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/dyads_m2/peak-motifs_dyads_m2.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/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 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
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=20; shift=0; ncol=24; wwwTTGAystagATCAAtww---- ; Alignment reference a 12 8 11 1 0 3 27 0 6 6 15 5 26 2 0 28 26 4 11 9 0 0 0 0 c 4 5 4 0 1 0 0 12 9 4 3 5 1 0 26 0 2 0 2 1 0 0 0 0 g 3 3 4 1 0 25 0 3 7 3 5 14 1 0 0 0 0 5 0 5 0 0 0 0 t 9 12 9 26 27 0 1 13 6 15 5 4 0 26 2 0 0 19 15 13 0 0 0 0

3061_FNR_RegulonDB_7.5__rc_shift3 (3061_FNR_RegulonDB_7.5__rc) 0.915 0.641 6.428 0.637 0.948 1.060 0.962 1 1 1 1 1 1 1 1.000 1
; dyads_m2 versus 3061_FNR_RegulonDB_7.5__rc; m=1/8; ncol2=14; w=14; offset=3; strand=R; shift=3; score= 1; ---TTGATrtwrAtCAa------- ; cor=0.915; Ncor=0.641; logoDP=6.428; NIcor=0.637; NsEucl=0.948; SSD=1.060; NSW=0.962; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1 a 0 0 0 2 2 6 79 6 29 12 29 35 57 14 2 64 48 0 0 0 0 0 0 0 c 0 0 0 0 0 5 0 11 11 11 16 3 13 8 58 6 10 0 0 0 0 0 0 0 g 0 0 0 8 1 72 0 0 23 12 10 28 3 14 10 8 8 0 0 0 0 0 0 0 t 0 0 0 73 80 0 4 66 20 48 28 17 10 47 13 5 17 0 0 0 0 0 0 0

1999_PB0144.1_JASPAR_CORE_2009__shift8 (1999_PB0144.1_JASPAR_CORE_2009_) 0.839 0.420 5.565 0.431 0.932 1.343 0.944 2 7 2 4 3 3 3 3.429 2
; dyads_m2 versus 1999_PB0144.1_JASPAR_CORE_2009_; m=2/8; ncol2=16; w=12; offset=8; strand=D; shift=8; score= 3.4286; --------swrsATCAATCrctww ; cor=0.839; Ncor=0.420; logoDP=5.565; NIcor=0.431; NsEucl=0.932; SSD=1.343; NSW=0.944; rcor=2; rNcor=7; rlogoDP=2; rNIcor=4; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.429; match_rank=2 a 0 0 0 0 0 0 0 0 23 44 42 17 81 4 2 94 93 3 11 68 24 9 33 34 c 0 0 0 0 0 0 0 0 27 8 14 34 2 1 90 1 1 2 71 2 35 24 18 16 g 0 0 0 0 0 0 0 0 39 23 32 39 1 1 4 1 4 5 1 28 19 20 11 19 t 0 0 0 0 0 0 0 0 11 25 12 10 16 94 4 4 2 91 17 3 23 46 38 32

2042_PB0188.1_JASPAR_CORE_2009__shift8 (2042_PB0188.1_JASPAR_CORE_2009_) 0.832 0.416 5.073 0.430 0.932 1.342 0.944 3 8 3 5 2 2 2 3.571 3
; dyads_m2 versus 2042_PB0188.1_JASPAR_CORE_2009_; m=3/8; ncol2=16; w=12; offset=8; strand=D; shift=8; score= 3.5714; --------sdrsWTCAATCrstww ; cor=0.832; Ncor=0.416; logoDP=5.073; NIcor=0.430; NsEucl=0.932; SSD=1.342; NSW=0.944; rcor=3; rNcor=8; rlogoDP=3; rNIcor=5; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=3.571; match_rank=3 a 0 0 0 0 0 0 0 0 22 34 40 24 70 5 2 93 93 3 12 59 14 12 36 33 c 0 0 0 0 0 0 0 0 30 5 16 26 3 2 85 1 1 2 69 2 38 18 20 17 g 0 0 0 0 0 0 0 0 37 34 35 39 1 1 6 1 3 5 1 36 27 24 11 20 t 0 0 0 0 0 0 0 0 12 27 10 10 26 92 7 5 2 90 18 4 21 46 33 30

1000_UP00185_UniPROBE_20120919__shift6 (1000_UP00185_UniPROBE_20120919_) 0.765 0.466 5.022 0.471 0.927 2.111 0.925 5 3 4 2 4 5 5 4.000 4
; dyads_m2 versus 1000_UP00185_UniPROBE_20120919_; m=4/8; ncol2=17; w=14; offset=6; strand=D; shift=6; score= 4; ------yyaymCATCAAwmwwmm- ; cor=0.765; Ncor=0.466; logoDP=5.022; NIcor=0.471; NsEucl=0.927; SSD=2.111; NSW=0.925; rcor=5; rNcor=3; rlogoDP=4; rNIcor=2; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=4.000; match_rank=4 a 0 0 0 0 0 0 21 6 59 12 37 11 86 3 3 93 74 31 32 39 36 26 37 0 c 0 0 0 0 0 0 28 50 4 40 39 73 2 1 95 3 6 5 32 14 13 29 35 0 g 0 0 0 0 0 0 15 15 14 9 11 9 7 1 1 2 3 6 15 9 15 24 21 0 t 0 0 0 0 0 0 36 29 23 39 13 7 5 95 1 2 17 58 21 38 36 21 7 0

7440_HNF6_f1_HOCOMOCO_v9__rc_shift7 (7440_HNF6_f1_HOCOMOCO_v9__rc) 0.805 0.524 0.878 -0.127 0.927 1.821 0.930 4 2 8 8 5 4 4 5.000 5
; dyads_m2 versus 7440_HNF6_f1_HOCOMOCO_v9__rc; m=5/8; ncol2=13; w=13; offset=7; strand=R; shift=7; score= 5; -------whwaARTCAATAw---- ; cor=0.805; Ncor=0.524; logoDP=0.878; NIcor=-0.127; NsEucl=0.927; SSD=1.821; NSW=0.930; rcor=4; rNcor=2; rlogoDP=8; rNIcor=8; rNsEucl=5; rSSD=4; rNSW=4; rank_mean=5.000; match_rank=5 a 0 0 0 0 0 0 0 9 9 11 16 19 17 0 0 20 24 0 17 13 0 0 0 0 c 0 0 0 0 0 0 0 3 7 2 0 2 0 1 24 3 0 0 1 0 0 0 0 0 g 0 0 0 0 0 0 0 5 2 3 3 1 7 0 0 1 0 0 4 4 0 0 0 0 t 0 0 0 0 0 0 0 7 6 8 5 2 0 23 0 0 0 24 2 7 0 0 0 0

2984_PH0134.1_JASPAR_CORE_2009__shift6 (2984_PH0134.1_JASPAR_CORE_2009_) 0.764 0.465 5.021 0.471 0.926 2.119 0.924 6 4 5 3 6 6 6 5.143 6
; dyads_m2 versus 2984_PH0134.1_JASPAR_CORE_2009_; m=6/8; ncol2=17; w=14; offset=6; strand=D; shift=6; score= 5.1429; ------yyaymCATCAAwmwwmm- ; cor=0.764; Ncor=0.465; logoDP=5.021; NIcor=0.471; NsEucl=0.926; SSD=2.119; NSW=0.924; rcor=6; rNcor=4; rlogoDP=5; rNIcor=3; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=5.143; match_rank=6 a 0 0 0 0 0 0 21 6 59 12 37 11 86 3 3 93 74 31 32 39 36 26 37 0 c 0 0 0 0 0 0 28 49 3 40 39 73 2 1 95 3 6 5 32 14 14 29 35 0 g 0 0 0 0 0 0 15 15 14 9 11 9 7 1 1 2 3 6 15 9 15 24 21 0 t 0 0 0 0 0 0 36 29 23 39 13 7 5 95 1 2 17 58 21 38 36 21 7 0

1924_PB0063.1_JASPAR_CORE_2009__shift7 (1924_PB0063.1_JASPAR_CORE_2009_) 0.750 0.424 4.768 0.416 0.921 2.123 0.918 8 6 7 6 7 7 7 6.857 7
; dyads_m2 versus 1924_PB0063.1_JASPAR_CORE_2009_; m=7/8; ncol2=16; w=13; offset=7; strand=D; shift=7; score= 6.8571; -------wtwrgAACAATwwwtw- ; cor=0.750; Ncor=0.424; logoDP=4.768; NIcor=0.416; NsEucl=0.921; SSD=2.123; NSW=0.918; rcor=8; rNcor=6; rlogoDP=7; rNIcor=6; rNsEucl=7; rSSD=7; rNSW=7; rank_mean=6.857; match_rank=7 a 0 0 0 0 0 0 0 27 19 37 50 13 83 96 2 94 95 4 47 42 36 21 30 0 c 0 0 0 0 0 0 0 12 24 14 11 9 2 1 90 1 1 3 2 9 10 20 16 0 g 0 0 0 0 0 0 0 17 18 16 28 62 13 1 1 1 3 1 8 12 18 12 7 0 t 0 0 0 0 0 0 0 44 40 33 11 16 3 2 7 4 1 93 44 38 36 47 46 0

3793_UP00096_UniPROBE_20120919__shift7 (3793_UP00096_UniPROBE_20120919_) 0.750 0.424 4.822 0.416 0.921 2.131 0.918 7 5 6 7 8 8 8 7.000 8
; dyads_m2 versus 3793_UP00096_UniPROBE_20120919_; m=8/8; ncol2=16; w=13; offset=7; strand=D; shift=7; score= 7; -------wtwrgAACAATwwwtw- ; cor=0.750; Ncor=0.424; logoDP=4.822; NIcor=0.416; NsEucl=0.921; SSD=2.131; NSW=0.918; rcor=7; rNcor=5; rlogoDP=6; rNIcor=7; rNsEucl=8; rSSD=8; rNSW=8; rank_mean=7.000; match_rank=8 a 0 0 0 0 0 0 0 27 18 37 50 13 83 96 2 94 95 3 47 42 36 21 30 0 c 0 0 0 0 0 0 0 12 24 14 11 9 1 1 90 1 1 3 2 9 10 20 17 0 g 0 0 0 0 0 0 0 17 18 16 28 62 13 1 1 1 3 1 7 12 18 12 7 0 t 0 0 0 0 0 0 0 44 40 33 11 16 3 2 7 4 1 93 44 37 36 47 46 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m2_shift0 (dyads_m2)																	; dyads_m2; m=0 (reference); ncol1=20; shift=0; ncol=24; wwwTTGAystagATCAAtww---- ; Alignment reference a 12 8 11 1 0 3 27 0 6 6 15 5 26 2 0 28 26 4 11 9 0 0 0 0 c 4 5 4 0 1 0 0 12 9 4 3 5 1 0 26 0 2 0 2 1 0 0 0 0 g 3 3 4 1 0 25 0 3 7 3 5 14 1 0 0 0 0 5 0 5 0 0 0 0 t 9 12 9 26 27 0 1 13 6 15 5 4 0 26 2 0 0 19 15 13 0 0 0 0
3061_FNR_RegulonDB_7.5__rc_shift3 (3061_FNR_RegulonDB_7.5__rc)	0.915	0.641	6.428	0.637	0.948	1.060	0.962	1	1	1	1	1	1	1	1.000	1	; dyads_m2 versus 3061_FNR_RegulonDB_7.5__rc; m=1/8; ncol2=14; w=14; offset=3; strand=R; shift=3; score= 1; ---TTGATrtwrAtCAa------- ; cor=0.915; Ncor=0.641; logoDP=6.428; NIcor=0.637; NsEucl=0.948; SSD=1.060; NSW=0.962; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1 a 0 0 0 2 2 6 79 6 29 12 29 35 57 14 2 64 48 0 0 0 0 0 0 0 c 0 0 0 0 0 5 0 11 11 11 16 3 13 8 58 6 10 0 0 0 0 0 0 0 g 0 0 0 8 1 72 0 0 23 12 10 28 3 14 10 8 8 0 0 0 0 0 0 0 t 0 0 0 73 80 0 4 66 20 48 28 17 10 47 13 5 17 0 0 0 0 0 0 0
1999_PB0144.1_JASPAR_CORE_2009__shift8 (1999_PB0144.1_JASPAR_CORE_2009_)	0.839	0.420	5.565	0.431	0.932	1.343	0.944	2	7	2	4	3	3	3	3.429	2	; dyads_m2 versus 1999_PB0144.1_JASPAR_CORE_2009_; m=2/8; ncol2=16; w=12; offset=8; strand=D; shift=8; score= 3.4286; --------swrsATCAATCrctww ; cor=0.839; Ncor=0.420; logoDP=5.565; NIcor=0.431; NsEucl=0.932; SSD=1.343; NSW=0.944; rcor=2; rNcor=7; rlogoDP=2; rNIcor=4; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.429; match_rank=2 a 0 0 0 0 0 0 0 0 23 44 42 17 81 4 2 94 93 3 11 68 24 9 33 34 c 0 0 0 0 0 0 0 0 27 8 14 34 2 1 90 1 1 2 71 2 35 24 18 16 g 0 0 0 0 0 0 0 0 39 23 32 39 1 1 4 1 4 5 1 28 19 20 11 19 t 0 0 0 0 0 0 0 0 11 25 12 10 16 94 4 4 2 91 17 3 23 46 38 32
2042_PB0188.1_JASPAR_CORE_2009__shift8 (2042_PB0188.1_JASPAR_CORE_2009_)	0.832	0.416	5.073	0.430	0.932	1.342	0.944	3	8	3	5	2	2	2	3.571	3	; dyads_m2 versus 2042_PB0188.1_JASPAR_CORE_2009_; m=3/8; ncol2=16; w=12; offset=8; strand=D; shift=8; score= 3.5714; --------sdrsWTCAATCrstww ; cor=0.832; Ncor=0.416; logoDP=5.073; NIcor=0.430; NsEucl=0.932; SSD=1.342; NSW=0.944; rcor=3; rNcor=8; rlogoDP=3; rNIcor=5; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=3.571; match_rank=3 a 0 0 0 0 0 0 0 0 22 34 40 24 70 5 2 93 93 3 12 59 14 12 36 33 c 0 0 0 0 0 0 0 0 30 5 16 26 3 2 85 1 1 2 69 2 38 18 20 17 g 0 0 0 0 0 0 0 0 37 34 35 39 1 1 6 1 3 5 1 36 27 24 11 20 t 0 0 0 0 0 0 0 0 12 27 10 10 26 92 7 5 2 90 18 4 21 46 33 30
1000_UP00185_UniPROBE_20120919__shift6 (1000_UP00185_UniPROBE_20120919_)	0.765	0.466	5.022	0.471	0.927	2.111	0.925	5	3	4	2	4	5	5	4.000	4	; dyads_m2 versus 1000_UP00185_UniPROBE_20120919_; m=4/8; ncol2=17; w=14; offset=6; strand=D; shift=6; score= 4; ------yyaymCATCAAwmwwmm- ; cor=0.765; Ncor=0.466; logoDP=5.022; NIcor=0.471; NsEucl=0.927; SSD=2.111; NSW=0.925; rcor=5; rNcor=3; rlogoDP=4; rNIcor=2; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=4.000; match_rank=4 a 0 0 0 0 0 0 21 6 59 12 37 11 86 3 3 93 74 31 32 39 36 26 37 0 c 0 0 0 0 0 0 28 50 4 40 39 73 2 1 95 3 6 5 32 14 13 29 35 0 g 0 0 0 0 0 0 15 15 14 9 11 9 7 1 1 2 3 6 15 9 15 24 21 0 t 0 0 0 0 0 0 36 29 23 39 13 7 5 95 1 2 17 58 21 38 36 21 7 0
7440_HNF6_f1_HOCOMOCO_v9__rc_shift7 (7440_HNF6_f1_HOCOMOCO_v9__rc)	0.805	0.524	0.878	-0.127	0.927	1.821	0.930	4	2	8	8	5	4	4	5.000	5	; dyads_m2 versus 7440_HNF6_f1_HOCOMOCO_v9__rc; m=5/8; ncol2=13; w=13; offset=7; strand=R; shift=7; score= 5; -------whwaARTCAATAw---- ; cor=0.805; Ncor=0.524; logoDP=0.878; NIcor=-0.127; NsEucl=0.927; SSD=1.821; NSW=0.930; rcor=4; rNcor=2; rlogoDP=8; rNIcor=8; rNsEucl=5; rSSD=4; rNSW=4; rank_mean=5.000; match_rank=5 a 0 0 0 0 0 0 0 9 9 11 16 19 17 0 0 20 24 0 17 13 0 0 0 0 c 0 0 0 0 0 0 0 3 7 2 0 2 0 1 24 3 0 0 1 0 0 0 0 0 g 0 0 0 0 0 0 0 5 2 3 3 1 7 0 0 1 0 0 4 4 0 0 0 0 t 0 0 0 0 0 0 0 7 6 8 5 2 0 23 0 0 0 24 2 7 0 0 0 0
2984_PH0134.1_JASPAR_CORE_2009__shift6 (2984_PH0134.1_JASPAR_CORE_2009_)	0.764	0.465	5.021	0.471	0.926	2.119	0.924	6	4	5	3	6	6	6	5.143	6	; dyads_m2 versus 2984_PH0134.1_JASPAR_CORE_2009_; m=6/8; ncol2=17; w=14; offset=6; strand=D; shift=6; score= 5.1429; ------yyaymCATCAAwmwwmm- ; cor=0.764; Ncor=0.465; logoDP=5.021; NIcor=0.471; NsEucl=0.926; SSD=2.119; NSW=0.924; rcor=6; rNcor=4; rlogoDP=5; rNIcor=3; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=5.143; match_rank=6 a 0 0 0 0 0 0 21 6 59 12 37 11 86 3 3 93 74 31 32 39 36 26 37 0 c 0 0 0 0 0 0 28 49 3 40 39 73 2 1 95 3 6 5 32 14 14 29 35 0 g 0 0 0 0 0 0 15 15 14 9 11 9 7 1 1 2 3 6 15 9 15 24 21 0 t 0 0 0 0 0 0 36 29 23 39 13 7 5 95 1 2 17 58 21 38 36 21 7 0
1924_PB0063.1_JASPAR_CORE_2009__shift7 (1924_PB0063.1_JASPAR_CORE_2009_)	0.750	0.424	4.768	0.416	0.921	2.123	0.918	8	6	7	6	7	7	7	6.857	7	; dyads_m2 versus 1924_PB0063.1_JASPAR_CORE_2009_; m=7/8; ncol2=16; w=13; offset=7; strand=D; shift=7; score= 6.8571; -------wtwrgAACAATwwwtw- ; cor=0.750; Ncor=0.424; logoDP=4.768; NIcor=0.416; NsEucl=0.921; SSD=2.123; NSW=0.918; rcor=8; rNcor=6; rlogoDP=7; rNIcor=6; rNsEucl=7; rSSD=7; rNSW=7; rank_mean=6.857; match_rank=7 a 0 0 0 0 0 0 0 27 19 37 50 13 83 96 2 94 95 4 47 42 36 21 30 0 c 0 0 0 0 0 0 0 12 24 14 11 9 2 1 90 1 1 3 2 9 10 20 16 0 g 0 0 0 0 0 0 0 17 18 16 28 62 13 1 1 1 3 1 8 12 18 12 7 0 t 0 0 0 0 0 0 0 44 40 33 11 16 3 2 7 4 1 93 44 38 36 47 46 0
3793_UP00096_UniPROBE_20120919__shift7 (3793_UP00096_UniPROBE_20120919_)	0.750	0.424	4.822	0.416	0.921	2.131	0.918	7	5	6	7	8	8	8	7.000	8	; dyads_m2 versus 3793_UP00096_UniPROBE_20120919_; m=8/8; ncol2=16; w=13; offset=7; strand=D; shift=7; score= 7; -------wtwrgAACAATwwwtw- ; cor=0.750; Ncor=0.424; logoDP=4.822; NIcor=0.416; NsEucl=0.921; SSD=2.131; NSW=0.918; rcor=7; rNcor=5; rlogoDP=6; rNIcor=7; rNsEucl=8; rSSD=8; rNSW=8; rank_mean=7.000; match_rank=8 a 0 0 0 0 0 0 0 27 18 37 50 13 83 96 2 94 95 3 47 42 36 21 30 0 c 0 0 0 0 0 0 0 12 24 14 11 9 1 1 90 1 1 3 2 9 10 20 17 0 g 0 0 0 0 0 0 0 17 18 16 28 62 13 1 1 1 3 1 7 12 18 12 7 0 t 0 0 0 0 0 0 0 44 40 33 11 16 3 2 7 4 1 93 44 37 36 47 46 0