445; NsEucl=0.859; SSD=1.955; NSW=0.860; rcor=9; rNcor=3; rlogoDP=2; rNIcor=1; rNsEucl=10; rSSD=9; rNSW=10; rank_mean=6.286; match_rank=6 a 0 0 0 4 12 48 96 4 92 4 0 0 0 0 0 c 0 0 0 20 60 16 0 0 0 0 0 0 0 0 0 g 0 0 0 4 4 16 0 92 0 92 0 0 0 0 0 t 0 0 0 68 20 16 0 0 4 0 0 0 0 0 0
6749_4hn6_A_3D-footprint_20130124__rc_shift4 (6749_4hn6_A_3D-footprint_20130124__rc)	0.861	0.431	0.148	-0.136	0.863	1.342	0.888	2	5	9	9	9	5	6	6.429	7	; oligos_6nt_mkv3 versus 6749_4hn6_A_3D-footprint_20130124__rc; m=7/10; ncol2=6; w=6; offset=2; strand=R; shift=4; score= 6.4286; ----GnagAG----- ; cor=0.861; Ncor=0.431; logoDP=0.148; NIcor=-0.136; NsEucl=0.863; SSD=1.342; NSW=0.888; rcor=2; rNcor=5; rlogoDP=9; rNIcor=9; rNsEucl=9; rSSD=5; rNSW=6; rank_mean=6.429; match_rank=7 a 0 0 0 0 0 24 60 15 80 10 0 0 0 0 0 c 0 0 0 0 0 24 10 20 5 0 0 0 0 0 0 g 0 0 0 0 96 24 21 50 5 80 0 0 0 0 0 t 0 0 0 0 0 24 5 11 6 6 0 0 0 0 0
2554_MA0293.1_JASPAR_CORE_2009__shift6 (2554_MA0293.1_JASPAR_CORE_2009_)	0.774	0.413	4.982	0.387	0.879	1.865	0.883	8	9	6	5	4	8	8	6.857	8	; oligos_6nt_mkv3 versus 2554_MA0293.1_JASPAR_CORE_2009_; m=8/10; ncol2=11; w=8; offset=4; strand=D; shift=6; score= 6.8571; ------mmAGATCtw ; cor=0.774; Ncor=0.413; logoDP=4.982; NIcor=0.387; NsEucl=0.879; SSD=1.865; NSW=0.883; rcor=8; rNcor=9; rlogoDP=6; rNIcor=5; rNsEucl=4; rSSD=8; rNSW=8; rank_mean=6.857; match_rank=8 a 0 0 0 0 0 0 31 33 72 10 100 3 1 14 30 c 0 0 0 0 0 0 25 25 11 2 0 0 90 19 23 g 0 0 0 0 0 0 23 22 10 86 0 0 3 14 21 t 0 0 0 0 0 0 21 20 7 2 0 97 7 53 26
5048_ZmHOX2a_2__Athamap_20091028__rc_shift7 (5048_ZmHOX2a_2__Athamap_20091028__rc)	0.780	0.455	0.100	-0.141	0.871	1.623	0.884	7	2	10	10	7	6	7	7.000	9	; oligos_6nt_mkv3 versus 5048_ZmHOX2a_2__Athamap_20091028__rc; m=9/10; ncol2=7; w=7; offset=5; strand=R; shift=7; score= 7; -------cmGATCa- ; cor=0.780; Ncor=0.455; logoDP=0.100; NIcor=-0.141; NsEucl=0.871; SSD=1.623; NSW=0.884; rcor=7; rNcor=2; rlogoDP=10; rNIcor=10; rNsEucl=7; rSSD=6; rNSW=7; rank_mean=7.000; match_rank=9 a 0 0 0 0 0 0 0 6 16 0 27 0 0 15 0 c 0 0 0 0 0 0 0 14 7 0 0 0 27 5 0 g 0 0 0 0 0 0 0 4 4 27 0 0 0 2 0 t 0 0 0 0 0 0 0 3 0 0 0 27 0 5 0
2560_MA0302.1_JASPAR_CORE_2009__shift6 (2560_MA0302.1_JASPAR_CORE_2009_)	0.756	0.403	6.109	0.380	0.873	2.059	0.871	10	10	3	6	6	10	9	7.714	10	; oligos_6nt_mkv3 versus 2560_MA0302.1_JASPAR_CORE_2009_; m=10/10; ncol2=11; w=8; offset=4; strand=D; shift=6; score= 7.7143; ------ahAGATCya ; cor=0.756; Ncor=0.403; logoDP=6.109; NIcor=0.380; NsEucl=0.873; SSD=2.059; NSW=0.871; rcor=10; rNcor=10; rlogoDP=3; rNIcor=6; rNsEucl=6; rSSD=10; rNSW=9; rank_mean=7.714; match_rank=10 a 0 0 0 0 0 0 36 31 80 3 98 0 0 5 40 c 0 0 0 0 0 0 21 26 4 0 0 0 99 28 20 g 0 0 0 0 0 0 24 18 12 96 0 0 0 3 23 t 0 0 0 0 0 0 20 26 4 0 2 99 0 64 17