One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 E2F/regulonE2F.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.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 E2F/regulonE2F.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift0 ; 6 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_test_vs_ctrl_m1_shift0 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; kykTGGCGGGAArag ; Alignment reference a 10 6 7 3 1 2 1 0 2 0 42 35 11 20 7 c 7 11 2 3 2 2 42 2 3 3 1 0 0 7 8 g 14 6 12 4 41 40 1 40 39 41 1 6 28 10 23 t 13 21 23 34 0 0 0 2 0 0 0 3 5 7 6

1437_M01839_TRANSFAC_2012.1__shift3 (1437_M01839_TRANSFAC_2012.1_) 0.987 0.461 7.416 0.461 0.965 0.118 0.992 1 43 2 10 1 1 1 8.429 1
; dyads_test_vs_ctrl_m1 versus 1437_M01839_TRANSFAC_2012.1_; m=1/5; ncol2=7; w=7; offset=3; strand=D; shift=3; score= 8.4286; ---WGGCGGG----- ; cor=0.987; Ncor=0.461; logoDP=7.416; NIcor=0.461; NsEucl=0.965; SSD=0.118; NSW=0.992; rcor=1; rNcor=43; rlogoDP=2; rNIcor=10; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=8.429; match_rank=1 a 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 7 0 1 1 0 0 0 0 0 g 0 0 0 0 7 7 0 7 6 6 0 0 0 0 0 t 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0

5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc_shift1 (5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc) 0.927 0.680 1.454 -0.088 0.944 0.771 0.965 4 1 33 38 2 5 2 12.143 3
; dyads_test_vs_ctrl_m1 versus 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc; m=2/5; ncol2=11; w=11; offset=1; strand=R; shift=1; score=12.1429; -wwkgGCGGGAA--- ; cor=0.927; Ncor=0.680; logoDP=1.454; NIcor=-0.088; NsEucl=0.944; SSD=0.771; NSW=0.965; rcor=4; rNcor=1; rlogoDP=33; rNIcor=38; rNsEucl=2; rSSD=5; rNSW=2; rank_mean=12.143; match_rank=3 a 0 2 2 0 1 0 0 0 0 0 4 4 0 0 0 c 0 0 0 0 1 0 5 0 1 0 0 0 0 0 0 g 0 0 0 2 3 5 0 5 4 5 0 0 0 0 0 t 0 3 3 3 0 0 0 0 0 0 1 1 0 0 0

5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028__rc_shift5 (5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028__rc) 0.931 0.497 0.452 -0.177 0.923 0.752 0.953 2 35 43 52 8 4 7 21.571 13
; dyads_test_vs_ctrl_m1 versus 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028__rc; m=3/5; ncol2=8; w=8; offset=5; strand=R; shift=5; score=21.5714; -----GCGGGAAw-- ; cor=0.931; Ncor=0.497; logoDP=0.452; NIcor=-0.177; NsEucl=0.923; SSD=0.752; NSW=0.953; rcor=2; rNcor=35; rlogoDP=43; rNIcor=52; rNsEucl=8; rSSD=4; rNSW=7; rank_mean=21.571; match_rank=13 a 0 0 0 0 0 0 0 0 0 0 3 3 2 0 0 c 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 g 0 0 0 0 0 3 0 3 3 3 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0

5015_E2Fb_Athamap_20091028__rc_shift5 (5015_E2Fb_Athamap_20091028__rc) 0.928 0.495 0.450 -0.176 0.921 0.799 0.950 3 36 44 51 9 6 8 22.429 18
; dyads_test_vs_ctrl_m1 versus 5015_E2Fb_Athamap_20091028__rc; m=4/5; ncol2=8; w=8; offset=5; strand=R; shift=5; score=22.4286; -----GCGGGAAW-- ; cor=0.928; Ncor=0.495; logoDP=0.450; NIcor=-0.176; NsEucl=0.921; SSD=0.799; NSW=0.950; rcor=3; rNcor=36; rlogoDP=44; rNIcor=51; rNsEucl=9; rSSD=6; rNSW=8; rank_mean=22.429; match_rank=18 a 0 0 0 0 0 0 0 0 0 0 4 4 3 0 0 c 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 g 0 0 0 0 0 4 0 4 4 4 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0

802_M01114_TRANSFAC_2012.1__rc_shift4 (802_M01114_TRANSFAC_2012.1__rc) 0.834 0.612 0.869 -0.122 0.918 1.636 0.926 17 5 37 44 10 30 19 23.143 20
; dyads_test_vs_ctrl_m1 versus 802_M01114_TRANSFAC_2012.1__rc; m=5/5; ncol2=11; w=11; offset=4; strand=R; shift=4; score=23.1429; ----ssCGsSAAArr ; cor=0.834; Ncor=0.612; logoDP=0.869; NIcor=-0.122; NsEucl=0.918; SSD=1.636; NSW=0.926; rcor=17; rNcor=5; rlogoDP=37; rNIcor=44; rNsEucl=10; rSSD=30; rNSW=19; rank_mean=23.143; match_rank=20 a 0 0 0 0 3 0 0 0 0 0 15 15 13 6 7 c 0 0 0 0 4 5 15 0 5 4 0 0 0 3 1 g 0 0 0 0 8 10 0 15 10 11 0 0 0 4 4 t 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m1_shift0 (dyads_test_vs_ctrl_m1)																	; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; kykTGGCGGGAArag ; Alignment reference a 10 6 7 3 1 2 1 0 2 0 42 35 11 20 7 c 7 11 2 3 2 2 42 2 3 3 1 0 0 7 8 g 14 6 12 4 41 40 1 40 39 41 1 6 28 10 23 t 13 21 23 34 0 0 0 2 0 0 0 3 5 7 6
1437_M01839_TRANSFAC_2012.1__shift3 (1437_M01839_TRANSFAC_2012.1_)	0.987	0.461	7.416	0.461	0.965	0.118	0.992	1	43	2	10	1	1	1	8.429	1	; dyads_test_vs_ctrl_m1 versus 1437_M01839_TRANSFAC_2012.1_; m=1/5; ncol2=7; w=7; offset=3; strand=D; shift=3; score= 8.4286; ---WGGCGGG----- ; cor=0.987; Ncor=0.461; logoDP=7.416; NIcor=0.461; NsEucl=0.965; SSD=0.118; NSW=0.992; rcor=1; rNcor=43; rlogoDP=2; rNIcor=10; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=8.429; match_rank=1 a 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 7 0 1 1 0 0 0 0 0 g 0 0 0 0 7 7 0 7 6 6 0 0 0 0 0 t 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0
5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc_shift1 (5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc)	0.927	0.680	1.454	-0.088	0.944	0.771	0.965	4	1	33	38	2	5	2	12.143	3	; dyads_test_vs_ctrl_m1 versus 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc; m=2/5; ncol2=11; w=11; offset=1; strand=R; shift=1; score=12.1429; -wwkgGCGGGAA--- ; cor=0.927; Ncor=0.680; logoDP=1.454; NIcor=-0.088; NsEucl=0.944; SSD=0.771; NSW=0.965; rcor=4; rNcor=1; rlogoDP=33; rNIcor=38; rNsEucl=2; rSSD=5; rNSW=2; rank_mean=12.143; match_rank=3 a 0 2 2 0 1 0 0 0 0 0 4 4 0 0 0 c 0 0 0 0 1 0 5 0 1 0 0 0 0 0 0 g 0 0 0 2 3 5 0 5 4 5 0 0 0 0 0 t 0 3 3 3 0 0 0 0 0 0 1 1 0 0 0
5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028__rc_shift5 (5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028__rc)	0.931	0.497	0.452	-0.177	0.923	0.752	0.953	2	35	43	52	8	4	7	21.571	13	; dyads_test_vs_ctrl_m1 versus 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028__rc; m=3/5; ncol2=8; w=8; offset=5; strand=R; shift=5; score=21.5714; -----GCGGGAAw-- ; cor=0.931; Ncor=0.497; logoDP=0.452; NIcor=-0.177; NsEucl=0.923; SSD=0.752; NSW=0.953; rcor=2; rNcor=35; rlogoDP=43; rNIcor=52; rNsEucl=8; rSSD=4; rNSW=7; rank_mean=21.571; match_rank=13 a 0 0 0 0 0 0 0 0 0 0 3 3 2 0 0 c 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 g 0 0 0 0 0 3 0 3 3 3 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
5015_E2Fb_Athamap_20091028__rc_shift5 (5015_E2Fb_Athamap_20091028__rc)	0.928	0.495	0.450	-0.176	0.921	0.799	0.950	3	36	44	51	9	6	8	22.429	18	; dyads_test_vs_ctrl_m1 versus 5015_E2Fb_Athamap_20091028__rc; m=4/5; ncol2=8; w=8; offset=5; strand=R; shift=5; score=22.4286; -----GCGGGAAW-- ; cor=0.928; Ncor=0.495; logoDP=0.450; NIcor=-0.176; NsEucl=0.921; SSD=0.799; NSW=0.950; rcor=3; rNcor=36; rlogoDP=44; rNIcor=51; rNsEucl=9; rSSD=6; rNSW=8; rank_mean=22.429; match_rank=18 a 0 0 0 0 0 0 0 0 0 0 4 4 3 0 0 c 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 g 0 0 0 0 0 4 0 4 4 4 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
802_M01114_TRANSFAC_2012.1__rc_shift4 (802_M01114_TRANSFAC_2012.1__rc)	0.834	0.612	0.869	-0.122	0.918	1.636	0.926	17	5	37	44	10	30	19	23.143	20	; dyads_test_vs_ctrl_m1 versus 802_M01114_TRANSFAC_2012.1__rc; m=5/5; ncol2=11; w=11; offset=4; strand=R; shift=4; score=23.1429; ----ssCGsSAAArr ; cor=0.834; Ncor=0.612; logoDP=0.869; NIcor=-0.122; NsEucl=0.918; SSD=1.636; NSW=0.926; rcor=17; rNcor=5; rlogoDP=37; rNIcor=44; rNsEucl=10; rSSD=30; rNSW=19; rank_mean=23.143; match_rank=20 a 0 0 0 0 3 0 0 0 0 0 15 15 13 6 7 c 0 0 0 0 4 5 15 0 5 4 0 0 0 3 1 g 0 0 0 0 8 10 0 15 10 11 0 0 0 4 4 t 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m5_shift0 ; 3 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_5-7nt_m5_shift0 (oligos_5-7nt_m5)
; oligos_5-7nt_m5; m=0 (reference); ncol1=20; shift=0; ncol=20; chctTCCCGCCAmawcbcyc ; Alignment reference a 3 8 4 3 0 0 0 2 0 0 0 24 18 18 7 3 3 5 3 2 c 14 7 15 5 0 26 23 25 0 27 26 3 7 3 6 15 10 15 13 17 g 6 3 3 2 0 1 2 0 26 0 1 0 0 4 3 6 7 1 3 3 t 4 9 5 17 27 0 2 0 1 0 0 0 2 2 11 3 7 6 8 5

5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__shift3 (5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_) 0.922 0.507 9.355 0.508 0.940 0.885 0.960 7 32 1 7 5 10 5 9.571 2
; oligos_5-7nt_m5 versus 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_; m=1/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 9.5714; ---TTCCCGCcmww------ ; cor=0.922; Ncor=0.507; logoDP=9.355; NIcor=0.508; NsEucl=0.940; SSD=0.885; NSW=0.960; rcor=7; rNcor=32; rlogoDP=1; rNIcor=7; rNsEucl=5; rSSD=10; rNSW=5; rank_mean=9.571; match_rank=2 a 0 0 0 1 1 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 c 0 0 0 0 0 5 4 5 0 5 3 2 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 0 0 0 0 0 t 0 0 0 4 4 0 0 0 0 0 1 0 2 2 0 0 0 0 0 0

802_M01114_TRANSFAC_2012.1__shift0 (802_M01114_TRANSFAC_2012.1_) 0.804 0.442 7.380 0.426 0.911 1.937 0.912 26 45 3 15 19 43 30 25.857 27
; oligos_5-7nt_m5 versus 802_M01114_TRANSFAC_2012.1_; m=2/2; ncol2=11; w=11; offset=0; strand=D; shift=0; score=25.8571; yyTTTSsCGss--------- ; cor=0.804; Ncor=0.442; logoDP=7.380; NIcor=0.426; NsEucl=0.911; SSD=1.937; NSW=0.912; rcor=26; rNcor=45; rlogoDP=3; rNIcor=15; rNsEucl=19; rSSD=43; rNSW=30; rank_mean=25.857; match_rank=27 a 3 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 4 4 0 0 0 11 10 15 0 10 8 0 0 0 0 0 0 0 0 0 g 1 3 0 0 0 4 5 0 15 5 4 0 0 0 0 0 0 0 0 0 t 7 6 13 15 15 0 0 0 0 0 3 0 0 0 0 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
oligos_5-7nt_m5_shift0 (oligos_5-7nt_m5)																	; oligos_5-7nt_m5; m=0 (reference); ncol1=20; shift=0; ncol=20; chctTCCCGCCAmawcbcyc ; Alignment reference a 3 8 4 3 0 0 0 2 0 0 0 24 18 18 7 3 3 5 3 2 c 14 7 15 5 0 26 23 25 0 27 26 3 7 3 6 15 10 15 13 17 g 6 3 3 2 0 1 2 0 26 0 1 0 0 4 3 6 7 1 3 3 t 4 9 5 17 27 0 2 0 1 0 0 0 2 2 11 3 7 6 8 5
5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__shift3 (5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_)	0.922	0.507	9.355	0.508	0.940	0.885	0.960	7	32	1	7	5	10	5	9.571	2	; oligos_5-7nt_m5 versus 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_; m=1/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 9.5714; ---TTCCCGCcmww------ ; cor=0.922; Ncor=0.507; logoDP=9.355; NIcor=0.508; NsEucl=0.940; SSD=0.885; NSW=0.960; rcor=7; rNcor=32; rlogoDP=1; rNIcor=7; rNsEucl=5; rSSD=10; rNSW=5; rank_mean=9.571; match_rank=2 a 0 0 0 1 1 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 c 0 0 0 0 0 5 4 5 0 5 3 2 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 0 0 0 0 0 t 0 0 0 4 4 0 0 0 0 0 1 0 2 2 0 0 0 0 0 0
802_M01114_TRANSFAC_2012.1__shift0 (802_M01114_TRANSFAC_2012.1_)	0.804	0.442	7.380	0.426	0.911	1.937	0.912	26	45	3	15	19	43	30	25.857	27	; oligos_5-7nt_m5 versus 802_M01114_TRANSFAC_2012.1_; m=2/2; ncol2=11; w=11; offset=0; strand=D; shift=0; score=25.8571; yyTTTSsCGss--------- ; cor=0.804; Ncor=0.442; logoDP=7.380; NIcor=0.426; NsEucl=0.911; SSD=1.937; NSW=0.912; rcor=26; rNcor=45; rlogoDP=3; rNIcor=15; rNsEucl=19; rSSD=43; rNSW=30; rank_mean=25.857; match_rank=27 a 3 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 4 4 0 0 0 11 10 15 0 10 8 0 0 0 0 0 0 0 0 0 g 1 3 0 0 0 4 5 0 15 5 4 0 0 0 0 0 0 0 0 0 t 7 6 13 15 15 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m4_shift0 ; 10 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_5-7nt_m4_shift0 (oligos_5-7nt_m4)
; oligos_5-7nt_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; rgATGGGCCCATsy ; Alignment reference a 6 3 12 2 0 0 1 0 0 2 13 3 2 3 c 3 4 1 3 3 0 0 15 17 12 0 1 7 5 g 5 8 1 0 12 17 16 1 0 3 2 1 5 3 t 3 2 3 12 2 0 0 1 0 0 2 12 3 6

11811_TCP2_M1648_1.02_CISBP_1.02__rc_shift2 (11811_TCP2_M1648_1.02_CISBP_1.02__rc) 0.813 0.581 4.560 0.578 0.913 1.519 0.924 21 10 12 1 15 25 21 15.000 4
; oligos_5-7nt_m4 versus 11811_TCP2_M1648_1.02_CISBP_1.02__rc; m=1/9; ncol2=10; w=10; offset=2; strand=R; shift=2; score= 15; --gtGGkmCCac-- ; cor=0.813; Ncor=0.581; logoDP=4.560; NIcor=0.578; NsEucl=0.913; SSD=1.519; NSW=0.924; rcor=21; rNcor=10; rlogoDP=12; rNIcor=1; rNsEucl=15; rSSD=25; rNSW=21; rank_mean=15.000; match_rank=4 a 0 0 22 9 4 0 7 33 2 12 57 18 0 0 c 0 0 16 20 0 0 8 52 98 84 15 43 0 0 g 0 0 43 15 84 98 52 8 0 0 19 17 0 0 t 0 0 19 56 12 2 33 7 0 4 9 22 0 0

11280_LOC_Os02g42380_M1657_1.02_CISBP_1.02__shift2 (11280_LOC_Os02g42380_M1657_1.02_CISBP_1.02_) 0.810 0.579 5.310 0.577 0.912 1.562 0.922 23 12 10 2 17 27 24 16.429 6
; oligos_5-7nt_m4 versus 11280_LOC_Os02g42380_M1657_1.02_CISBP_1.02_; m=2/9; ncol2=10; w=10; offset=2; strand=D; shift=2; score=16.4286; --kkGGgcCCmm-- ; cor=0.810; Ncor=0.579; logoDP=5.310; NIcor=0.577; NsEucl=0.912; SSD=1.562; NSW=0.922; rcor=23; rNcor=12; rlogoDP=10; rNIcor=2; rNsEucl=17; rSSD=27; rNSW=24; rank_mean=16.429; match_rank=6 a 0 0 18 7 0 0.0000 13 11 0.0000 7 45 28 0 0 c 0 0 13 15 0 0.0000 10 66 1.0000 93 33 41 0 0 g 0 0 41 33 93 1.0000 66 10 0.0000 0 15 13 0 0 t 0 0 28 45 7 0.0000 11 13 0.0000 0 7 18 0 0

11547_OsI_08196_M1658_1.02_CISBP_1.02__shift4 (11547_OsI_08196_M1658_1.02_CISBP_1.02_) 0.839 0.479 6.088 0.469 0.895 1.412 0.912 16 38 7 9 35 20 31 22.286 17
; oligos_5-7nt_m4 versus 11547_OsI_08196_M1658_1.02_CISBP_1.02_; m=3/9; ncol2=8; w=8; offset=4; strand=D; shift=4; score=22.2857; ----GGGCCCAC-- ; cor=0.839; Ncor=0.479; logoDP=6.088; NIcor=0.469; NsEucl=0.895; SSD=1.412; NSW=0.912; rcor=16; rNcor=38; rlogoDP=7; rNIcor=9; rNsEucl=35; rSSD=20; rNSW=31; rank_mean=22.286; match_rank=17 a 0 0 0 0 0 5 9 0 0 0 90 0 0 0 c 0 0 0 0 0 0 9 86 100 100 5 86 0 0 g 0 0 0 0 95 95 73 5 0 0 5 7 0 0 t 0 0 0 0 5 0 9 9 0 0 0 7 0 0

11598_PK14653.1_M1643_1.02_CISBP_1.02__shift2 (11598_PK14653.1_M1643_1.02_CISBP_1.02_) 0.777 0.555 3.644 0.562 0.904 1.826 0.909 37 18 18 5 26 41 34 25.571 26
; oligos_5-7nt_m4 versus 11598_PK14653.1_M1643_1.02_CISBP_1.02_; m=4/9; ncol2=10; w=10; offset=2; strand=D; shift=2; score=25.5714; --gTGGGCCCAc-- ; cor=0.777; Ncor=0.555; logoDP=3.644; NIcor=0.562; NsEucl=0.904; SSD=1.826; NSW=0.909; rcor=37; rNcor=18; rlogoDP=18; rNIcor=5; rNsEucl=26; rSSD=41; rNSW=34; rank_mean=25.571; match_rank=26 a 0 0 9 5 0 9 8 12 8 9 68 16 0 0 c 0 0 14 11 0 0 11 69 83 91 16 61 0 0 g 0 0 61 16 91 84 69 11 0 0 11 14 0 0 t 0 0 16 68 9 7 12 8 9 0 5 9 0 0

11809_TCP20_M1647_1.02_CISBP_1.02__rc_shift0 (11809_TCP20_M1647_1.02_CISBP_1.02__rc) 0.781 0.558 0.976 -0.012 0.908 1.682 0.916 33 17 34 34 24 32 26 28.571 30
; oligos_5-7nt_m4 versus 11809_TCP20_M1647_1.02_CISBP_1.02__rc; m=5/9; ncol2=10; w=10; offset=0; strand=R; shift=0; score=28.5714; tkGTGGGsCC---- ; cor=0.781; Ncor=0.558; logoDP=0.976; NIcor=-0.012; NsEucl=0.908; SSD=1.682; NSW=0.916; rcor=33; rNcor=17; rlogoDP=34; rNIcor=34; rNsEucl=24; rSSD=32; rNSW=26; rank_mean=28.571; match_rank=30 a 24 21 7 4 3 0 7 13 7 12 0 0 0 0 c 24 15 8 8 0 0 0 42 79 80 0 0 0 0 g 23 34 83 6 96 100 88 36 2 3 0 0 0 0 t 29 30 2 82 1 0 5 9 12 5 0 0 0 0

11146_Glyma19g26560.1_M1661_1.02_CISBP_1.02__shift3 (11146_Glyma19g26560.1_M1661_1.02_CISBP_1.02_) 0.751 0.483 5.083 0.472 0.886 2.105 0.883 51 37 11 8 41 44 47 34.143 40
; oligos_5-7nt_m4 versus 11146_Glyma19g26560.1_M1661_1.02_CISBP_1.02_; m=6/9; ncol2=9; w=9; offset=3; strand=D; shift=3; score=34.1429; ---gGGsCCCAC-- ; cor=0.751; Ncor=0.483; logoDP=5.083; NIcor=0.472; NsEucl=0.886; SSD=2.105; NSW=0.883; rcor=51; rNcor=37; rlogoDP=11; rNIcor=8; rNsEucl=41; rSSD=44; rNSW=47; rank_mean=34.143; match_rank=40 a 0 0 0 10 2 9 11 4 0 0 89 2 0 0 c 0 0 0 20 1 2 31 88 100 98 2 84 0 0 g 0 0 0 48 91 86 44 3 0 0 8 5 0 0 t 0 0 0 22 6 3 14 5 0 2 1 9 0 0

11940_XM_002867953.1_M1653_1.02_CISBP_1.02__shift4 (11940_XM_002867953.1_M1653_1.02_CISBP_1.02_) 0.771 0.441 6.700 0.428 0.871 2.124 0.867 40 46 4 14 49 45 49 35.286 44
; oligos_5-7nt_m4 versus 11940_XM_002867953.1_M1653_1.02_CISBP_1.02_; m=7/9; ncol2=8; w=8; offset=4; strand=D; shift=4; score=35.2857; ----GGsmCCAC-- ; cor=0.771; Ncor=0.441; logoDP=6.700; NIcor=0.428; NsEucl=0.871; SSD=2.124; NSW=0.867; rcor=40; rNcor=46; rlogoDP=4; rNIcor=14; rNsEucl=49; rSSD=45; rNSW=49; rank_mean=35.286; match_rank=44 a 0 0 0 0 0 0 0 33 0 0 100 0 0 0 c 0 0 0 0 0 0 34 67 100 100 0 100 0 0 g 0 0 0 0 100 100 66 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0

11944_XM_002893560.1_M1651_1.02_CISBP_1.02__shift2 (11944_XM_002893560.1_M1651_1.02_CISBP_1.02_) 0.756 0.540 0.668 0.573 0.889 2.449 0.878 48 21 42 3 40 52 48 36.286 48
; oligos_5-7nt_m4 versus 11944_XM_002893560.1_M1651_1.02_CISBP_1.02_; m=8/9; ncol2=10; w=10; offset=2; strand=D; shift=2; score=36.2857; --rtkkbvmmay-- ; cor=0.756; Ncor=0.540; logoDP=0.668; NIcor=0.573; NsEucl=0.889; SSD=2.449; NSW=0.878; rcor=48; rNcor=21; rlogoDP=42; rNIcor=3; rNsEucl=40; rSSD=52; rNSW=48; rank_mean=36.286; match_rank=48 a 0 0 33 11 15 6 15 26 27 26 43 17 0 0 c 0 0 20 24 3 12 26 32 55 56 22 30 0 0 g 0 0 30 22 56 55 33 27 12 4 24 20 0 0 t 0 0 17 43 26 27 26 15 6 14 11 33 0 0

11937_XM_002865836.1_M1654_1.02_CISBP_1.02__XM_002876964.1_M1652_1.02_CISBP_1.02__rc_shift2 (11937_XM_002865836.1_M1654_1.02_CISBP_1.02__XM_002876964.1_M1652_1.02_CISBP_1.02__rc) 0.752 0.430 1.956 0.033 0.866 2.289 0.857 49 48 30 33 51 50 51 44.571 52
; oligos_5-7nt_m4 versus 11937_XM_002865836.1_M1654_1.02_CISBP_1.02__XM_002876964.1_M1652_1.02_CISBP_1.02__rc; m=9/9; ncol2=8; w=8; offset=2; strand=R; shift=2; score=44.5714; --GTGGGsYC---- ; cor=0.752; Ncor=0.430; logoDP=1.956; NIcor=0.033; NsEucl=0.866; SSD=2.289; NSW=0.857; rcor=49; rNcor=48; rlogoDP=30; rNIcor=33; rNsEucl=51; rSSD=50; rNSW=51; rank_mean=44.571; match_rank=52 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 50 75 100 0 0 0 0 g 0 0 100 0 100 100 100 50 0 0 0 0 0 0 t 0 0 0 100 0 0 0 0 25 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
oligos_5-7nt_m4_shift0 (oligos_5-7nt_m4)																	; oligos_5-7nt_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; rgATGGGCCCATsy ; Alignment reference a 6 3 12 2 0 0 1 0 0 2 13 3 2 3 c 3 4 1 3 3 0 0 15 17 12 0 1 7 5 g 5 8 1 0 12 17 16 1 0 3 2 1 5 3 t 3 2 3 12 2 0 0 1 0 0 2 12 3 6
11811_TCP2_M1648_1.02_CISBP_1.02__rc_shift2 (11811_TCP2_M1648_1.02_CISBP_1.02__rc)	0.813	0.581	4.560	0.578	0.913	1.519	0.924	21	10	12	1	15	25	21	15.000	4	; oligos_5-7nt_m4 versus 11811_TCP2_M1648_1.02_CISBP_1.02__rc; m=1/9; ncol2=10; w=10; offset=2; strand=R; shift=2; score= 15; --gtGGkmCCac-- ; cor=0.813; Ncor=0.581; logoDP=4.560; NIcor=0.578; NsEucl=0.913; SSD=1.519; NSW=0.924; rcor=21; rNcor=10; rlogoDP=12; rNIcor=1; rNsEucl=15; rSSD=25; rNSW=21; rank_mean=15.000; match_rank=4 a 0 0 22 9 4 0 7 33 2 12 57 18 0 0 c 0 0 16 20 0 0 8 52 98 84 15 43 0 0 g 0 0 43 15 84 98 52 8 0 0 19 17 0 0 t 0 0 19 56 12 2 33 7 0 4 9 22 0 0
11280_LOC_Os02g42380_M1657_1.02_CISBP_1.02__shift2 (11280_LOC_Os02g42380_M1657_1.02_CISBP_1.02_)	0.810	0.579	5.310	0.577	0.912	1.562	0.922	23	12	10	2	17	27	24	16.429	6	; oligos_5-7nt_m4 versus 11280_LOC_Os02g42380_M1657_1.02_CISBP_1.02_; m=2/9; ncol2=10; w=10; offset=2; strand=D; shift=2; score=16.4286; --kkGGgcCCmm-- ; cor=0.810; Ncor=0.579; logoDP=5.310; NIcor=0.577; NsEucl=0.912; SSD=1.562; NSW=0.922; rcor=23; rNcor=12; rlogoDP=10; rNIcor=2; rNsEucl=17; rSSD=27; rNSW=24; rank_mean=16.429; match_rank=6 a 0 0 18 7 0 0.0000 13 11 0.0000 7 45 28 0 0 c 0 0 13 15 0 0.0000 10 66 1.0000 93 33 41 0 0 g 0 0 41 33 93 1.0000 66 10 0.0000 0 15 13 0 0 t 0 0 28 45 7 0.0000 11 13 0.0000 0 7 18 0 0
11547_OsI_08196_M1658_1.02_CISBP_1.02__shift4 (11547_OsI_08196_M1658_1.02_CISBP_1.02_)	0.839	0.479	6.088	0.469	0.895	1.412	0.912	16	38	7	9	35	20	31	22.286	17	; oligos_5-7nt_m4 versus 11547_OsI_08196_M1658_1.02_CISBP_1.02_; m=3/9; ncol2=8; w=8; offset=4; strand=D; shift=4; score=22.2857; ----GGGCCCAC-- ; cor=0.839; Ncor=0.479; logoDP=6.088; NIcor=0.469; NsEucl=0.895; SSD=1.412; NSW=0.912; rcor=16; rNcor=38; rlogoDP=7; rNIcor=9; rNsEucl=35; rSSD=20; rNSW=31; rank_mean=22.286; match_rank=17 a 0 0 0 0 0 5 9 0 0 0 90 0 0 0 c 0 0 0 0 0 0 9 86 100 100 5 86 0 0 g 0 0 0 0 95 95 73 5 0 0 5 7 0 0 t 0 0 0 0 5 0 9 9 0 0 0 7 0 0
11598_PK14653.1_M1643_1.02_CISBP_1.02__shift2 (11598_PK14653.1_M1643_1.02_CISBP_1.02_)	0.777	0.555	3.644	0.562	0.904	1.826	0.909	37	18	18	5	26	41	34	25.571	26	; oligos_5-7nt_m4 versus 11598_PK14653.1_M1643_1.02_CISBP_1.02_; m=4/9; ncol2=10; w=10; offset=2; strand=D; shift=2; score=25.5714; --gTGGGCCCAc-- ; cor=0.777; Ncor=0.555; logoDP=3.644; NIcor=0.562; NsEucl=0.904; SSD=1.826; NSW=0.909; rcor=37; rNcor=18; rlogoDP=18; rNIcor=5; rNsEucl=26; rSSD=41; rNSW=34; rank_mean=25.571; match_rank=26 a 0 0 9 5 0 9 8 12 8 9 68 16 0 0 c 0 0 14 11 0 0 11 69 83 91 16 61 0 0 g 0 0 61 16 91 84 69 11 0 0 11 14 0 0 t 0 0 16 68 9 7 12 8 9 0 5 9 0 0
11809_TCP20_M1647_1.02_CISBP_1.02__rc_shift0 (11809_TCP20_M1647_1.02_CISBP_1.02__rc)	0.781	0.558	0.976	-0.012	0.908	1.682	0.916	33	17	34	34	24	32	26	28.571	30	; oligos_5-7nt_m4 versus 11809_TCP20_M1647_1.02_CISBP_1.02__rc; m=5/9; ncol2=10; w=10; offset=0; strand=R; shift=0; score=28.5714; tkGTGGGsCC---- ; cor=0.781; Ncor=0.558; logoDP=0.976; NIcor=-0.012; NsEucl=0.908; SSD=1.682; NSW=0.916; rcor=33; rNcor=17; rlogoDP=34; rNIcor=34; rNsEucl=24; rSSD=32; rNSW=26; rank_mean=28.571; match_rank=30 a 24 21 7 4 3 0 7 13 7 12 0 0 0 0 c 24 15 8 8 0 0 0 42 79 80 0 0 0 0 g 23 34 83 6 96 100 88 36 2 3 0 0 0 0 t 29 30 2 82 1 0 5 9 12 5 0 0 0 0
11146_Glyma19g26560.1_M1661_1.02_CISBP_1.02__shift3 (11146_Glyma19g26560.1_M1661_1.02_CISBP_1.02_)	0.751	0.483	5.083	0.472	0.886	2.105	0.883	51	37	11	8	41	44	47	34.143	40	; oligos_5-7nt_m4 versus 11146_Glyma19g26560.1_M1661_1.02_CISBP_1.02_; m=6/9; ncol2=9; w=9; offset=3; strand=D; shift=3; score=34.1429; ---gGGsCCCAC-- ; cor=0.751; Ncor=0.483; logoDP=5.083; NIcor=0.472; NsEucl=0.886; SSD=2.105; NSW=0.883; rcor=51; rNcor=37; rlogoDP=11; rNIcor=8; rNsEucl=41; rSSD=44; rNSW=47; rank_mean=34.143; match_rank=40 a 0 0 0 10 2 9 11 4 0 0 89 2 0 0 c 0 0 0 20 1 2 31 88 100 98 2 84 0 0 g 0 0 0 48 91 86 44 3 0 0 8 5 0 0 t 0 0 0 22 6 3 14 5 0 2 1 9 0 0
11940_XM_002867953.1_M1653_1.02_CISBP_1.02__shift4 (11940_XM_002867953.1_M1653_1.02_CISBP_1.02_)	0.771	0.441	6.700	0.428	0.871	2.124	0.867	40	46	4	14	49	45	49	35.286	44	; oligos_5-7nt_m4 versus 11940_XM_002867953.1_M1653_1.02_CISBP_1.02_; m=7/9; ncol2=8; w=8; offset=4; strand=D; shift=4; score=35.2857; ----GGsmCCAC-- ; cor=0.771; Ncor=0.441; logoDP=6.700; NIcor=0.428; NsEucl=0.871; SSD=2.124; NSW=0.867; rcor=40; rNcor=46; rlogoDP=4; rNIcor=14; rNsEucl=49; rSSD=45; rNSW=49; rank_mean=35.286; match_rank=44 a 0 0 0 0 0 0 0 33 0 0 100 0 0 0 c 0 0 0 0 0 0 34 67 100 100 0 100 0 0 g 0 0 0 0 100 100 66 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0
11944_XM_002893560.1_M1651_1.02_CISBP_1.02__shift2 (11944_XM_002893560.1_M1651_1.02_CISBP_1.02_)	0.756	0.540	0.668	0.573	0.889	2.449	0.878	48	21	42	3	40	52	48	36.286	48	; oligos_5-7nt_m4 versus 11944_XM_002893560.1_M1651_1.02_CISBP_1.02_; m=8/9; ncol2=10; w=10; offset=2; strand=D; shift=2; score=36.2857; --rtkkbvmmay-- ; cor=0.756; Ncor=0.540; logoDP=0.668; NIcor=0.573; NsEucl=0.889; SSD=2.449; NSW=0.878; rcor=48; rNcor=21; rlogoDP=42; rNIcor=3; rNsEucl=40; rSSD=52; rNSW=48; rank_mean=36.286; match_rank=48 a 0 0 33 11 15 6 15 26 27 26 43 17 0 0 c 0 0 20 24 3 12 26 32 55 56 22 30 0 0 g 0 0 30 22 56 55 33 27 12 4 24 20 0 0 t 0 0 17 43 26 27 26 15 6 14 11 33 0 0
11937_XM_002865836.1_M1654_1.02_CISBP_1.02__XM_002876964.1_M1652_1.02_CISBP_1.02__rc_shift2 (11937_XM_002865836.1_M1654_1.02_CISBP_1.02__XM_002876964.1_M1652_1.02_CISBP_1.02__rc)	0.752	0.430	1.956	0.033	0.866	2.289	0.857	49	48	30	33	51	50	51	44.571	52	; oligos_5-7nt_m4 versus 11937_XM_002865836.1_M1654_1.02_CISBP_1.02__XM_002876964.1_M1652_1.02_CISBP_1.02__rc; m=9/9; ncol2=8; w=8; offset=2; strand=R; shift=2; score=44.5714; --GTGGGsYC---- ; cor=0.752; Ncor=0.430; logoDP=1.956; NIcor=0.033; NsEucl=0.866; SSD=2.289; NSW=0.857; rcor=49; rNcor=48; rlogoDP=30; rNIcor=33; rNsEucl=51; rSSD=50; rNSW=51; rank_mean=44.571; match_rank=52 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 50 75 100 0 0 0 0 g 0 0 100 0 100 100 100 50 0 0 0 0 0 0 t 0 0 0 100 0 0 0 0 25 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m4_shift0 ; 30 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_test_vs_ctrl_m4_shift0 (dyads_test_vs_ctrl_m4)
; dyads_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=0; ncol=14; rsGAGGmGGCsg-- ; Alignment reference a 27 22 6 82 1 11 29 2 2 4 23 21 0 0 c 19 26 3 10 4 3 33 4 1 79 24 17 0 0 g 34 36 83 2 89 76 22 89 93 8 35 43 0 0 t 16 12 4 2 2 6 12 1 0 5 14 15 0 0

1584_M01999_TRANSFAC_2012.1__shift4 (1584_M01999_TRANSFAC_2012.1_) 0.848 0.565 5.363 0.568 0.901 1.248 0.922 15 15 9 4 32 16 23 16.286 5
; dyads_test_vs_ctrl_m4 versus 1584_M01999_TRANSFAC_2012.1_; m=1/29; ncol2=8; w=8; offset=4; strand=D; shift=4; score=16.2857; ----GGCGGCTb-- ; cor=0.848; Ncor=0.565; logoDP=5.363; NIcor=0.568; NsEucl=0.901; SSD=1.248; NSW=0.922; rcor=15; rNcor=15; rlogoDP=9; rNIcor=4; rNsEucl=32; rSSD=16; rNSW=23; rank_mean=16.286; match_rank=5 a 0 0 0 0 0 0 0 0 0 0 1 0 0 0 c 0 0 0 0 0 0 7 0 0 6 0 3 0 0 g 0 0 0 0 7 6 0 7 7 0 1 2 0 0 t 0 0 0 0 0 1 0 0 0 1 5 2 0 0

5032_NtERF2_Athamap_20091028__rc_shift4 (5032_NtERF2_Athamap_20091028__rc) 0.871 0.508 2.089 0.232 0.914 0.730 0.948 11 30 29 28 13 3 9 17.571 8
; dyads_test_vs_ctrl_m4 versus 5032_NtERF2_Athamap_20091028__rc; m=2/29; ncol2=7; w=7; offset=4; strand=R; shift=4; score=17.5714; ----GGCGGCr--- ; cor=0.871; Ncor=0.508; logoDP=2.089; NIcor=0.232; NsEucl=0.914; SSD=0.730; NSW=0.948; rcor=11; rNcor=30; rlogoDP=29; rNIcor=28; rNsEucl=13; rSSD=3; rNSW=9; rank_mean=17.571; match_rank=8 a 0 0 0 0 0 0 0 1 0 1 4 0 0 0 c 0 0 0 0 1 2 13 2 3 12 1 0 0 0 g 0 0 0 0 13 10 0 11 10 1 7 0 0 0 t 0 0 0 0 0 2 1 0 1 0 2 0 0 0

10654_AT3G23230_M0024_1.02_CISBP_1.02__rc_shift4 (10654_AT3G23230_M0024_1.02_CISBP_1.02__rc) 0.870 0.580 0.223 -0.140 0.926 0.710 0.956 12 11 50 46 6 2 6 19.000 10
; dyads_test_vs_ctrl_m4 versus 10654_AT3G23230_M0024_1.02_CISBP_1.02__rc; m=3/29; ncol2=8; w=8; offset=4; strand=R; shift=4; score= 19; ----GgCGGCks-- ; cor=0.870; Ncor=0.580; logoDP=0.223; NIcor=-0.140; NsEucl=0.926; SSD=0.710; NSW=0.956; rcor=12; rNcor=11; rlogoDP=50; rNIcor=46; rNsEucl=6; rSSD=2; rNSW=6; rank_mean=19.000; match_rank=10 a 0 0 0 0 10 19 1 7 5 4 17 20 0 0 c 0 0 0 0 10 17 76 1 17 80 22 27 0 0 g 0 0 0 0 68 45 4 77 75 6 36 32 0 0 t 0 0 0 0 12 19 19 15 3 10 25 21 0 0

755_M01057_TRANSFAC_2012.1__rc_shift4 (755_M01057_TRANSFAC_2012.1__rc) 0.877 0.512 2.625 0.220 0.904 0.897 0.936 9 28 25 29 27 11 13 20.286 11
; dyads_test_vs_ctrl_m4 versus 755_M01057_TRANSFAC_2012.1__rc; m=4/29; ncol2=7; w=7; offset=4; strand=R; shift=4; score=20.2857; ----GGCGGCG--- ; cor=0.877; Ncor=0.512; logoDP=2.625; NIcor=0.220; NsEucl=0.904; SSD=0.897; NSW=0.936; rcor=9; rNcor=28; rlogoDP=25; rNIcor=29; rNsEucl=27; rSSD=11; rNSW=13; rank_mean=20.286; match_rank=11 a 0 0 0 0 0 0 0 1 0 1 4 0 0 0 c 0 0 0 0 1 2 32 2 6 31 1 0 0 0 g 0 0 0 0 32 28 0 30 26 1 26 0 0 0 t 0 0 0 0 0 3 1 0 1 0 2 0 0 0

10683_ATERF-4_M0022_1.02_CISBP_1.02__rc_shift4 (10683_ATERF-4_M0022_1.02_CISBP_1.02__rc) 0.875 0.584 0.364 -0.174 0.918 0.868 0.946 10 8 48 50 11 9 10 20.857 12
; dyads_test_vs_ctrl_m4 versus 10683_ATERF-4_M0022_1.02_CISBP_1.02__rc; m=5/29; ncol2=8; w=8; offset=4; strand=R; shift=4; score=20.8571; ----GgCGGCGg-- ; cor=0.875; Ncor=0.584; logoDP=0.364; NIcor=-0.174; NsEucl=0.918; SSD=0.868; NSW=0.946; rcor=10; rNcor=8; rlogoDP=48; rNIcor=50; rNsEucl=11; rSSD=9; rNSW=10; rank_mean=20.857; match_rank=12 a 0 0 0 0 4 15 0 0 1 1 9 9 0 0 c 0 0 0 0 4 13 99 1 8 95 12 22 0 0 g 0 0 0 0 80 66 1 98 90 2 73 52 0 0 t 0 0 0 0 12 6 0 1 1 2 6 17 0 0

10682_ATERF-1_M0028_1.02_CISBP_1.02__rc_shift3 (10682_ATERF-1_M0028_1.02_CISBP_1.02__rc) 0.791 0.593 0.964 0.175 0.912 1.251 0.931 29 6 35 31 16 17 17 21.571 14
; dyads_test_vs_ctrl_m4 versus 10682_ATERF-1_M0028_1.02_CISBP_1.02__rc; m=6/29; ncol2=9; w=9; offset=3; strand=R; shift=3; score=21.5714; ---kGrcGGCks-- ; cor=0.791; Ncor=0.593; logoDP=0.964; NIcor=0.175; NsEucl=0.912; SSD=1.251; NSW=0.931; rcor=29; rNcor=6; rlogoDP=35; rNIcor=31; rNsEucl=16; rSSD=17; rNSW=17; rank_mean=21.571; match_rank=14 a 0 0 0 23 12 28 8 6 6 0 12 20 0 0 c 0 0 0 14 7 13 62 3 5 95 11 26 0 0 g 0 0 0 32 68 35 9 78 83 0 47 32 0 0 t 0 0 0 31 13 24 21 13 6 5 30 22 0 0

8786_MA0123_JASPAR_2014__rc_shift4 (8786_MA0123_JASPAR_2014__rc) 0.816 0.466 2.230 0.242 0.913 0.971 0.939 20 39 28 27 14 12 11 21.571 15
; dyads_test_vs_ctrl_m4 versus 8786_MA0123_JASPAR_2014__rc; m=7/29; ncol2=10; w=8; offset=4; strand=R; shift=4; score=21.5714; ----ggggGCrsCG ; cor=0.816; Ncor=0.466; logoDP=2.230; NIcor=0.242; NsEucl=0.913; SSD=0.971; NSW=0.939; rcor=20; rNcor=39; rlogoDP=28; rNIcor=27; rNsEucl=14; rSSD=12; rNSW=11; rank_mean=21.571; match_rank=15 a 0 0 0 0 12 10 10 10 0 0 25 0 0 0 c 0 0 0 0 7 5 11 6 4 45 1 29 37 0 g 0 0 0 0 26 31 25 28 45 3 23 20 0 49 t 0 0 0 0 4 3 3 5 0 1 0 0 12 0

10843_CRF2_M0029_1.02_CISBP_1.02__rc_shift4 (10843_CRF2_M0029_1.02_CISBP_1.02__rc) 0.879 0.586 0.369 -0.154 0.911 1.021 0.936 8 7 47 49 18 13 12 22.000 16
; dyads_test_vs_ctrl_m4 versus 10843_CRF2_M0029_1.02_CISBP_1.02__rc; m=8/29; ncol2=8; w=8; offset=4; strand=R; shift=4; score= 22; ----GGCGGCGs-- ; cor=0.879; Ncor=0.586; logoDP=0.369; NIcor=-0.154; NsEucl=0.911; SSD=1.021; NSW=0.936; rcor=8; rNcor=7; rlogoDP=47; rNIcor=49; rNsEucl=18; rSSD=13; rNSW=12; rank_mean=22.000; match_rank=16 a 0 0 0 0 9 5 0 0 0 0 3 13 0 0 c 0 0 0 0 6 0 100 0 2 100 8 35 0 0 g 0 0 0 0 73 93 0 100 98 0 78 48 0 0 t 0 0 0 0 12 2 0 0 0 0 11 4 0 0

7202_ATERF1_ArabidopsisPBM_20140210__shift4 (7202_ATERF1_ArabidopsisPBM_20140210_) 0.807 0.461 2.357 0.446 0.909 1.060 0.934 25 42 27 11 22 15 16 22.571 19
; dyads_test_vs_ctrl_m4 versus 7202_ATERF1_ArabidopsisPBM_20140210_; m=9/29; ncol2=10; w=8; offset=4; strand=D; shift=4; score=22.5714; ----GGcGsCGsCb ; cor=0.807; Ncor=0.461; logoDP=2.357; NIcor=0.446; NsEucl=0.909; SSD=1.060; NSW=0.934; rcor=25; rNcor=42; rlogoDP=27; rNIcor=11; rNsEucl=22; rSSD=15; rNSW=16; rank_mean=22.571; match_rank=19 a 0 0 0 0 5 4 19 3 4 6 7 8 6 9 c 0 0 0 0 3 15 60 2 48 85 9 52 80 37 g 0 0 0 0 83 71 15 93 38 5 73 35 10 29 t 0 0 0 0 9 10 6 2 10 4 11 5 4 25

2148_M03201_TRANSFAC_2012.1__rc_shift2 (2148_M03201_TRANSFAC_2012.1__rc) 0.782 0.651 3.457 0.321 0.906 1.751 0.912 32 2 20 18 25 36 29 23.143 21
; dyads_test_vs_ctrl_m4 versus 2148_M03201_TRANSFAC_2012.1__rc; m=10/29; ncol2=10; w=10; offset=2; strand=R; shift=2; score=23.1429; --krGsCGGCAw-- ; cor=0.782; Ncor=0.651; logoDP=3.457; NIcor=0.321; NsEucl=0.906; SSD=1.751; NSW=0.912; rcor=32; rNcor=2; rlogoDP=20; rNIcor=18; rNsEucl=25; rSSD=36; rNSW=29; rank_mean=23.143; match_rank=21 a 0 0 1 41 15 1 0 0 0 0 69 28 0 0 c 0 0 22 7 0 32 100 0 0 100 20 17 0 0 g 0 0 49 31 85 56 0 100 100 0 11 22 0 0 t 0 0 28 21 0 11 0 0 0 0 0 33 0 0

10845_CRF4_M0033_1.02_CISBP_1.02__rc_shift4 (10845_CRF4_M0033_1.02_CISBP_1.02__rc) 0.865 0.576 0.437 -0.122 0.909 1.056 0.934 13 13 45 43 21 14 15 23.429 22
; dyads_test_vs_ctrl_m4 versus 10845_CRF4_M0033_1.02_CISBP_1.02__rc; m=11/29; ncol2=8; w=8; offset=4; strand=R; shift=4; score=23.4286; ----GGCGGCGs-- ; cor=0.865; Ncor=0.576; logoDP=0.437; NIcor=-0.122; NsEucl=0.909; SSD=1.056; NSW=0.934; rcor=13; rNcor=13; rlogoDP=45; rNIcor=43; rNsEucl=21; rSSD=14; rNSW=15; rank_mean=23.429; match_rank=22 a 0 0 0 0 5 11 0 0 0 0 6 7 0 0 c 0 0 0 0 6 7 99 0 3 100 6 53 0 0 g 0 0 0 0 79 75 1 100 97 0 77 33 0 0 t 0 0 0 0 10 7 0 0 0 0 11 7 0 0

10844_CRF3_M0041_1.02_CISBP_1.02__rc_shift3 (10844_CRF3_M0041_1.02_CISBP_1.02__rc) 0.776 0.582 0.947 0.198 0.909 1.332 0.926 38 9 36 30 20 18 18 24.143 23
; dyads_test_vs_ctrl_m4 versus 10844_CRF3_M0041_1.02_CISBP_1.02__rc; m=12/29; ncol2=9; w=9; offset=3; strand=R; shift=3; score=24.1429; ---tggcGGCgs-- ; cor=0.776; Ncor=0.582; logoDP=0.947; NIcor=0.198; NsEucl=0.909; SSD=1.332; NSW=0.926; rcor=38; rNcor=9; rlogoDP=36; rNIcor=30; rNsEucl=20; rSSD=18; rNSW=18; rank_mean=24.143; match_rank=23 a 0 0 0 21 19 24 11 7 5 0 14 20 0 0 c 0 0 0 21 13 14 62 6 5 94 16 30 0 0 g 0 0 0 24 46 42 10 77 88 0 48 31 0 0 t 0 0 0 34 22 20 17 10 2 6 22 19 0 0

11540_ORA59_M0005_1.02_CISBP_1.02__rc_shift3 (11540_ORA59_M0005_1.02_CISBP_1.02__rc) 0.818 0.545 3.669 0.287 0.893 1.453 0.909 19 19 17 21 38 23 33 24.286 24
; dyads_test_vs_ctrl_m4 versus 11540_ORA59_M0005_1.02_CISBP_1.02__rc; m=13/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=24.2857; ---cGGCGGCk--- ; cor=0.818; Ncor=0.545; logoDP=3.669; NIcor=0.287; NsEucl=0.893; SSD=1.453; NSW=0.909; rcor=19; rNcor=19; rlogoDP=17; rNIcor=21; rNsEucl=38; rSSD=23; rNSW=33; rank_mean=24.286; match_rank=24 a 0 0 0 17 0 0 0 0 0 0 0 0 0 0 c 0 0 0 49 0 5 98 0 0 100 19 0 0 0 g 0 0 0 10 100 95 0 88 100 0 46 0 0 0 t 0 0 0 24 0 0 2 12 0 0 35 0 0 0

10686_ATERF13_M0020_1.02_CISBP_1.02__rc_shift3 (10686_ATERF13_M0020_1.02_CISBP_1.02__rc) 0.803 0.535 3.371 0.289 0.894 1.431 0.911 27 24 22 20 37 22 32 26.286 28
; dyads_test_vs_ctrl_m4 versus 10686_ATERF13_M0020_1.02_CISBP_1.02__rc; m=14/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=26.2857; ---yGgCGGCs--- ; cor=0.803; Ncor=0.535; logoDP=3.371; NIcor=0.289; NsEucl=0.894; SSD=1.431; NSW=0.911; rcor=27; rNcor=24; rlogoDP=22; rNIcor=20; rNsEucl=37; rSSD=22; rNSW=32; rank_mean=26.286; match_rank=28 a 0 0 0 15 0 11 0 0 0 0 2 0 0 0 c 0 0 0 28 0 15 98 2 3 95 28 0 0 0 g 0 0 0 10 100 64 2 98 95 5 48 0 0 0 t 0 0 0 47 0 10 0 0 2 0 22 0 0 0

7216_DEAR4_2_ArabidopsisPBM_20140210__rc_shift3 (7216_DEAR4_2_ArabidopsisPBM_20140210__rc) 0.813 0.563 0.777 -0.074 0.901 1.573 0.913 22 16 39 37 31 29 28 28.857 31
; dyads_test_vs_ctrl_m4 versus 7216_DEAR4_2_ArabidopsisPBM_20140210__rc; m=15/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score=28.8571; ---aGGCGGCGCy- ; cor=0.813; Ncor=0.563; logoDP=0.777; NIcor=-0.074; NsEucl=0.901; SSD=1.573; NSW=0.913; rcor=22; rNcor=16; rlogoDP=39; rNIcor=37; rNsEucl=31; rSSD=29; rNSW=28; rank_mean=28.857; match_rank=31 a 0 0 0 61 9 7 3 1 0 1 2 8 12 0 c 0 0 0 15 2 8 95 1 8 87 2 76 37 0 g 0 0 0 21 86 84 1 98 91 0 94 13 22 0 t 0 0 0 3 3 1 1 0 1 12 2 3 29 0

7219_DREB2C_ArabidopsisPBM_20140210__rc_shift4 (7219_DREB2C_ArabidopsisPBM_20140210__rc) 0.809 0.462 4.093 0.428 0.885 1.685 0.895 24 40 13 13 43 33 38 29.143 32
; dyads_test_vs_ctrl_m4 versus 7219_DREB2C_ArabidopsisPBM_20140210__rc; m=16/29; ncol2=10; w=8; offset=4; strand=R; shift=4; score=29.1429; ----gGCGGCCGCc ; cor=0.809; Ncor=0.462; logoDP=4.093; NIcor=0.428; NsEucl=0.885; SSD=1.685; NSW=0.895; rcor=24; rNcor=40; rlogoDP=13; rNIcor=13; rNsEucl=43; rSSD=33; rNSW=38; rank_mean=29.143; match_rank=32 a 0 0 0 0 13 2 0 1 3 0 0 4 3 14 c 0 0 0 0 7 2 96 5 0 97 94 0 92 67 g 0 0 0 0 67 93 0 94 97 0 5 96 2 5 t 0 0 0 0 13 3 4 0 0 3 1 0 3 14

10960_ERF1_M0025_1.02_CISBP_1.02__rc_shift2 (10960_ERF1_M0025_1.02_CISBP_1.02__rc) 0.750 0.625 3.700 0.318 0.895 2.197 0.890 52 4 16 19 34 46 41 30.286 34
; dyads_test_vs_ctrl_m4 versus 10960_ERF1_M0025_1.02_CISBP_1.02__rc; m=17/29; ncol2=10; w=10; offset=2; strand=R; shift=2; score=30.2857; --ryGGCGGCks-- ; cor=0.750; Ncor=0.625; logoDP=3.700; NIcor=0.318; NsEucl=0.895; SSD=2.197; NSW=0.890; rcor=52; rNcor=4; rlogoDP=16; rNIcor=19; rNsEucl=34; rSSD=46; rNSW=41; rank_mean=30.286; match_rank=34 a 0 0 35 7 0 0 0 0 0 0 10 17 0 0 c 0 0 24 49 0 0 100 0 0 100 10 27 0 0 g 0 0 26 8 100 100 0 100 100 0 50 38 0 0 t 0 0 15 36 0 0 0 0 0 0 30 18 0 0

10961_ERF2_M0038_1.02_CISBP_1.02__rc_shift3 (10961_ERF2_M0038_1.02_CISBP_1.02__rc) 0.778 0.539 0.181 -0.139 0.909 1.346 0.925 35 22 51 45 23 19 20 30.714 35
; dyads_test_vs_ctrl_m4 versus 10961_ERF2_M0038_1.02_CISBP_1.02__rc; m=18/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score=30.7143; ---tGgCGGCksd- ; cor=0.778; Ncor=0.539; logoDP=0.181; NIcor=-0.139; NsEucl=0.909; SSD=1.346; NSW=0.925; rcor=35; rNcor=22; rlogoDP=51; rNIcor=45; rNsEucl=23; rSSD=19; rNSW=20; rank_mean=30.714; match_rank=35 a 0 0 0 22 11 21 4 8 7 6 15 23 27 0 c 0 0 0 22 9 15 77 4 14 73 24 27 21 0 g 0 0 0 22 68 46 3 71 70 8 32 27 26 0 t 0 0 0 34 12 18 16 17 9 13 29 23 26 0

2154_M03207_TRANSFAC_2012.1__rc_shift2 (2154_M03207_TRANSFAC_2012.1__rc) 0.760 0.633 3.741 0.272 0.894 2.226 0.889 46 3 15 24 36 48 43 30.714 36
; dyads_test_vs_ctrl_m4 versus 2154_M03207_TRANSFAC_2012.1__rc; m=19/29; ncol2=10; w=10; offset=2; strand=R; shift=2; score=30.7143; --GTGGCGGCmw-- ; cor=0.760; Ncor=0.633; logoDP=3.741; NIcor=0.272; NsEucl=0.894; SSD=2.226; NSW=0.889; rcor=46; rNcor=3; rlogoDP=15; rNIcor=24; rNsEucl=36; rSSD=48; rNSW=43; rank_mean=30.714; match_rank=36 a 0 0 1 0 1 0 0 0 0 0 38 27 0 0 c 0 0 2 6 0 19 100 0 0 100 49 18 0 0 g 0 0 93 20 99 69 0 100 100 0 13 22 0 0 t 0 0 4 74 0 12 0 0 0 0 0 33 0 0

9050_MA0567_JASPAR_2014__rc_shift3 (9050_MA0567_JASPAR_2014__rc) 0.791 0.527 3.336 0.280 0.885 1.686 0.895 30 27 23 23 44 34 39 31.429 37
; dyads_test_vs_ctrl_m4 versus 9050_MA0567_JASPAR_2014__rc; m=20/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=31.4286; ---tGGCGGCk--- ; cor=0.791; Ncor=0.527; logoDP=3.336; NIcor=0.280; NsEucl=0.885; SSD=1.686; NSW=0.895; rcor=30; rNcor=27; rlogoDP=23; rNIcor=23; rNsEucl=44; rSSD=34; rNSW=39; rank_mean=31.429; match_rank=37 a 0 0 0 12 1 4 1 0 1 1 1 0 0 0 c 0 0 0 24 1 2 97 0 1 98 3 0 0 0 g 0 0 0 5 98 92 0 96 98 1 54 0 0 0 t 0 0 0 58 1 2 2 4 0 1 42 0 0 0

10660_AT4G00270_M1620_1.02_CISBP_1.02__rc_shift5 (10660_AT4G00270_M1620_1.02_CISBP_1.02__rc) 0.793 0.427 3.622 0.352 0.874 1.557 0.889 28 50 19 17 48 26 42 32.857 38
; dyads_test_vs_ctrl_m4 versus 10660_AT4G00270_M1620_1.02_CISBP_1.02__rc; m=21/29; ncol2=8; w=7; offset=5; strand=R; shift=5; score=32.8571; -----gCGGCCGg- ; cor=0.793; Ncor=0.427; logoDP=3.622; NIcor=0.352; NsEucl=0.874; SSD=1.557; NSW=0.889; rcor=28; rNcor=50; rlogoDP=19; rNIcor=17; rNsEucl=48; rSSD=26; rNSW=42; rank_mean=32.857; match_rank=38 a 0 0 0 0 0 14 3 0 0 0 0 5 16 0 c 0 0 0 0 0 4 97 0 0 100 97 0 4 0 g 0 0 0 0 0 61 0 100 95 0 0 81 56 0 t 0 0 0 0 0 21 0 0 5 0 3 14 24 0

7246_ORA47_2_ArabidopsisPBM_20140210__rc_shift3 (7246_ORA47_2_ArabidopsisPBM_20140210__rc) 0.783 0.542 0.682 -0.090 0.896 1.768 0.902 31 20 41 39 33 37 35 33.714 39
; dyads_test_vs_ctrl_m4 versus 7246_ORA47_2_ArabidopsisPBM_20140210__rc; m=22/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score=33.7143; ---rGkCGGCGCm- ; cor=0.783; Ncor=0.542; logoDP=0.682; NIcor=-0.090; NsEucl=0.896; SSD=1.768; NSW=0.902; rcor=31; rNcor=20; rlogoDP=41; rNIcor=39; rNsEucl=33; rSSD=37; rNSW=35; rank_mean=33.714; match_rank=39 a 0 0 0 42 2 5 2 0 0 0 4 5 47 0 c 0 0 0 13 1 5 97 1 4 92 1 73 30 0 g 0 0 0 25 93 65 0 98 96 1 93 13 6 0 t 0 0 0 20 4 25 1 1 0 7 2 9 17 0

10565_0100010458_M0076_1.02_CISBP_1.02__rc_shift3 (10565_0100010458_M0076_1.02_CISBP_1.02__rc) 0.767 0.511 3.866 0.284 0.881 1.803 0.887 42 29 14 22 47 40 46 34.286 41
; dyads_test_vs_ctrl_m4 versus 10565_0100010458_M0076_1.02_CISBP_1.02__rc; m=23/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=34.2857; ---yGGCGGCg--- ; cor=0.767; Ncor=0.511; logoDP=3.866; NIcor=0.284; NsEucl=0.881; SSD=1.803; NSW=0.887; rcor=42; rNcor=29; rlogoDP=14; rNIcor=22; rNsEucl=47; rSSD=40; rNSW=46; rank_mean=34.286; match_rank=41 a 0 0 0 6 0 5 0 0 0 0 8 0 0 0 c 0 0 0 32 0 22 100 2 8 100 13 0 0 0 g 0 0 0 3 100 71 0 98 92 0 61 0 0 0 t 0 0 0 59 0 2 0 0 0 0 18 0 0 0

11601_PK19363.1_M0004_1.02_CISBP_1.02__rc_shift3 (11601_PK19363.1_M0004_1.02_CISBP_1.02__rc) 0.757 0.505 2.923 0.261 0.886 1.670 0.896 47 34 24 26 42 31 37 34.429 42
; dyads_test_vs_ctrl_m4 versus 11601_PK19363.1_M0004_1.02_CISBP_1.02__rc; m=24/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=34.4286; ---yGgCGGCG--- ; cor=0.757; Ncor=0.505; logoDP=2.923; NIcor=0.261; NsEucl=0.886; SSD=1.670; NSW=0.896; rcor=47; rNcor=34; rlogoDP=24; rNIcor=26; rNsEucl=42; rSSD=31; rNSW=37; rank_mean=34.429; match_rank=42 a 0 0 0 14 6 17 0 0 0 1 6 0 0 0 c 0 0 0 30 1 14 99 1 11 95 7 0 0 0 g 0 0 0 7 77 63 1 97 87 1 72 0 0 0 t 0 0 0 49 16 6 0 2 2 3 15 0 0 0

10963_ERF5_M0039_1.02_CISBP_1.02__rc_shift3 (10963_ERF5_M0039_1.02_CISBP_1.02__rc) 0.767 0.531 0.162 -0.143 0.904 1.488 0.917 43 25 52 47 28 24 25 34.857 43
; dyads_test_vs_ctrl_m4 versus 10963_ERF5_M0039_1.02_CISBP_1.02__rc; m=25/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score=34.8571; ---kggcggCksd- ; cor=0.767; Ncor=0.531; logoDP=0.162; NIcor=-0.143; NsEucl=0.904; SSD=1.488; NSW=0.917; rcor=43; rNcor=25; rlogoDP=52; rNIcor=47; rNsEucl=28; rSSD=24; rNSW=25; rank_mean=34.857; match_rank=43 a 0 0 0 21 12 24 8 7 9 5 17 23 25 0 c 0 0 0 17 11 21 59 7 18 75 19 27 21 0 g 0 0 0 29 60 35 12 67 61 6 36 27 27 0 t 0 0 0 33 17 20 21 19 12 14 28 23 27 0

10962_ERF3_M0011_1.02_CISBP_1.02__rc_shift3 (10962_ERF3_M0011_1.02_CISBP_1.02__rc) 0.761 0.507 3.404 0.266 0.882 1.787 0.888 45 33 21 25 45 38 44 35.857 45
; dyads_test_vs_ctrl_m4 versus 10962_ERF3_M0011_1.02_CISBP_1.02__rc; m=26/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=35.8571; ---yGgCGGCG--- ; cor=0.761; Ncor=0.507; logoDP=3.404; NIcor=0.266; NsEucl=0.882; SSD=1.787; NSW=0.888; rcor=45; rNcor=33; rlogoDP=21; rNIcor=25; rNsEucl=45; rSSD=38; rNSW=44; rank_mean=35.857; match_rank=45 a 0 0 0 12 2 11 0 0 0 0 8 0 0 0 c 0 0 0 28 0 19 99 1 11 99 8 0 0 0 g 0 0 0 2 90 64 0 99 89 0 76 0 0 0 t 0 0 0 58 8 6 1 0 0 1 8 0 0 0

10649_AT2G33710_M0018_1.02_CISBP_1.02__rc_shift3 (10649_AT2G33710_M0018_1.02_CISBP_1.02__rc) 0.762 0.528 0.278 -0.143 0.902 1.571 0.913 44 26 49 48 30 28 27 36.000 47
; dyads_test_vs_ctrl_m4 versus 10649_AT2G33710_M0018_1.02_CISBP_1.02__rc; m=27/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score= 36; ---tggCGGCgsc- ; cor=0.762; Ncor=0.528; logoDP=0.278; NIcor=-0.143; NsEucl=0.902; SSD=1.571; NSW=0.913; rcor=44; rNcor=26; rlogoDP=49; rNIcor=48; rNsEucl=30; rSSD=28; rNSW=27; rank_mean=36.000; match_rank=47 a 0 0 0 15 6 21 3 0 0 7 5 12 18 0 c 0 0 0 24 4 10 90 0 0 92 12 34 39 0 g 0 0 0 13 66 52 3 95 100 0 61 44 24 0 t 0 0 0 48 24 17 4 5 0 1 22 10 19 0

7221_ERF1_ArabidopsisPBM_20140210__rc_shift3 (7221_ERF1_ArabidopsisPBM_20140210__rc) 0.774 0.536 0.373 -0.115 0.892 1.900 0.894 39 23 46 41 39 42 40 38.571 50
; dyads_test_vs_ctrl_m4 versus 7221_ERF1_ArabidopsisPBM_20140210__rc; m=28/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score=38.5714; ---tGGCGGCGsy- ; cor=0.774; Ncor=0.536; logoDP=0.373; NIcor=-0.115; NsEucl=0.892; SSD=1.900; NSW=0.894; rcor=39; rNcor=23; rlogoDP=46; rNIcor=41; rNsEucl=39; rSSD=42; rNSW=40; rank_mean=38.571; match_rank=50 a 0 0 0 12 1 3 1 1 1 1 2 15 23 0 c 0 0 0 24 1 2 97 0 3 97 1 46 27 0 g 0 0 0 5 97 90 0 95 96 1 82 33 12 0 t 0 0 0 59 1 5 2 4 0 1 15 6 38 0

4995_ABI4_Athamap_20091028__rc_shift4 (4995_ABI4_Athamap_20091028__rc) 0.751 0.429 2.548 0.138 0.882 1.788 0.888 50 49 26 32 46 39 45 41.000 51
; dyads_test_vs_ctrl_m4 versus 4995_ABI4_Athamap_20091028__rc; m=29/29; ncol2=10; w=8; offset=4; strand=R; shift=4; score= 41; ----sggGGCGGyG ; cor=0.751; Ncor=0.429; logoDP=2.548; NIcor=0.138; NsEucl=0.882; SSD=1.788; NSW=0.888; rcor=50; rNcor=49; rlogoDP=26; rNIcor=32; rNsEucl=46; rSSD=39; rNSW=45; rank_mean=41.000; match_rank=51 a 0 0 0 0 4 2 1 0 0 0 0 0 0 1 c 0 0 0 0 6 4 5 0 0 20 0 0 9 0 g 0 0 0 0 7 13 14 20 21 0 21 21 0 20 t 0 0 0 0 4 2 1 1 0 1 0 0 12 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m4_shift0 (dyads_test_vs_ctrl_m4)																	; dyads_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=0; ncol=14; rsGAGGmGGCsg-- ; Alignment reference a 27 22 6 82 1 11 29 2 2 4 23 21 0 0 c 19 26 3 10 4 3 33 4 1 79 24 17 0 0 g 34 36 83 2 89 76 22 89 93 8 35 43 0 0 t 16 12 4 2 2 6 12 1 0 5 14 15 0 0
1584_M01999_TRANSFAC_2012.1__shift4 (1584_M01999_TRANSFAC_2012.1_)	0.848	0.565	5.363	0.568	0.901	1.248	0.922	15	15	9	4	32	16	23	16.286	5	; dyads_test_vs_ctrl_m4 versus 1584_M01999_TRANSFAC_2012.1_; m=1/29; ncol2=8; w=8; offset=4; strand=D; shift=4; score=16.2857; ----GGCGGCTb-- ; cor=0.848; Ncor=0.565; logoDP=5.363; NIcor=0.568; NsEucl=0.901; SSD=1.248; NSW=0.922; rcor=15; rNcor=15; rlogoDP=9; rNIcor=4; rNsEucl=32; rSSD=16; rNSW=23; rank_mean=16.286; match_rank=5 a 0 0 0 0 0 0 0 0 0 0 1 0 0 0 c 0 0 0 0 0 0 7 0 0 6 0 3 0 0 g 0 0 0 0 7 6 0 7 7 0 1 2 0 0 t 0 0 0 0 0 1 0 0 0 1 5 2 0 0
5032_NtERF2_Athamap_20091028__rc_shift4 (5032_NtERF2_Athamap_20091028__rc)	0.871	0.508	2.089	0.232	0.914	0.730	0.948	11	30	29	28	13	3	9	17.571	8	; dyads_test_vs_ctrl_m4 versus 5032_NtERF2_Athamap_20091028__rc; m=2/29; ncol2=7; w=7; offset=4; strand=R; shift=4; score=17.5714; ----GGCGGCr--- ; cor=0.871; Ncor=0.508; logoDP=2.089; NIcor=0.232; NsEucl=0.914; SSD=0.730; NSW=0.948; rcor=11; rNcor=30; rlogoDP=29; rNIcor=28; rNsEucl=13; rSSD=3; rNSW=9; rank_mean=17.571; match_rank=8 a 0 0 0 0 0 0 0 1 0 1 4 0 0 0 c 0 0 0 0 1 2 13 2 3 12 1 0 0 0 g 0 0 0 0 13 10 0 11 10 1 7 0 0 0 t 0 0 0 0 0 2 1 0 1 0 2 0 0 0
10654_AT3G23230_M0024_1.02_CISBP_1.02__rc_shift4 (10654_AT3G23230_M0024_1.02_CISBP_1.02__rc)	0.870	0.580	0.223	-0.140	0.926	0.710	0.956	12	11	50	46	6	2	6	19.000	10	; dyads_test_vs_ctrl_m4 versus 10654_AT3G23230_M0024_1.02_CISBP_1.02__rc; m=3/29; ncol2=8; w=8; offset=4; strand=R; shift=4; score= 19; ----GgCGGCks-- ; cor=0.870; Ncor=0.580; logoDP=0.223; NIcor=-0.140; NsEucl=0.926; SSD=0.710; NSW=0.956; rcor=12; rNcor=11; rlogoDP=50; rNIcor=46; rNsEucl=6; rSSD=2; rNSW=6; rank_mean=19.000; match_rank=10 a 0 0 0 0 10 19 1 7 5 4 17 20 0 0 c 0 0 0 0 10 17 76 1 17 80 22 27 0 0 g 0 0 0 0 68 45 4 77 75 6 36 32 0 0 t 0 0 0 0 12 19 19 15 3 10 25 21 0 0
755_M01057_TRANSFAC_2012.1__rc_shift4 (755_M01057_TRANSFAC_2012.1__rc)	0.877	0.512	2.625	0.220	0.904	0.897	0.936	9	28	25	29	27	11	13	20.286	11	; dyads_test_vs_ctrl_m4 versus 755_M01057_TRANSFAC_2012.1__rc; m=4/29; ncol2=7; w=7; offset=4; strand=R; shift=4; score=20.2857; ----GGCGGCG--- ; cor=0.877; Ncor=0.512; logoDP=2.625; NIcor=0.220; NsEucl=0.904; SSD=0.897; NSW=0.936; rcor=9; rNcor=28; rlogoDP=25; rNIcor=29; rNsEucl=27; rSSD=11; rNSW=13; rank_mean=20.286; match_rank=11 a 0 0 0 0 0 0 0 1 0 1 4 0 0 0 c 0 0 0 0 1 2 32 2 6 31 1 0 0 0 g 0 0 0 0 32 28 0 30 26 1 26 0 0 0 t 0 0 0 0 0 3 1 0 1 0 2 0 0 0
10683_ATERF-4_M0022_1.02_CISBP_1.02__rc_shift4 (10683_ATERF-4_M0022_1.02_CISBP_1.02__rc)	0.875	0.584	0.364	-0.174	0.918	0.868	0.946	10	8	48	50	11	9	10	20.857	12	; dyads_test_vs_ctrl_m4 versus 10683_ATERF-4_M0022_1.02_CISBP_1.02__rc; m=5/29; ncol2=8; w=8; offset=4; strand=R; shift=4; score=20.8571; ----GgCGGCGg-- ; cor=0.875; Ncor=0.584; logoDP=0.364; NIcor=-0.174; NsEucl=0.918; SSD=0.868; NSW=0.946; rcor=10; rNcor=8; rlogoDP=48; rNIcor=50; rNsEucl=11; rSSD=9; rNSW=10; rank_mean=20.857; match_rank=12 a 0 0 0 0 4 15 0 0 1 1 9 9 0 0 c 0 0 0 0 4 13 99 1 8 95 12 22 0 0 g 0 0 0 0 80 66 1 98 90 2 73 52 0 0 t 0 0 0 0 12 6 0 1 1 2 6 17 0 0
10682_ATERF-1_M0028_1.02_CISBP_1.02__rc_shift3 (10682_ATERF-1_M0028_1.02_CISBP_1.02__rc)	0.791	0.593	0.964	0.175	0.912	1.251	0.931	29	6	35	31	16	17	17	21.571	14	; dyads_test_vs_ctrl_m4 versus 10682_ATERF-1_M0028_1.02_CISBP_1.02__rc; m=6/29; ncol2=9; w=9; offset=3; strand=R; shift=3; score=21.5714; ---kGrcGGCks-- ; cor=0.791; Ncor=0.593; logoDP=0.964; NIcor=0.175; NsEucl=0.912; SSD=1.251; NSW=0.931; rcor=29; rNcor=6; rlogoDP=35; rNIcor=31; rNsEucl=16; rSSD=17; rNSW=17; rank_mean=21.571; match_rank=14 a 0 0 0 23 12 28 8 6 6 0 12 20 0 0 c 0 0 0 14 7 13 62 3 5 95 11 26 0 0 g 0 0 0 32 68 35 9 78 83 0 47 32 0 0 t 0 0 0 31 13 24 21 13 6 5 30 22 0 0
8786_MA0123_JASPAR_2014__rc_shift4 (8786_MA0123_JASPAR_2014__rc)	0.816	0.466	2.230	0.242	0.913	0.971	0.939	20	39	28	27	14	12	11	21.571	15	; dyads_test_vs_ctrl_m4 versus 8786_MA0123_JASPAR_2014__rc; m=7/29; ncol2=10; w=8; offset=4; strand=R; shift=4; score=21.5714; ----ggggGCrsCG ; cor=0.816; Ncor=0.466; logoDP=2.230; NIcor=0.242; NsEucl=0.913; SSD=0.971; NSW=0.939; rcor=20; rNcor=39; rlogoDP=28; rNIcor=27; rNsEucl=14; rSSD=12; rNSW=11; rank_mean=21.571; match_rank=15 a 0 0 0 0 12 10 10 10 0 0 25 0 0 0 c 0 0 0 0 7 5 11 6 4 45 1 29 37 0 g 0 0 0 0 26 31 25 28 45 3 23 20 0 49 t 0 0 0 0 4 3 3 5 0 1 0 0 12 0
10843_CRF2_M0029_1.02_CISBP_1.02__rc_shift4 (10843_CRF2_M0029_1.02_CISBP_1.02__rc)	0.879	0.586	0.369	-0.154	0.911	1.021	0.936	8	7	47	49	18	13	12	22.000	16	; dyads_test_vs_ctrl_m4 versus 10843_CRF2_M0029_1.02_CISBP_1.02__rc; m=8/29; ncol2=8; w=8; offset=4; strand=R; shift=4; score= 22; ----GGCGGCGs-- ; cor=0.879; Ncor=0.586; logoDP=0.369; NIcor=-0.154; NsEucl=0.911; SSD=1.021; NSW=0.936; rcor=8; rNcor=7; rlogoDP=47; rNIcor=49; rNsEucl=18; rSSD=13; rNSW=12; rank_mean=22.000; match_rank=16 a 0 0 0 0 9 5 0 0 0 0 3 13 0 0 c 0 0 0 0 6 0 100 0 2 100 8 35 0 0 g 0 0 0 0 73 93 0 100 98 0 78 48 0 0 t 0 0 0 0 12 2 0 0 0 0 11 4 0 0
7202_ATERF1_ArabidopsisPBM_20140210__shift4 (7202_ATERF1_ArabidopsisPBM_20140210_)	0.807	0.461	2.357	0.446	0.909	1.060	0.934	25	42	27	11	22	15	16	22.571	19	; dyads_test_vs_ctrl_m4 versus 7202_ATERF1_ArabidopsisPBM_20140210_; m=9/29; ncol2=10; w=8; offset=4; strand=D; shift=4; score=22.5714; ----GGcGsCGsCb ; cor=0.807; Ncor=0.461; logoDP=2.357; NIcor=0.446; NsEucl=0.909; SSD=1.060; NSW=0.934; rcor=25; rNcor=42; rlogoDP=27; rNIcor=11; rNsEucl=22; rSSD=15; rNSW=16; rank_mean=22.571; match_rank=19 a 0 0 0 0 5 4 19 3 4 6 7 8 6 9 c 0 0 0 0 3 15 60 2 48 85 9 52 80 37 g 0 0 0 0 83 71 15 93 38 5 73 35 10 29 t 0 0 0 0 9 10 6 2 10 4 11 5 4 25
2148_M03201_TRANSFAC_2012.1__rc_shift2 (2148_M03201_TRANSFAC_2012.1__rc)	0.782	0.651	3.457	0.321	0.906	1.751	0.912	32	2	20	18	25	36	29	23.143	21	; dyads_test_vs_ctrl_m4 versus 2148_M03201_TRANSFAC_2012.1__rc; m=10/29; ncol2=10; w=10; offset=2; strand=R; shift=2; score=23.1429; --krGsCGGCAw-- ; cor=0.782; Ncor=0.651; logoDP=3.457; NIcor=0.321; NsEucl=0.906; SSD=1.751; NSW=0.912; rcor=32; rNcor=2; rlogoDP=20; rNIcor=18; rNsEucl=25; rSSD=36; rNSW=29; rank_mean=23.143; match_rank=21 a 0 0 1 41 15 1 0 0 0 0 69 28 0 0 c 0 0 22 7 0 32 100 0 0 100 20 17 0 0 g 0 0 49 31 85 56 0 100 100 0 11 22 0 0 t 0 0 28 21 0 11 0 0 0 0 0 33 0 0
10845_CRF4_M0033_1.02_CISBP_1.02__rc_shift4 (10845_CRF4_M0033_1.02_CISBP_1.02__rc)	0.865	0.576	0.437	-0.122	0.909	1.056	0.934	13	13	45	43	21	14	15	23.429	22	; dyads_test_vs_ctrl_m4 versus 10845_CRF4_M0033_1.02_CISBP_1.02__rc; m=11/29; ncol2=8; w=8; offset=4; strand=R; shift=4; score=23.4286; ----GGCGGCGs-- ; cor=0.865; Ncor=0.576; logoDP=0.437; NIcor=-0.122; NsEucl=0.909; SSD=1.056; NSW=0.934; rcor=13; rNcor=13; rlogoDP=45; rNIcor=43; rNsEucl=21; rSSD=14; rNSW=15; rank_mean=23.429; match_rank=22 a 0 0 0 0 5 11 0 0 0 0 6 7 0 0 c 0 0 0 0 6 7 99 0 3 100 6 53 0 0 g 0 0 0 0 79 75 1 100 97 0 77 33 0 0 t 0 0 0 0 10 7 0 0 0 0 11 7 0 0
10844_CRF3_M0041_1.02_CISBP_1.02__rc_shift3 (10844_CRF3_M0041_1.02_CISBP_1.02__rc)	0.776	0.582	0.947	0.198	0.909	1.332	0.926	38	9	36	30	20	18	18	24.143	23	; dyads_test_vs_ctrl_m4 versus 10844_CRF3_M0041_1.02_CISBP_1.02__rc; m=12/29; ncol2=9; w=9; offset=3; strand=R; shift=3; score=24.1429; ---tggcGGCgs-- ; cor=0.776; Ncor=0.582; logoDP=0.947; NIcor=0.198; NsEucl=0.909; SSD=1.332; NSW=0.926; rcor=38; rNcor=9; rlogoDP=36; rNIcor=30; rNsEucl=20; rSSD=18; rNSW=18; rank_mean=24.143; match_rank=23 a 0 0 0 21 19 24 11 7 5 0 14 20 0 0 c 0 0 0 21 13 14 62 6 5 94 16 30 0 0 g 0 0 0 24 46 42 10 77 88 0 48 31 0 0 t 0 0 0 34 22 20 17 10 2 6 22 19 0 0
11540_ORA59_M0005_1.02_CISBP_1.02__rc_shift3 (11540_ORA59_M0005_1.02_CISBP_1.02__rc)	0.818	0.545	3.669	0.287	0.893	1.453	0.909	19	19	17	21	38	23	33	24.286	24	; dyads_test_vs_ctrl_m4 versus 11540_ORA59_M0005_1.02_CISBP_1.02__rc; m=13/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=24.2857; ---cGGCGGCk--- ; cor=0.818; Ncor=0.545; logoDP=3.669; NIcor=0.287; NsEucl=0.893; SSD=1.453; NSW=0.909; rcor=19; rNcor=19; rlogoDP=17; rNIcor=21; rNsEucl=38; rSSD=23; rNSW=33; rank_mean=24.286; match_rank=24 a 0 0 0 17 0 0 0 0 0 0 0 0 0 0 c 0 0 0 49 0 5 98 0 0 100 19 0 0 0 g 0 0 0 10 100 95 0 88 100 0 46 0 0 0 t 0 0 0 24 0 0 2 12 0 0 35 0 0 0
10686_ATERF13_M0020_1.02_CISBP_1.02__rc_shift3 (10686_ATERF13_M0020_1.02_CISBP_1.02__rc)	0.803	0.535	3.371	0.289	0.894	1.431	0.911	27	24	22	20	37	22	32	26.286	28	; dyads_test_vs_ctrl_m4 versus 10686_ATERF13_M0020_1.02_CISBP_1.02__rc; m=14/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=26.2857; ---yGgCGGCs--- ; cor=0.803; Ncor=0.535; logoDP=3.371; NIcor=0.289; NsEucl=0.894; SSD=1.431; NSW=0.911; rcor=27; rNcor=24; rlogoDP=22; rNIcor=20; rNsEucl=37; rSSD=22; rNSW=32; rank_mean=26.286; match_rank=28 a 0 0 0 15 0 11 0 0 0 0 2 0 0 0 c 0 0 0 28 0 15 98 2 3 95 28 0 0 0 g 0 0 0 10 100 64 2 98 95 5 48 0 0 0 t 0 0 0 47 0 10 0 0 2 0 22 0 0 0
7216_DEAR4_2_ArabidopsisPBM_20140210__rc_shift3 (7216_DEAR4_2_ArabidopsisPBM_20140210__rc)	0.813	0.563	0.777	-0.074	0.901	1.573	0.913	22	16	39	37	31	29	28	28.857	31	; dyads_test_vs_ctrl_m4 versus 7216_DEAR4_2_ArabidopsisPBM_20140210__rc; m=15/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score=28.8571; ---aGGCGGCGCy- ; cor=0.813; Ncor=0.563; logoDP=0.777; NIcor=-0.074; NsEucl=0.901; SSD=1.573; NSW=0.913; rcor=22; rNcor=16; rlogoDP=39; rNIcor=37; rNsEucl=31; rSSD=29; rNSW=28; rank_mean=28.857; match_rank=31 a 0 0 0 61 9 7 3 1 0 1 2 8 12 0 c 0 0 0 15 2 8 95 1 8 87 2 76 37 0 g 0 0 0 21 86 84 1 98 91 0 94 13 22 0 t 0 0 0 3 3 1 1 0 1 12 2 3 29 0
7219_DREB2C_ArabidopsisPBM_20140210__rc_shift4 (7219_DREB2C_ArabidopsisPBM_20140210__rc)	0.809	0.462	4.093	0.428	0.885	1.685	0.895	24	40	13	13	43	33	38	29.143	32	; dyads_test_vs_ctrl_m4 versus 7219_DREB2C_ArabidopsisPBM_20140210__rc; m=16/29; ncol2=10; w=8; offset=4; strand=R; shift=4; score=29.1429; ----gGCGGCCGCc ; cor=0.809; Ncor=0.462; logoDP=4.093; NIcor=0.428; NsEucl=0.885; SSD=1.685; NSW=0.895; rcor=24; rNcor=40; rlogoDP=13; rNIcor=13; rNsEucl=43; rSSD=33; rNSW=38; rank_mean=29.143; match_rank=32 a 0 0 0 0 13 2 0 1 3 0 0 4 3 14 c 0 0 0 0 7 2 96 5 0 97 94 0 92 67 g 0 0 0 0 67 93 0 94 97 0 5 96 2 5 t 0 0 0 0 13 3 4 0 0 3 1 0 3 14
10960_ERF1_M0025_1.02_CISBP_1.02__rc_shift2 (10960_ERF1_M0025_1.02_CISBP_1.02__rc)	0.750	0.625	3.700	0.318	0.895	2.197	0.890	52	4	16	19	34	46	41	30.286	34	; dyads_test_vs_ctrl_m4 versus 10960_ERF1_M0025_1.02_CISBP_1.02__rc; m=17/29; ncol2=10; w=10; offset=2; strand=R; shift=2; score=30.2857; --ryGGCGGCks-- ; cor=0.750; Ncor=0.625; logoDP=3.700; NIcor=0.318; NsEucl=0.895; SSD=2.197; NSW=0.890; rcor=52; rNcor=4; rlogoDP=16; rNIcor=19; rNsEucl=34; rSSD=46; rNSW=41; rank_mean=30.286; match_rank=34 a 0 0 35 7 0 0 0 0 0 0 10 17 0 0 c 0 0 24 49 0 0 100 0 0 100 10 27 0 0 g 0 0 26 8 100 100 0 100 100 0 50 38 0 0 t 0 0 15 36 0 0 0 0 0 0 30 18 0 0
10961_ERF2_M0038_1.02_CISBP_1.02__rc_shift3 (10961_ERF2_M0038_1.02_CISBP_1.02__rc)	0.778	0.539	0.181	-0.139	0.909	1.346	0.925	35	22	51	45	23	19	20	30.714	35	; dyads_test_vs_ctrl_m4 versus 10961_ERF2_M0038_1.02_CISBP_1.02__rc; m=18/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score=30.7143; ---tGgCGGCksd- ; cor=0.778; Ncor=0.539; logoDP=0.181; NIcor=-0.139; NsEucl=0.909; SSD=1.346; NSW=0.925; rcor=35; rNcor=22; rlogoDP=51; rNIcor=45; rNsEucl=23; rSSD=19; rNSW=20; rank_mean=30.714; match_rank=35 a 0 0 0 22 11 21 4 8 7 6 15 23 27 0 c 0 0 0 22 9 15 77 4 14 73 24 27 21 0 g 0 0 0 22 68 46 3 71 70 8 32 27 26 0 t 0 0 0 34 12 18 16 17 9 13 29 23 26 0
2154_M03207_TRANSFAC_2012.1__rc_shift2 (2154_M03207_TRANSFAC_2012.1__rc)	0.760	0.633	3.741	0.272	0.894	2.226	0.889	46	3	15	24	36	48	43	30.714	36	; dyads_test_vs_ctrl_m4 versus 2154_M03207_TRANSFAC_2012.1__rc; m=19/29; ncol2=10; w=10; offset=2; strand=R; shift=2; score=30.7143; --GTGGCGGCmw-- ; cor=0.760; Ncor=0.633; logoDP=3.741; NIcor=0.272; NsEucl=0.894; SSD=2.226; NSW=0.889; rcor=46; rNcor=3; rlogoDP=15; rNIcor=24; rNsEucl=36; rSSD=48; rNSW=43; rank_mean=30.714; match_rank=36 a 0 0 1 0 1 0 0 0 0 0 38 27 0 0 c 0 0 2 6 0 19 100 0 0 100 49 18 0 0 g 0 0 93 20 99 69 0 100 100 0 13 22 0 0 t 0 0 4 74 0 12 0 0 0 0 0 33 0 0
9050_MA0567_JASPAR_2014__rc_shift3 (9050_MA0567_JASPAR_2014__rc)	0.791	0.527	3.336	0.280	0.885	1.686	0.895	30	27	23	23	44	34	39	31.429	37	; dyads_test_vs_ctrl_m4 versus 9050_MA0567_JASPAR_2014__rc; m=20/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=31.4286; ---tGGCGGCk--- ; cor=0.791; Ncor=0.527; logoDP=3.336; NIcor=0.280; NsEucl=0.885; SSD=1.686; NSW=0.895; rcor=30; rNcor=27; rlogoDP=23; rNIcor=23; rNsEucl=44; rSSD=34; rNSW=39; rank_mean=31.429; match_rank=37 a 0 0 0 12 1 4 1 0 1 1 1 0 0 0 c 0 0 0 24 1 2 97 0 1 98 3 0 0 0 g 0 0 0 5 98 92 0 96 98 1 54 0 0 0 t 0 0 0 58 1 2 2 4 0 1 42 0 0 0
10660_AT4G00270_M1620_1.02_CISBP_1.02__rc_shift5 (10660_AT4G00270_M1620_1.02_CISBP_1.02__rc)	0.793	0.427	3.622	0.352	0.874	1.557	0.889	28	50	19	17	48	26	42	32.857	38	; dyads_test_vs_ctrl_m4 versus 10660_AT4G00270_M1620_1.02_CISBP_1.02__rc; m=21/29; ncol2=8; w=7; offset=5; strand=R; shift=5; score=32.8571; -----gCGGCCGg- ; cor=0.793; Ncor=0.427; logoDP=3.622; NIcor=0.352; NsEucl=0.874; SSD=1.557; NSW=0.889; rcor=28; rNcor=50; rlogoDP=19; rNIcor=17; rNsEucl=48; rSSD=26; rNSW=42; rank_mean=32.857; match_rank=38 a 0 0 0 0 0 14 3 0 0 0 0 5 16 0 c 0 0 0 0 0 4 97 0 0 100 97 0 4 0 g 0 0 0 0 0 61 0 100 95 0 0 81 56 0 t 0 0 0 0 0 21 0 0 5 0 3 14 24 0
7246_ORA47_2_ArabidopsisPBM_20140210__rc_shift3 (7246_ORA47_2_ArabidopsisPBM_20140210__rc)	0.783	0.542	0.682	-0.090	0.896	1.768	0.902	31	20	41	39	33	37	35	33.714	39	; dyads_test_vs_ctrl_m4 versus 7246_ORA47_2_ArabidopsisPBM_20140210__rc; m=22/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score=33.7143; ---rGkCGGCGCm- ; cor=0.783; Ncor=0.542; logoDP=0.682; NIcor=-0.090; NsEucl=0.896; SSD=1.768; NSW=0.902; rcor=31; rNcor=20; rlogoDP=41; rNIcor=39; rNsEucl=33; rSSD=37; rNSW=35; rank_mean=33.714; match_rank=39 a 0 0 0 42 2 5 2 0 0 0 4 5 47 0 c 0 0 0 13 1 5 97 1 4 92 1 73 30 0 g 0 0 0 25 93 65 0 98 96 1 93 13 6 0 t 0 0 0 20 4 25 1 1 0 7 2 9 17 0
10565_0100010458_M0076_1.02_CISBP_1.02__rc_shift3 (10565_0100010458_M0076_1.02_CISBP_1.02__rc)	0.767	0.511	3.866	0.284	0.881	1.803	0.887	42	29	14	22	47	40	46	34.286	41	; dyads_test_vs_ctrl_m4 versus 10565_0100010458_M0076_1.02_CISBP_1.02__rc; m=23/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=34.2857; ---yGGCGGCg--- ; cor=0.767; Ncor=0.511; logoDP=3.866; NIcor=0.284; NsEucl=0.881; SSD=1.803; NSW=0.887; rcor=42; rNcor=29; rlogoDP=14; rNIcor=22; rNsEucl=47; rSSD=40; rNSW=46; rank_mean=34.286; match_rank=41 a 0 0 0 6 0 5 0 0 0 0 8 0 0 0 c 0 0 0 32 0 22 100 2 8 100 13 0 0 0 g 0 0 0 3 100 71 0 98 92 0 61 0 0 0 t 0 0 0 59 0 2 0 0 0 0 18 0 0 0
11601_PK19363.1_M0004_1.02_CISBP_1.02__rc_shift3 (11601_PK19363.1_M0004_1.02_CISBP_1.02__rc)	0.757	0.505	2.923	0.261	0.886	1.670	0.896	47	34	24	26	42	31	37	34.429	42	; dyads_test_vs_ctrl_m4 versus 11601_PK19363.1_M0004_1.02_CISBP_1.02__rc; m=24/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=34.4286; ---yGgCGGCG--- ; cor=0.757; Ncor=0.505; logoDP=2.923; NIcor=0.261; NsEucl=0.886; SSD=1.670; NSW=0.896; rcor=47; rNcor=34; rlogoDP=24; rNIcor=26; rNsEucl=42; rSSD=31; rNSW=37; rank_mean=34.429; match_rank=42 a 0 0 0 14 6 17 0 0 0 1 6 0 0 0 c 0 0 0 30 1 14 99 1 11 95 7 0 0 0 g 0 0 0 7 77 63 1 97 87 1 72 0 0 0 t 0 0 0 49 16 6 0 2 2 3 15 0 0 0
10963_ERF5_M0039_1.02_CISBP_1.02__rc_shift3 (10963_ERF5_M0039_1.02_CISBP_1.02__rc)	0.767	0.531	0.162	-0.143	0.904	1.488	0.917	43	25	52	47	28	24	25	34.857	43	; dyads_test_vs_ctrl_m4 versus 10963_ERF5_M0039_1.02_CISBP_1.02__rc; m=25/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score=34.8571; ---kggcggCksd- ; cor=0.767; Ncor=0.531; logoDP=0.162; NIcor=-0.143; NsEucl=0.904; SSD=1.488; NSW=0.917; rcor=43; rNcor=25; rlogoDP=52; rNIcor=47; rNsEucl=28; rSSD=24; rNSW=25; rank_mean=34.857; match_rank=43 a 0 0 0 21 12 24 8 7 9 5 17 23 25 0 c 0 0 0 17 11 21 59 7 18 75 19 27 21 0 g 0 0 0 29 60 35 12 67 61 6 36 27 27 0 t 0 0 0 33 17 20 21 19 12 14 28 23 27 0
10962_ERF3_M0011_1.02_CISBP_1.02__rc_shift3 (10962_ERF3_M0011_1.02_CISBP_1.02__rc)	0.761	0.507	3.404	0.266	0.882	1.787	0.888	45	33	21	25	45	38	44	35.857	45	; dyads_test_vs_ctrl_m4 versus 10962_ERF3_M0011_1.02_CISBP_1.02__rc; m=26/29; ncol2=8; w=8; offset=3; strand=R; shift=3; score=35.8571; ---yGgCGGCG--- ; cor=0.761; Ncor=0.507; logoDP=3.404; NIcor=0.266; NsEucl=0.882; SSD=1.787; NSW=0.888; rcor=45; rNcor=33; rlogoDP=21; rNIcor=25; rNsEucl=45; rSSD=38; rNSW=44; rank_mean=35.857; match_rank=45 a 0 0 0 12 2 11 0 0 0 0 8 0 0 0 c 0 0 0 28 0 19 99 1 11 99 8 0 0 0 g 0 0 0 2 90 64 0 99 89 0 76 0 0 0 t 0 0 0 58 8 6 1 0 0 1 8 0 0 0
10649_AT2G33710_M0018_1.02_CISBP_1.02__rc_shift3 (10649_AT2G33710_M0018_1.02_CISBP_1.02__rc)	0.762	0.528	0.278	-0.143	0.902	1.571	0.913	44	26	49	48	30	28	27	36.000	47	; dyads_test_vs_ctrl_m4 versus 10649_AT2G33710_M0018_1.02_CISBP_1.02__rc; m=27/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score= 36; ---tggCGGCgsc- ; cor=0.762; Ncor=0.528; logoDP=0.278; NIcor=-0.143; NsEucl=0.902; SSD=1.571; NSW=0.913; rcor=44; rNcor=26; rlogoDP=49; rNIcor=48; rNsEucl=30; rSSD=28; rNSW=27; rank_mean=36.000; match_rank=47 a 0 0 0 15 6 21 3 0 0 7 5 12 18 0 c 0 0 0 24 4 10 90 0 0 92 12 34 39 0 g 0 0 0 13 66 52 3 95 100 0 61 44 24 0 t 0 0 0 48 24 17 4 5 0 1 22 10 19 0
7221_ERF1_ArabidopsisPBM_20140210__rc_shift3 (7221_ERF1_ArabidopsisPBM_20140210__rc)	0.774	0.536	0.373	-0.115	0.892	1.900	0.894	39	23	46	41	39	42	40	38.571	50	; dyads_test_vs_ctrl_m4 versus 7221_ERF1_ArabidopsisPBM_20140210__rc; m=28/29; ncol2=10; w=9; offset=3; strand=R; shift=3; score=38.5714; ---tGGCGGCGsy- ; cor=0.774; Ncor=0.536; logoDP=0.373; NIcor=-0.115; NsEucl=0.892; SSD=1.900; NSW=0.894; rcor=39; rNcor=23; rlogoDP=46; rNIcor=41; rNsEucl=39; rSSD=42; rNSW=40; rank_mean=38.571; match_rank=50 a 0 0 0 12 1 3 1 1 1 1 2 15 23 0 c 0 0 0 24 1 2 97 0 3 97 1 46 27 0 g 0 0 0 5 97 90 0 95 96 1 82 33 12 0 t 0 0 0 59 1 5 2 4 0 1 15 6 38 0
4995_ABI4_Athamap_20091028__rc_shift4 (4995_ABI4_Athamap_20091028__rc)	0.751	0.429	2.548	0.138	0.882	1.788	0.888	50	49	26	32	46	39	45	41.000	51	; dyads_test_vs_ctrl_m4 versus 4995_ABI4_Athamap_20091028__rc; m=29/29; ncol2=10; w=8; offset=4; strand=R; shift=4; score= 41; ----sggGGCGGyG ; cor=0.751; Ncor=0.429; logoDP=2.548; NIcor=0.138; NsEucl=0.882; SSD=1.788; NSW=0.888; rcor=50; rNcor=49; rlogoDP=26; rNIcor=32; rNsEucl=46; rSSD=39; rNSW=45; rank_mean=41.000; match_rank=51 a 0 0 0 0 4 2 1 0 0 0 0 0 0 1 c 0 0 0 0 6 4 5 0 0 20 0 0 9 0 g 0 0 0 0 7 13 14 20 21 0 21 21 0 20 t 0 0 0 0 4 2 1 1 0 1 0 0 12 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m1_shift0 ; 3 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_5-7nt_m1_shift0 (oligos_5-7nt_m1)
; oligos_5-7nt_m1; m=0 (reference); ncol1=20; shift=0; ncol=20; grrggwTkTGGCGGGAAgrg ; Alignment reference a 5 9 10 8 3 13 3 5 1 0 2 1 0 2 0 33 29 7 13 6 c 4 3 3 8 6 4 6 2 1 2 0 32 0 3 4 1 0 1 6 8 g 21 17 17 13 21 8 2 10 2 33 33 1 34 30 31 1 5 23 9 17 t 5 6 5 6 5 10 24 18 31 0 0 1 1 0 0 0 1 4 7 4

5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc_shift6 (5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc) 0.922 0.507 1.522 -0.041 0.941 0.852 0.961 6 31 32 35 3 7 3 16.714 7
; oligos_5-7nt_m1 versus 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc; m=1/2; ncol2=11; w=11; offset=6; strand=R; shift=6; score=16.7143; ------wwkgGCGGGAA--- ; cor=0.922; Ncor=0.507; logoDP=1.522; NIcor=-0.041; NsEucl=0.941; SSD=0.852; NSW=0.961; rcor=6; rNcor=31; rlogoDP=32; rNIcor=35; rNsEucl=3; rSSD=7; rNSW=3; rank_mean=16.714; match_rank=7 a 0 0 0 0 0 0 2 2 0 1 0 0 0 0 0 4 4 0 0 0 c 0 0 0 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 2 3 5 0 5 4 5 0 0 0 0 0 t 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 1 1 0 0 0

802_M01114_TRANSFAC_2012.1__rc_shift9 (802_M01114_TRANSFAC_2012.1__rc) 0.826 0.454 0.824 -0.091 0.916 1.709 0.922 18 44 38 40 12 35 22 29.857 33
; oligos_5-7nt_m1 versus 802_M01114_TRANSFAC_2012.1__rc; m=2/2; ncol2=11; w=11; offset=9; strand=R; shift=9; score=29.8571; ---------ssCGsSAAArr ; cor=0.826; Ncor=0.454; logoDP=0.824; NIcor=-0.091; NsEucl=0.916; SSD=1.709; NSW=0.922; rcor=18; rNcor=44; rlogoDP=38; rNIcor=40; rNsEucl=12; rSSD=35; rNSW=22; rank_mean=29.857; match_rank=33 a 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 15 15 13 6 7 c 0 0 0 0 0 0 0 0 0 4 5 15 0 5 4 0 0 0 3 1 g 0 0 0 0 0 0 0 0 0 8 10 0 15 10 11 0 0 0 4 4 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-7nt_m1_shift0 (oligos_5-7nt_m1)																	; oligos_5-7nt_m1; m=0 (reference); ncol1=20; shift=0; ncol=20; grrggwTkTGGCGGGAAgrg ; Alignment reference a 5 9 10 8 3 13 3 5 1 0 2 1 0 2 0 33 29 7 13 6 c 4 3 3 8 6 4 6 2 1 2 0 32 0 3 4 1 0 1 6 8 g 21 17 17 13 21 8 2 10 2 33 33 1 34 30 31 1 5 23 9 17 t 5 6 5 6 5 10 24 18 31 0 0 1 1 0 0 0 1 4 7 4
5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc_shift6 (5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc)	0.922	0.507	1.522	-0.041	0.941	0.852	0.961	6	31	32	35	3	7	3	16.714	7	; oligos_5-7nt_m1 versus 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc; m=1/2; ncol2=11; w=11; offset=6; strand=R; shift=6; score=16.7143; ------wwkgGCGGGAA--- ; cor=0.922; Ncor=0.507; logoDP=1.522; NIcor=-0.041; NsEucl=0.941; SSD=0.852; NSW=0.961; rcor=6; rNcor=31; rlogoDP=32; rNIcor=35; rNsEucl=3; rSSD=7; rNSW=3; rank_mean=16.714; match_rank=7 a 0 0 0 0 0 0 2 2 0 1 0 0 0 0 0 4 4 0 0 0 c 0 0 0 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 2 3 5 0 5 4 5 0 0 0 0 0 t 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 1 1 0 0 0
802_M01114_TRANSFAC_2012.1__rc_shift9 (802_M01114_TRANSFAC_2012.1__rc)	0.826	0.454	0.824	-0.091	0.916	1.709	0.922	18	44	38	40	12	35	22	29.857	33	; oligos_5-7nt_m1 versus 802_M01114_TRANSFAC_2012.1__rc; m=2/2; ncol2=11; w=11; offset=9; strand=R; shift=9; score=29.8571; ---------ssCGsSAAArr ; cor=0.826; Ncor=0.454; logoDP=0.824; NIcor=-0.091; NsEucl=0.916; SSD=1.709; NSW=0.922; rcor=18; rNcor=44; rlogoDP=38; rNIcor=40; rNsEucl=12; rSSD=35; rNSW=22; rank_mean=29.857; match_rank=33 a 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 15 15 13 6 7 c 0 0 0 0 0 0 0 0 0 4 5 15 0 5 4 0 0 0 3 1 g 0 0 0 0 0 0 0 0 0 8 10 0 15 10 11 0 0 0 4 4 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m3_shift0 ; 3 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_5-7nt_m3_shift0 (oligos_5-7nt_m3)
; oligos_5-7nt_m3; m=0 (reference); ncol1=22; shift=0; ncol=22; grgsgdtkTGGCGGGAArwgkg ; Alignment reference a 5 11 7 6 5 10 5 7 0 1 0 0 0 1 0 32 27 12 17 5 6 6 c 4 3 2 8 6 5 6 0 2 1 1 29 0 1 2 0 0 1 2 4 5 4 g 20 13 19 12 15 9 3 10 1 29 31 1 30 30 30 0 5 15 5 17 13 17 t 3 5 4 6 6 8 18 15 29 1 0 2 2 0 0 0 0 4 8 6 8 5

5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc_shift6 (5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc) 0.923 0.462 1.647 -0.057 0.940 0.864 0.961 5 41 31 36 4 8 4 18.429 9
; oligos_5-7nt_m3 versus 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc; m=1/2; ncol2=11; w=11; offset=6; strand=R; shift=6; score=18.4286; ------wwkgGCGGGAA----- ; cor=0.923; Ncor=0.462; logoDP=1.647; NIcor=-0.057; NsEucl=0.940; SSD=0.864; NSW=0.961; rcor=5; rNcor=41; rlogoDP=31; rNIcor=36; rNsEucl=4; rSSD=8; rNSW=4; rank_mean=18.429; match_rank=9 a 0 0 0 0 0 0 2 2 0 1 0 0 0 0 0 4 4 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 2 3 5 0 5 4 5 0 0 0 0 0 0 0 t 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 1 1 0 0 0 0 0

802_M01114_TRANSFAC_2012.1__rc_shift9 (802_M01114_TRANSFAC_2012.1__rc) 0.861 0.430 0.690 -0.117 0.923 1.420 0.935 14 47 40 42 7 21 14 26.429 29
; oligos_5-7nt_m3 versus 802_M01114_TRANSFAC_2012.1__rc; m=2/2; ncol2=11; w=11; offset=9; strand=R; shift=9; score=26.4286; ---------ssCGsSAAArr-- ; cor=0.861; Ncor=0.430; logoDP=0.690; NIcor=-0.117; NsEucl=0.923; SSD=1.420; NSW=0.935; rcor=14; rNcor=47; rlogoDP=40; rNIcor=42; rNsEucl=7; rSSD=21; rNSW=14; rank_mean=26.429; match_rank=29 a 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 15 15 13 6 7 0 0 c 0 0 0 0 0 0 0 0 0 4 5 15 0 5 4 0 0 0 3 1 0 0 g 0 0 0 0 0 0 0 0 0 8 10 0 15 10 11 0 0 0 4 4 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3 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_5-7nt_m3_shift0 (oligos_5-7nt_m3)																	; oligos_5-7nt_m3; m=0 (reference); ncol1=22; shift=0; ncol=22; grgsgdtkTGGCGGGAArwgkg ; Alignment reference a 5 11 7 6 5 10 5 7 0 1 0 0 0 1 0 32 27 12 17 5 6 6 c 4 3 2 8 6 5 6 0 2 1 1 29 0 1 2 0 0 1 2 4 5 4 g 20 13 19 12 15 9 3 10 1 29 31 1 30 30 30 0 5 15 5 17 13 17 t 3 5 4 6 6 8 18 15 29 1 0 2 2 0 0 0 0 4 8 6 8 5
5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc_shift6 (5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc)	0.923	0.462	1.647	-0.057	0.940	0.864	0.961	5	41	31	36	4	8	4	18.429	9	; oligos_5-7nt_m3 versus 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__rc; m=1/2; ncol2=11; w=11; offset=6; strand=R; shift=6; score=18.4286; ------wwkgGCGGGAA----- ; cor=0.923; Ncor=0.462; logoDP=1.647; NIcor=-0.057; NsEucl=0.940; SSD=0.864; NSW=0.961; rcor=5; rNcor=41; rlogoDP=31; rNIcor=36; rNsEucl=4; rSSD=8; rNSW=4; rank_mean=18.429; match_rank=9 a 0 0 0 0 0 0 2 2 0 1 0 0 0 0 0 4 4 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 2 3 5 0 5 4 5 0 0 0 0 0 0 0 t 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 1 1 0 0 0 0 0
802_M01114_TRANSFAC_2012.1__rc_shift9 (802_M01114_TRANSFAC_2012.1__rc)	0.861	0.430	0.690	-0.117	0.923	1.420	0.935	14	47	40	42	7	21	14	26.429	29	; oligos_5-7nt_m3 versus 802_M01114_TRANSFAC_2012.1__rc; m=2/2; ncol2=11; w=11; offset=9; strand=R; shift=9; score=26.4286; ---------ssCGsSAAArr-- ; cor=0.861; Ncor=0.430; logoDP=0.690; NIcor=-0.117; NsEucl=0.923; SSD=1.420; NSW=0.935; rcor=14; rNcor=47; rlogoDP=40; rNIcor=42; rNsEucl=7; rSSD=21; rNSW=14; rank_mean=26.429; match_rank=29 a 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 15 15 13 6 7 0 0 c 0 0 0 0 0 0 0 0 0 4 5 15 0 5 4 0 0 0 3 1 0 0 g 0 0 0 0 0 0 0 0 0 8 10 0 15 10 11 0 0 0 4 4 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3 0 0

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m3_shift0 ; 4 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_test_vs_ctrl_m3_shift0 (dyads_test_vs_ctrl_m3)
; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; gwctTCCAGCCCAad ; Alignment reference a 4 6 5 1 0 2 1 15 1 1 0 3 19 10 6 c 5 4 13 3 2 18 21 5 0 20 20 18 2 4 4 g 8 4 4 4 1 0 0 1 20 1 2 1 0 4 6 t 5 8 0 14 19 2 0 1 1 0 0 0 1 4 6

5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__shift3 (5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_) 0.779 0.572 6.027 0.536 0.904 2.241 0.898 34 14 8 6 29 49 36 25.143 25
; dyads_test_vs_ctrl_m3 versus 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_; m=1/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score=25.1429; ---TTCCCGCcmww- ; cor=0.779; Ncor=0.572; logoDP=6.027; NIcor=0.536; NsEucl=0.904; SSD=2.241; NSW=0.898; rcor=34; rNcor=14; rlogoDP=8; rNIcor=6; rNsEucl=29; rSSD=49; rNSW=36; rank_mean=25.143; match_rank=25 a 0 0 0 1 1 0 0 0 0 0 0 3 3 3 0 c 0 0 0 0 0 5 4 5 0 5 3 2 0 0 0 g 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 t 0 0 0 4 4 0 0 0 0 0 1 0 2 2 0

5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028__shift2 (5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_) 0.778 0.415 6.644 0.429 0.869 2.197 0.863 36 51 5 12 50 47 50 35.857 46
; dyads_test_vs_ctrl_m3 versus 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_; m=2/3; ncol2=8; w=8; offset=2; strand=D; shift=2; score=35.8571; --wTTCCCGC----- ; cor=0.778; Ncor=0.415; logoDP=6.644; NIcor=0.429; NsEucl=0.869; SSD=2.197; NSW=0.863; rcor=36; rNcor=51; rlogoDP=5; rNIcor=12; rNsEucl=50; rSSD=47; rNSW=50; rank_mean=35.857; match_rank=46 a 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 3 3 3 0 3 0 0 0 0 0 g 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 t 0 0 2 3 3 0 0 0 0 0 0 0 0 0 0

5015_E2Fb_Athamap_20091028__shift2 (5015_E2Fb_Athamap_20091028_) 0.768 0.410 6.640 0.425 0.866 2.305 0.856 41 52 6 16 52 51 52 38.571 49
; dyads_test_vs_ctrl_m3 versus 5015_E2Fb_Athamap_20091028_; m=3/3; ncol2=8; w=8; offset=2; strand=D; shift=2; score=38.5714; --WTTCCCGC----- ; cor=0.768; Ncor=0.410; logoDP=6.640; NIcor=0.425; NsEucl=0.866; SSD=2.305; NSW=0.856; rcor=41; rNcor=52; rlogoDP=6; rNIcor=16; rNsEucl=52; rSSD=51; rNSW=52; rank_mean=38.571; match_rank=49 a 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 4 4 4 0 4 0 0 0 0 0 g 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 t 0 0 3 4 4 0 0 0 0 0 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
dyads_test_vs_ctrl_m3_shift0 (dyads_test_vs_ctrl_m3)																	; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; gwctTCCAGCCCAad ; Alignment reference a 4 6 5 1 0 2 1 15 1 1 0 3 19 10 6 c 5 4 13 3 2 18 21 5 0 20 20 18 2 4 4 g 8 4 4 4 1 0 0 1 20 1 2 1 0 4 6 t 5 8 0 14 19 2 0 1 1 0 0 0 1 4 6
5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028__shift3 (5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_)	0.779	0.572	6.027	0.536	0.904	2.241	0.898	34	14	8	6	29	49	36	25.143	25	; dyads_test_vs_ctrl_m3 versus 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_; m=1/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score=25.1429; ---TTCCCGCcmww- ; cor=0.779; Ncor=0.572; logoDP=6.027; NIcor=0.536; NsEucl=0.904; SSD=2.241; NSW=0.898; rcor=34; rNcor=14; rlogoDP=8; rNIcor=6; rNsEucl=29; rSSD=49; rNSW=36; rank_mean=25.143; match_rank=25 a 0 0 0 1 1 0 0 0 0 0 0 3 3 3 0 c 0 0 0 0 0 5 4 5 0 5 3 2 0 0 0 g 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 t 0 0 0 4 4 0 0 0 0 0 1 0 2 2 0
5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028__shift2 (5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_)	0.778	0.415	6.644	0.429	0.869	2.197	0.863	36	51	5	12	50	47	50	35.857	46	; dyads_test_vs_ctrl_m3 versus 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_; m=2/3; ncol2=8; w=8; offset=2; strand=D; shift=2; score=35.8571; --wTTCCCGC----- ; cor=0.778; Ncor=0.415; logoDP=6.644; NIcor=0.429; NsEucl=0.869; SSD=2.197; NSW=0.863; rcor=36; rNcor=51; rlogoDP=5; rNIcor=12; rNsEucl=50; rSSD=47; rNSW=50; rank_mean=35.857; match_rank=46 a 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 3 3 3 0 3 0 0 0 0 0 g 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 t 0 0 2 3 3 0 0 0 0 0 0 0 0 0 0
5015_E2Fb_Athamap_20091028__shift2 (5015_E2Fb_Athamap_20091028_)	0.768	0.410	6.640	0.425	0.866	2.305	0.856	41	52	6	16	52	51	52	38.571	49	; dyads_test_vs_ctrl_m3 versus 5015_E2Fb_Athamap_20091028_; m=3/3; ncol2=8; w=8; offset=2; strand=D; shift=2; score=38.5714; --WTTCCCGC----- ; cor=0.768; Ncor=0.410; logoDP=6.640; NIcor=0.425; NsEucl=0.866; SSD=2.305; NSW=0.856; rcor=41; rNcor=52; rlogoDP=6; rNIcor=16; rNsEucl=52; rSSD=51; rNSW=52; rank_mean=38.571; match_rank=49 a 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 4 4 4 0 4 0 0 0 0 0 g 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 t 0 0 3 4 4 0 0 0 0 0 0 0 0 0 0