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_7nt_m5/peak-motifs_positions_7nt_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/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_footprintDB

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift3 ; 7 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_7nt_m5_shift3 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=11; shift=3; ncol=15; ---wkCACTCCAsg- ; Alignment reference a 0 0 0 2 1 0 6 0 0 0 0 6 0 1 0 c 0 0 0 0 0 6 0 6 0 6 6 0 2 1 0 g 0 0 0 0 2 0 0 0 0 0 0 0 4 3 0 t 0 0 0 4 3 0 0 0 6 0 0 0 0 1 0

2858_PF0171.1_JASPAR_CORE_2009__shift7 (2858_PF0171.1_JASPAR_CORE_2009_) 0.926 0.432 8.320 0.414 0.921 0.612 0.956 1 3 2 3 1 2 2 2.000 1
; positions_7nt_m5 versus 2858_PF0171.1_JASPAR_CORE_2009_; m=1/6; ncol2=11; w=7; offset=4; strand=D; shift=7; score= 2; -------CTCCAsGT ; cor=0.926; Ncor=0.432; logoDP=8.320; NIcor=0.414; NsEucl=0.921; SSD=0.612; NSW=0.956; rcor=1; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 43 368 69 0 0 c 0 0 0 0 0 0 0 368 0 368 268 0 125 0 0 g 0 0 0 0 0 0 0 0 0 0 20 0 118 368 0 t 0 0 0 0 0 0 0 0 368 0 37 0 56 0 368

5958_1a0a_B_3D-footprint_20130124__shift9 (5958_1a0a_B_3D-footprint_20130124_) 0.924 0.420 5.834 0.422 0.911 0.393 0.961 2 4 4 2 2 1 1 2.286 2
; positions_7nt_m5 versus 5958_1a0a_B_3D-footprint_20130124_; m=2/6; ncol2=5; w=5; offset=6; strand=D; shift=9; score= 2.2857; ---------CCAcg- ; cor=0.924; Ncor=0.420; logoDP=5.834; NIcor=0.422; NsEucl=0.911; SSD=0.393; NSW=0.961; rcor=2; rNcor=4; rlogoDP=4; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=2.286; match_rank=2 a 0 0 0 0 0 0 0 0 0 0 0 96 13 16 0 c 0 0 0 0 0 0 0 0 0 96 96 0 57 13 0 g 0 0 0 0 0 0 0 0 0 0 0 0 13 54 0 t 0 0 0 0 0 0 0 0 0 0 0 0 13 13 0

5978_1am9_AB_3D-footprint_20130124__shift3 (5978_1am9_AB_3D-footprint_20130124_) 0.772 0.702 12.376 0.660 0.881 2.840 0.858 6 1 1 1 3 6 6 3.429 3
; positions_7nt_m5 versus 5978_1am9_AB_3D-footprint_20130124_; m=3/6; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 3.4286; ---aTCACCCCAC-- ; cor=0.772; Ncor=0.702; logoDP=12.376; NIcor=0.660; NsEucl=0.881; SSD=2.840; NSW=0.858; rcor=6; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=6; rNSW=6; rank_mean=3.429; match_rank=3 a 0 0 0 38 0 0 96 0 1 0 0 96 0 0 0 c 0 0 0 19 0 96 0 96 76 96 96 0 96 0 0 g 0 0 0 19 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 20 96 0 0 0 19 0 0 0 0 0 0

2512_MA0130.1_JASPAR_CORE_2009__shift7 (2512_MA0130.1_JASPAR_CORE_2009_) 0.800 0.437 6.779 0.396 0.856 1.496 0.875 5 2 3 4 6 3 5 4.000 4
; positions_7nt_m5 versus 2512_MA0130.1_JASPAR_CORE_2009_; m=4/6; ncol2=6; w=6; offset=4; strand=D; shift=7; score= 4; -------mTCCAC-- ; cor=0.800; Ncor=0.437; logoDP=6.779; NIcor=0.396; NsEucl=0.856; SSD=1.496; NSW=0.875; rcor=5; rNcor=2; rlogoDP=3; rNIcor=4; rNsEucl=6; rSSD=3; rNSW=5; rank_mean=4.000; match_rank=4 a 0 0 0 0 0 0 0 7 3 0 0 16 0 0 0 c 0 0 0 0 0 0 0 6 2 16 16 0 15 0 0 g 0 0 0 0 0 0 0 3 0 0 0 0 1 0 0 t 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0

7286_ZAT18_ArabidopsisPBM_20140210__rc_shift0 (7286_ZAT18_ArabidopsisPBM_20140210__rc) 0.803 0.401 3.249 0.357 0.876 1.505 0.893 4 6 5 5 4 4 3 4.429 5
; positions_7nt_m5 versus 7286_ZAT18_ArabidopsisPBM_20140210__rc; m=5/6; ncol2=10; w=7; offset=-3; strand=R; shift=0; score= 4.4286; yAGTGCACTh----- ; cor=0.803; Ncor=0.401; logoDP=3.249; NIcor=0.357; NsEucl=0.876; SSD=1.505; NSW=0.893; rcor=4; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=4; rNSW=3; rank_mean=4.429; match_rank=5 a 12 71 3 3 10 4 73 3 17 31 0 0 0 0 0 c 26 4 5 18 6 81 6 88 8 34 0 0 0 0 0 g 12 8 88 6 80 5 18 5 4 3 0 0 0 0 0 t 50 17 4 73 4 10 3 4 71 32 0 0 0 0 0

6200_1lo1_A_3D-footprint_20130124__rc_shift7 (6200_1lo1_A_3D-footprint_20130124__rc) 0.806 0.403 1.973 0.015 0.874 1.561 0.888 3 5 6 6 5 5 4 4.857 6
; positions_7nt_m5 versus 6200_1lo1_A_3D-footprint_20130124__rc; m=6/6; ncol2=10; w=7; offset=4; strand=R; shift=7; score= 4.8571; -------cTCnAGGT ; cor=0.806; Ncor=0.403; logoDP=1.973; NIcor=0.015; NsEucl=0.874; SSD=1.561; NSW=0.888; rcor=3; rNcor=5; rlogoDP=6; rNIcor=6; rNsEucl=5; rSSD=5; rNSW=4; rank_mean=4.857; match_rank=6 a 0 0 0 0 0 0 0 13 0 0 24 96 0 0 0 c 0 0 0 0 0 0 0 54 0 96 24 0 0 0 0 g 0 0 0 0 0 0 0 13 0 0 24 0 96 96 0 t 0 0 0 0 0 0 0 16 96 0 24 0 0 0 96

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m5_shift3 (positions_7nt_m5)																	; positions_7nt_m5; m=0 (reference); ncol1=11; shift=3; ncol=15; ---wkCACTCCAsg- ; Alignment reference a 0 0 0 2 1 0 6 0 0 0 0 6 0 1 0 c 0 0 0 0 0 6 0 6 0 6 6 0 2 1 0 g 0 0 0 0 2 0 0 0 0 0 0 0 4 3 0 t 0 0 0 4 3 0 0 0 6 0 0 0 0 1 0
2858_PF0171.1_JASPAR_CORE_2009__shift7 (2858_PF0171.1_JASPAR_CORE_2009_)	0.926	0.432	8.320	0.414	0.921	0.612	0.956	1	3	2	3	1	2	2	2.000	1	; positions_7nt_m5 versus 2858_PF0171.1_JASPAR_CORE_2009_; m=1/6; ncol2=11; w=7; offset=4; strand=D; shift=7; score= 2; -------CTCCAsGT ; cor=0.926; Ncor=0.432; logoDP=8.320; NIcor=0.414; NsEucl=0.921; SSD=0.612; NSW=0.956; rcor=1; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 43 368 69 0 0 c 0 0 0 0 0 0 0 368 0 368 268 0 125 0 0 g 0 0 0 0 0 0 0 0 0 0 20 0 118 368 0 t 0 0 0 0 0 0 0 0 368 0 37 0 56 0 368
5958_1a0a_B_3D-footprint_20130124__shift9 (5958_1a0a_B_3D-footprint_20130124_)	0.924	0.420	5.834	0.422	0.911	0.393	0.961	2	4	4	2	2	1	1	2.286	2	; positions_7nt_m5 versus 5958_1a0a_B_3D-footprint_20130124_; m=2/6; ncol2=5; w=5; offset=6; strand=D; shift=9; score= 2.2857; ---------CCAcg- ; cor=0.924; Ncor=0.420; logoDP=5.834; NIcor=0.422; NsEucl=0.911; SSD=0.393; NSW=0.961; rcor=2; rNcor=4; rlogoDP=4; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=2.286; match_rank=2 a 0 0 0 0 0 0 0 0 0 0 0 96 13 16 0 c 0 0 0 0 0 0 0 0 0 96 96 0 57 13 0 g 0 0 0 0 0 0 0 0 0 0 0 0 13 54 0 t 0 0 0 0 0 0 0 0 0 0 0 0 13 13 0
5978_1am9_AB_3D-footprint_20130124__shift3 (5978_1am9_AB_3D-footprint_20130124_)	0.772	0.702	12.376	0.660	0.881	2.840	0.858	6	1	1	1	3	6	6	3.429	3	; positions_7nt_m5 versus 5978_1am9_AB_3D-footprint_20130124_; m=3/6; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 3.4286; ---aTCACCCCAC-- ; cor=0.772; Ncor=0.702; logoDP=12.376; NIcor=0.660; NsEucl=0.881; SSD=2.840; NSW=0.858; rcor=6; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=6; rNSW=6; rank_mean=3.429; match_rank=3 a 0 0 0 38 0 0 96 0 1 0 0 96 0 0 0 c 0 0 0 19 0 96 0 96 76 96 96 0 96 0 0 g 0 0 0 19 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 20 96 0 0 0 19 0 0 0 0 0 0
2512_MA0130.1_JASPAR_CORE_2009__shift7 (2512_MA0130.1_JASPAR_CORE_2009_)	0.800	0.437	6.779	0.396	0.856	1.496	0.875	5	2	3	4	6	3	5	4.000	4	; positions_7nt_m5 versus 2512_MA0130.1_JASPAR_CORE_2009_; m=4/6; ncol2=6; w=6; offset=4; strand=D; shift=7; score= 4; -------mTCCAC-- ; cor=0.800; Ncor=0.437; logoDP=6.779; NIcor=0.396; NsEucl=0.856; SSD=1.496; NSW=0.875; rcor=5; rNcor=2; rlogoDP=3; rNIcor=4; rNsEucl=6; rSSD=3; rNSW=5; rank_mean=4.000; match_rank=4 a 0 0 0 0 0 0 0 7 3 0 0 16 0 0 0 c 0 0 0 0 0 0 0 6 2 16 16 0 15 0 0 g 0 0 0 0 0 0 0 3 0 0 0 0 1 0 0 t 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0
7286_ZAT18_ArabidopsisPBM_20140210__rc_shift0 (7286_ZAT18_ArabidopsisPBM_20140210__rc)	0.803	0.401	3.249	0.357	0.876	1.505	0.893	4	6	5	5	4	4	3	4.429	5	; positions_7nt_m5 versus 7286_ZAT18_ArabidopsisPBM_20140210__rc; m=5/6; ncol2=10; w=7; offset=-3; strand=R; shift=0; score= 4.4286; yAGTGCACTh----- ; cor=0.803; Ncor=0.401; logoDP=3.249; NIcor=0.357; NsEucl=0.876; SSD=1.505; NSW=0.893; rcor=4; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=4; rNSW=3; rank_mean=4.429; match_rank=5 a 12 71 3 3 10 4 73 3 17 31 0 0 0 0 0 c 26 4 5 18 6 81 6 88 8 34 0 0 0 0 0 g 12 8 88 6 80 5 18 5 4 3 0 0 0 0 0 t 50 17 4 73 4 10 3 4 71 32 0 0 0 0 0
6200_1lo1_A_3D-footprint_20130124__rc_shift7 (6200_1lo1_A_3D-footprint_20130124__rc)	0.806	0.403	1.973	0.015	0.874	1.561	0.888	3	5	6	6	5	5	4	4.857	6	; positions_7nt_m5 versus 6200_1lo1_A_3D-footprint_20130124__rc; m=6/6; ncol2=10; w=7; offset=4; strand=R; shift=7; score= 4.8571; -------cTCnAGGT ; cor=0.806; Ncor=0.403; logoDP=1.973; NIcor=0.015; NsEucl=0.874; SSD=1.561; NSW=0.888; rcor=3; rNcor=5; rlogoDP=6; rNIcor=6; rNsEucl=5; rSSD=5; rNSW=4; rank_mean=4.857; match_rank=6 a 0 0 0 0 0 0 0 13 0 0 24 96 0 0 0 c 0 0 0 0 0 0 0 54 0 96 24 0 0 0 0 g 0 0 0 0 0 0 0 13 0 0 24 0 96 96 0 t 0 0 0 0 0 0 0 16 96 0 24 0 0 0 96