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/positions_8nt_m4/peak-motifs_positions_8nt_m4.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/positions_8nt_m4/peak-motifs_positions_8nt_m4_vs_db_footprintDB

One-to-n matrix alignment; reference matrix: positions_8nt_m4_shift5 ; 9 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
positions_8nt_m4_shift5 (positions_8nt_m4)
; positions_8nt_m4; m=0 (reference); ncol1=14; shift=5; ncol=19; -----sgAAGGGGGrGAya ; Alignment reference a 0 0 0 0 0 4 5 19 20 1 2 2 0 1 15 2 22 6 7 c 0 0 0 0 0 10 5 2 1 0 1 0 0 0 1 0 0 7 6 g 0 0 0 0 0 7 11 4 4 23 22 21 24 21 7 22 1 5 6 t 0 0 0 0 0 4 4 0 0 1 0 2 1 3 2 1 2 7 6

2529_MA0163.1_JASPAR_CORE_2009__shift0 (2529_MA0163.1_JASPAR_CORE_2009_) 0.884 0.419 4.896 0.422 0.925 0.910 0.949 1 8 3 5 1 1 1 2.857 1
; positions_8nt_m4 versus 2529_MA0163.1_JASPAR_CORE_2009_; m=1/8; ncol2=14; w=9; offset=-5; strand=D; shift=0; score= 2.8571; GGGGCCcwmGGGGG----- ; cor=0.884; Ncor=0.419; logoDP=4.896; NIcor=0.422; NsEucl=0.925; SSD=0.910; NSW=0.949; rcor=1; rNcor=8; rlogoDP=3; rNIcor=5; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.857; match_rank=1 a 0 3 0 0 0 0 4 12 11 2 0 0 0 2 0 0 0 0 0 c 0 0 0 0 14 15 10 0 5 0 0 0 0 0 0 0 0 0 0 g 18 14 18 17 4 1 1 0 2 14 18 18 16 16 0 0 0 0 0 t 0 1 0 1 0 2 3 6 0 2 0 0 2 0 0 0 0 0 0

2448_MA0057.1_JASPAR_CORE_2009__shift6 (2448_MA0057.1_JASPAR_CORE_2009_) 0.783 0.559 4.017 0.548 0.908 1.701 0.915 5 1 5 1 2 5 3 3.143 2
; positions_8nt_m4 versus 2448_MA0057.1_JASPAR_CORE_2009_; m=2/8; ncol2=10; w=10; offset=1; strand=D; shift=6; score= 3.1429; ------bkAKGGGkrr--- ; cor=0.783; Ncor=0.559; logoDP=4.017; NIcor=0.548; NsEucl=0.908; SSD=1.701; NSW=0.915; rcor=5; rNcor=1; rlogoDP=5; rNIcor=1; rNsEucl=2; rSSD=5; rNSW=3; rank_mean=3.143; match_rank=2 a 0 0 0 0 0 0 1 2 15 0 0 0 0 3 10 8 0 0 0 c 0 0 0 0 0 0 4 0 1 0 0 2 0 1 0 2 0 0 0 g 0 0 0 0 0 0 7 7 0 11 15 14 14 8 4 4 0 0 0 t 0 0 0 0 0 0 4 7 0 5 1 0 2 4 2 2 0 0 0

7511_MZF1_f1_HOCOMOCO_v9__shift10 (7511_MZF1_f1_HOCOMOCO_v9_) 0.796 0.455 5.176 0.430 0.890 1.538 0.904 3 4 1 4 5 3 4 3.429 3
; positions_8nt_m4 versus 7511_MZF1_f1_HOCOMOCO_v9_; m=3/8; ncol2=8; w=8; offset=5; strand=D; shift=10; score= 3.4286; ----------rkGGGGAw- ; cor=0.796; Ncor=0.455; logoDP=5.176; NIcor=0.430; NsEucl=0.890; SSD=1.538; NSW=0.904; rcor=3; rNcor=4; rlogoDP=1; rNIcor=4; rNsEucl=5; rSSD=3; rNSW=4; rank_mean=3.429; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 19 16 0 0 0 0 67 31 0 c 0 0 0 0 0 0 0 0 0 0 3 3 0 0 0 0 0 5 0 g 0 0 0 0 0 0 0 0 0 0 44 23 70 70 70 70 0 15 0 t 0 0 0 0 0 0 0 0 0 0 4 28 0 0 0 0 3 19 0

2562_MA0306.1_JASPAR_CORE_2009__rc_shift5 (2562_MA0306.1_JASPAR_CORE_2009__rc) 0.805 0.517 0.223 -0.161 0.906 1.431 0.921 2 2 8 6 3 2 2 3.571 4
; positions_8nt_m4 versus 2562_MA0306.1_JASPAR_CORE_2009__rc; m=4/8; ncol2=9; w=9; offset=0; strand=R; shift=5; score= 3.5714; -----wwwAGGGGw----- ; cor=0.805; Ncor=0.517; logoDP=0.223; NIcor=-0.161; NsEucl=0.906; SSD=1.431; NSW=0.921; rcor=2; rNcor=2; rlogoDP=8; rNIcor=6; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=3.571; match_rank=4 a 0 0 0 0 0 30 27 32 100 13 0 0 3 25 0 0 0 0 0 c 0 0 0 0 0 18 16 15 0 0 0 0 0 12 0 0 0 0 0 g 0 0 0 0 0 19 11 4 0 87 100 100 97 22 0 0 0 0 0 t 0 0 0 0 0 32 46 49 0 0 0 0 0 41 0 0 0 0 0

5131_YufM_DBTBS_1.0__shift8 (5131_YufM_DBTBS_1.0_) 0.792 0.453 4.969 0.432 0.890 1.553 0.903 4 5 2 3 6 4 5 4.143 5
; positions_8nt_m4 versus 5131_YufM_DBTBS_1.0_; m=5/8; ncol2=8; w=8; offset=3; strand=D; shift=8; score= 4.1429; --------ArGrGdws--- ; cor=0.792; Ncor=0.453; logoDP=4.969; NIcor=0.432; NsEucl=0.890; SSD=1.553; NSW=0.903; rcor=4; rNcor=5; rlogoDP=2; rNIcor=3; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=4.143; match_rank=5 a 0 0 0 0 0 0 0 0 3 1 0 2 0 1 2 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 g 0 0 0 0 0 0 0 0 0 2 3 1 3 1 0 2 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0

2642_MA0423.1_JASPAR_CORE_2009__rc_shift5 (2642_MA0423.1_JASPAR_CORE_2009__rc) 0.768 0.494 0.252 -0.179 0.894 1.826 0.899 6 3 7 8 4 6 6 5.714 6
; positions_8nt_m4 versus 2642_MA0423.1_JASPAR_CORE_2009__rc; m=6/8; ncol2=9; w=9; offset=0; strand=R; shift=5; score= 5.7143; -----dAwAGGGGk----- ; cor=0.768; Ncor=0.494; logoDP=0.252; NIcor=-0.179; NsEucl=0.894; SSD=1.826; NSW=0.899; rcor=6; rNcor=3; rlogoDP=7; rNIcor=8; rNsEucl=4; rSSD=6; rNSW=6; rank_mean=5.714; match_rank=6 a 0 0 0 0 0 34 75 32 100 0 0 9 2 13 0 0 0 0 0 c 0 0 0 0 0 5 4 8 0 0 0 0 1 23 0 0 0 0 0 g 0 0 0 0 0 28 0 0 0 100 100 91 97 28 0 0 0 0 0 t 0 0 0 0 0 32 21 60 0 0 0 0 0 35 0 0 0 0 0

7481_KLF8_f1_HOCOMOCO_v9__shift8 (7481_KLF8_f1_HOCOMOCO_v9_) 0.752 0.430 4.425 0.442 0.879 1.859 0.884 8 7 4 2 7 7 7 6.000 7
; positions_8nt_m4 versus 7481_KLF8_f1_HOCOMOCO_v9_; m=7/8; ncol2=8; w=8; offset=3; strand=D; shift=8; score= 6; --------mGkGkGTG--- ; cor=0.752; Ncor=0.430; logoDP=4.425; NIcor=0.442; NsEucl=0.879; SSD=1.859; NSW=0.884; rcor=8; rNcor=7; rlogoDP=4; rNIcor=2; rNsEucl=7; rSSD=7; rNSW=7; rank_mean=6.000; match_rank=7 a 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 2 0 0 0 0 0 1 1 0 0 0 g 0 0 0 0 0 0 0 0 0 4 3 5 3 5 0 4 0 0 0 t 0 0 0 0 0 0 0 0 0 1 2 0 2 0 4 0 0 0 0

2609_MA0372.1_JASPAR_CORE_2009__rc_shift6 (2609_MA0372.1_JASPAR_CORE_2009__rc) 0.756 0.432 0.363 -0.177 0.876 1.984 0.876 7 6 6 7 8 8 8 7.143 8
; positions_8nt_m4 versus 2609_MA0372.1_JASPAR_CORE_2009__rc; m=8/8; ncol2=8; w=8; offset=1; strand=R; shift=6; score= 7.1429; ------TwAGGGGt----- ; cor=0.756; Ncor=0.432; logoDP=0.363; NIcor=-0.177; NsEucl=0.876; SSD=1.984; NSW=0.876; rcor=7; rNcor=6; rlogoDP=6; rNIcor=7; rNsEucl=8; rSSD=8; rNSW=8; rank_mean=7.143; match_rank=8 a 0 0 0 0 0 0 13 28 100 0 0 0 0 19 0 0 0 0 0 c 0 0 0 0 0 0 7 7 0 0 0 0 0 14 0 0 0 0 0 g 0 0 0 0 0 0 7 1 0 100 100 100 100 14 0 0 0 0 0 t 0 0 0 0 0 0 74 63 0 0 0 0 0 53 0 0 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
positions_8nt_m4_shift5 (positions_8nt_m4)																	; positions_8nt_m4; m=0 (reference); ncol1=14; shift=5; ncol=19; -----sgAAGGGGGrGAya ; Alignment reference a 0 0 0 0 0 4 5 19 20 1 2 2 0 1 15 2 22 6 7 c 0 0 0 0 0 10 5 2 1 0 1 0 0 0 1 0 0 7 6 g 0 0 0 0 0 7 11 4 4 23 22 21 24 21 7 22 1 5 6 t 0 0 0 0 0 4 4 0 0 1 0 2 1 3 2 1 2 7 6
2529_MA0163.1_JASPAR_CORE_2009__shift0 (2529_MA0163.1_JASPAR_CORE_2009_)	0.884	0.419	4.896	0.422	0.925	0.910	0.949	1	8	3	5	1	1	1	2.857	1	; positions_8nt_m4 versus 2529_MA0163.1_JASPAR_CORE_2009_; m=1/8; ncol2=14; w=9; offset=-5; strand=D; shift=0; score= 2.8571; GGGGCCcwmGGGGG----- ; cor=0.884; Ncor=0.419; logoDP=4.896; NIcor=0.422; NsEucl=0.925; SSD=0.910; NSW=0.949; rcor=1; rNcor=8; rlogoDP=3; rNIcor=5; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.857; match_rank=1 a 0 3 0 0 0 0 4 12 11 2 0 0 0 2 0 0 0 0 0 c 0 0 0 0 14 15 10 0 5 0 0 0 0 0 0 0 0 0 0 g 18 14 18 17 4 1 1 0 2 14 18 18 16 16 0 0 0 0 0 t 0 1 0 1 0 2 3 6 0 2 0 0 2 0 0 0 0 0 0
2448_MA0057.1_JASPAR_CORE_2009__shift6 (2448_MA0057.1_JASPAR_CORE_2009_)	0.783	0.559	4.017	0.548	0.908	1.701	0.915	5	1	5	1	2	5	3	3.143	2	; positions_8nt_m4 versus 2448_MA0057.1_JASPAR_CORE_2009_; m=2/8; ncol2=10; w=10; offset=1; strand=D; shift=6; score= 3.1429; ------bkAKGGGkrr--- ; cor=0.783; Ncor=0.559; logoDP=4.017; NIcor=0.548; NsEucl=0.908; SSD=1.701; NSW=0.915; rcor=5; rNcor=1; rlogoDP=5; rNIcor=1; rNsEucl=2; rSSD=5; rNSW=3; rank_mean=3.143; match_rank=2 a 0 0 0 0 0 0 1 2 15 0 0 0 0 3 10 8 0 0 0 c 0 0 0 0 0 0 4 0 1 0 0 2 0 1 0 2 0 0 0 g 0 0 0 0 0 0 7 7 0 11 15 14 14 8 4 4 0 0 0 t 0 0 0 0 0 0 4 7 0 5 1 0 2 4 2 2 0 0 0
7511_MZF1_f1_HOCOMOCO_v9__shift10 (7511_MZF1_f1_HOCOMOCO_v9_)	0.796	0.455	5.176	0.430	0.890	1.538	0.904	3	4	1	4	5	3	4	3.429	3	; positions_8nt_m4 versus 7511_MZF1_f1_HOCOMOCO_v9_; m=3/8; ncol2=8; w=8; offset=5; strand=D; shift=10; score= 3.4286; ----------rkGGGGAw- ; cor=0.796; Ncor=0.455; logoDP=5.176; NIcor=0.430; NsEucl=0.890; SSD=1.538; NSW=0.904; rcor=3; rNcor=4; rlogoDP=1; rNIcor=4; rNsEucl=5; rSSD=3; rNSW=4; rank_mean=3.429; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 19 16 0 0 0 0 67 31 0 c 0 0 0 0 0 0 0 0 0 0 3 3 0 0 0 0 0 5 0 g 0 0 0 0 0 0 0 0 0 0 44 23 70 70 70 70 0 15 0 t 0 0 0 0 0 0 0 0 0 0 4 28 0 0 0 0 3 19 0
2562_MA0306.1_JASPAR_CORE_2009__rc_shift5 (2562_MA0306.1_JASPAR_CORE_2009__rc)	0.805	0.517	0.223	-0.161	0.906	1.431	0.921	2	2	8	6	3	2	2	3.571	4	; positions_8nt_m4 versus 2562_MA0306.1_JASPAR_CORE_2009__rc; m=4/8; ncol2=9; w=9; offset=0; strand=R; shift=5; score= 3.5714; -----wwwAGGGGw----- ; cor=0.805; Ncor=0.517; logoDP=0.223; NIcor=-0.161; NsEucl=0.906; SSD=1.431; NSW=0.921; rcor=2; rNcor=2; rlogoDP=8; rNIcor=6; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=3.571; match_rank=4 a 0 0 0 0 0 30 27 32 100 13 0 0 3 25 0 0 0 0 0 c 0 0 0 0 0 18 16 15 0 0 0 0 0 12 0 0 0 0 0 g 0 0 0 0 0 19 11 4 0 87 100 100 97 22 0 0 0 0 0 t 0 0 0 0 0 32 46 49 0 0 0 0 0 41 0 0 0 0 0
5131_YufM_DBTBS_1.0__shift8 (5131_YufM_DBTBS_1.0_)	0.792	0.453	4.969	0.432	0.890	1.553	0.903	4	5	2	3	6	4	5	4.143	5	; positions_8nt_m4 versus 5131_YufM_DBTBS_1.0_; m=5/8; ncol2=8; w=8; offset=3; strand=D; shift=8; score= 4.1429; --------ArGrGdws--- ; cor=0.792; Ncor=0.453; logoDP=4.969; NIcor=0.432; NsEucl=0.890; SSD=1.553; NSW=0.903; rcor=4; rNcor=5; rlogoDP=2; rNIcor=3; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=4.143; match_rank=5 a 0 0 0 0 0 0 0 0 3 1 0 2 0 1 2 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 g 0 0 0 0 0 0 0 0 0 2 3 1 3 1 0 2 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0
2642_MA0423.1_JASPAR_CORE_2009__rc_shift5 (2642_MA0423.1_JASPAR_CORE_2009__rc)	0.768	0.494	0.252	-0.179	0.894	1.826	0.899	6	3	7	8	4	6	6	5.714	6	; positions_8nt_m4 versus 2642_MA0423.1_JASPAR_CORE_2009__rc; m=6/8; ncol2=9; w=9; offset=0; strand=R; shift=5; score= 5.7143; -----dAwAGGGGk----- ; cor=0.768; Ncor=0.494; logoDP=0.252; NIcor=-0.179; NsEucl=0.894; SSD=1.826; NSW=0.899; rcor=6; rNcor=3; rlogoDP=7; rNIcor=8; rNsEucl=4; rSSD=6; rNSW=6; rank_mean=5.714; match_rank=6 a 0 0 0 0 0 34 75 32 100 0 0 9 2 13 0 0 0 0 0 c 0 0 0 0 0 5 4 8 0 0 0 0 1 23 0 0 0 0 0 g 0 0 0 0 0 28 0 0 0 100 100 91 97 28 0 0 0 0 0 t 0 0 0 0 0 32 21 60 0 0 0 0 0 35 0 0 0 0 0
7481_KLF8_f1_HOCOMOCO_v9__shift8 (7481_KLF8_f1_HOCOMOCO_v9_)	0.752	0.430	4.425	0.442	0.879	1.859	0.884	8	7	4	2	7	7	7	6.000	7	; positions_8nt_m4 versus 7481_KLF8_f1_HOCOMOCO_v9_; m=7/8; ncol2=8; w=8; offset=3; strand=D; shift=8; score= 6; --------mGkGkGTG--- ; cor=0.752; Ncor=0.430; logoDP=4.425; NIcor=0.442; NsEucl=0.879; SSD=1.859; NSW=0.884; rcor=8; rNcor=7; rlogoDP=4; rNIcor=2; rNsEucl=7; rSSD=7; rNSW=7; rank_mean=6.000; match_rank=7 a 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 2 0 0 0 0 0 1 1 0 0 0 g 0 0 0 0 0 0 0 0 0 4 3 5 3 5 0 4 0 0 0 t 0 0 0 0 0 0 0 0 0 1 2 0 2 0 4 0 0 0 0
2609_MA0372.1_JASPAR_CORE_2009__rc_shift6 (2609_MA0372.1_JASPAR_CORE_2009__rc)	0.756	0.432	0.363	-0.177	0.876	1.984	0.876	7	6	6	7	8	8	8	7.143	8	; positions_8nt_m4 versus 2609_MA0372.1_JASPAR_CORE_2009__rc; m=8/8; ncol2=8; w=8; offset=1; strand=R; shift=6; score= 7.1429; ------TwAGGGGt----- ; cor=0.756; Ncor=0.432; logoDP=0.363; NIcor=-0.177; NsEucl=0.876; SSD=1.984; NSW=0.876; rcor=7; rNcor=6; rlogoDP=6; rNIcor=7; rNsEucl=8; rSSD=8; rNSW=8; rank_mean=7.143; match_rank=8 a 0 0 0 0 0 0 13 28 100 0 0 0 0 19 0 0 0 0 0 c 0 0 0 0 0 0 7 7 0 0 0 0 0 14 0 0 0 0 0 g 0 0 0 0 0 0 7 1 0 100 100 100 100 14 0 0 0 0 0 t 0 0 0 0 0 0 74 63 0 0 0 0 0 53 0 0 0 0 0