One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 10/regulon10.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 10/regulon10.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m1_shift4 ; 13 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_shift4 (oligos_5-7nt_m1)
; oligos_5-7nt_m1; m=0 (reference); ncol1=14; shift=4; ncol=18; ----vrAAATATCTycwd ; Alignment reference a 0 0 0 0 17 23 49 52 50 1 47 4 7 3 12 13 15 14 c 0 0 0 0 16 8 0 0 1 1 1 1 44 6 15 15 13 10 g 0 0 0 0 15 15 2 0 1 3 3 0 0 1 5 12 10 14 t 0 0 0 0 5 7 2 1 1 48 2 48 2 43 21 13 15 15

CCA1_CCA1_ArabidopsisPBM_shift5 (CCA1_CCA1_ArabidopsisPBM) 0.987 0.705 8.672 0.704 0.969 0.191 0.990 2 13 6 11 2 2 2 5.429 1
; oligos_5-7nt_m1 versus CCA1_CCA1_ArabidopsisPBM; m=1/12; ncol2=10; w=10; offset=1; strand=D; shift=5; score= 5.4286; -----aAAATATCTt--- ; cor=0.987; Ncor=0.705; logoDP=8.672; NIcor=0.704; NsEucl=0.969; SSD=0.191; NSW=0.990; rcor=2; rNcor=13; rlogoDP=6; rNIcor=11; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=5.429; match_rank=1 a 0 0 0 0 0 60 93 96 98 4 100 0 0 3 17 0 0 0 c 0 0 0 0 0 8 0 0 0 0 0 1 100 9 21 0 0 0 g 0 0 0 0 0 10 1 4 2 0 0 0 0 1 11 0 0 0 t 0 0 0 0 0 22 6 0 0 96 0 99 0 87 51 0 0 0

RVE1_RVE1_ArabidopsisPBM_shift5 (RVE1_RVE1_ArabidopsisPBM) 0.976 0.697 7.901 0.701 0.963 0.268 0.987 3 14 10 12 3 3 3 6.857 2
; oligos_5-7nt_m1 versus RVE1_RVE1_ArabidopsisPBM; m=2/12; ncol2=10; w=10; offset=1; strand=D; shift=5; score= 6.8571; -----wAAATATCTk--- ; cor=0.976; Ncor=0.697; logoDP=7.901; NIcor=0.701; NsEucl=0.963; SSD=0.268; NSW=0.987; rcor=3; rNcor=14; rlogoDP=10; rNIcor=12; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=6.857; match_rank=2 a 0 0 0 0 0 65 92 92 98 7 99 0 1 2 9 0 0 0 c 0 0 0 0 0 4 0 0 0 0 1 1 98 10 20 0 0 0 g 0 0 0 0 0 6 2 7 1 4 0 0 0 4 28 0 0 0 t 0 0 0 0 0 25 6 1 1 89 0 99 1 84 43 0 0 0

CCA1_MA0972.1_JASPAR_shift6 (CCA1_MA0972.1_JASPAR) 0.995 0.569 8.536 0.567 0.974 0.088 0.994 1 34 7 27 1 1 1 10.286 6
; oligos_5-7nt_m1 versus CCA1_MA0972.1_JASPAR; m=3/12; ncol2=8; w=8; offset=2; strand=D; shift=6; score=10.2857; ------AAATATCT---- ; cor=0.995; Ncor=0.569; logoDP=8.536; NIcor=0.567; NsEucl=0.974; SSD=0.088; NSW=0.994; rcor=1; rNcor=34; rlogoDP=7; rNIcor=27; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=10.286; match_rank=6 a 0 0 0 0 0 0 934 960 985 35 992 1 5 21 0 0 0 0 c 0 0 0 0 0 0 1 1 4 0 5 12 991 91 0 0 0 0 g 0 0 0 0 0 0 10 37 10 5 1 1 0 14 0 0 0 0 t 0 0 0 0 0 0 54 2 1 960 2 986 4 874 0 0 0 0

CCA1_M01819_TRANSFAC_shift0 (CCA1_M01819_TRANSFAC) 0.873 0.631 8.927 0.624 0.931 1.613 0.938 20 20 5 18 9 40 21 19.000 13
; oligos_5-7nt_m1 versus CCA1_M01819_TRANSFAC; m=4/12; ncol2=17; w=13; offset=-4; strand=D; shift=0; score= 19; smharAAAAwATCTAar- ; cor=0.873; Ncor=0.631; logoDP=8.927; NIcor=0.624; NsEucl=0.931; SSD=1.613; NSW=0.938; rcor=20; rNcor=20; rlogoDP=5; rNIcor=18; rNsEucl=9; rSSD=40; rNSW=21; rank_mean=19.000; match_rank=13 a 0 3 2 3 3 6 7 7 7 3 7 0 0 1 5 3 2 0 c 4 3 2 1 0 0 0 0 0 0 0 0 7 0 0 1 1 0 g 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 1 2 0 t 0 0 2 1 1 0 0 0 0 4 0 7 0 6 1 1 1 0

PK02532.1_M1303_1.02_CISBP_rc_shift6 (PK02532.1_M1303_1.02_CISBP_rc) 0.945 0.608 2.859 0.029 0.940 0.593 0.967 4 27 38 49 5 8 6 19.571 15
; oligos_5-7nt_m1 versus PK02532.1_M1303_1.02_CISBP_rc; m=5/12; ncol2=9; w=9; offset=2; strand=R; shift=6; score=19.5714; ------wAATATCTn--- ; cor=0.945; Ncor=0.608; logoDP=2.859; NIcor=0.029; NsEucl=0.940; SSD=0.593; NSW=0.967; rcor=4; rNcor=27; rlogoDP=38; rNIcor=49; rNsEucl=5; rSSD=8; rNSW=6; rank_mean=19.571; match_rank=15 a 0 0 0 0 0 0 50 100 100 0 100 0 0 0 25 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 100 0 25 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 t 0 0 0 0 0 0 50 0 0 100 0 100 0 100 25 0 0 0

EPR1_M1317_1.02_CISBP_rc_shift5 (EPR1_M1317_1.02_CISBP_rc) 0.926 0.595 2.171 0.086 0.934 0.713 0.960 7 28 40 48 7 9 9 21.143 16
; oligos_5-7nt_m1 versus EPR1_M1317_1.02_CISBP_rc; m=6/12; ncol2=9; w=9; offset=1; strand=R; shift=5; score=21.1429; -----waAaTATCt---- ; cor=0.926; Ncor=0.595; logoDP=2.171; NIcor=0.086; NsEucl=0.934; SSD=0.713; NSW=0.960; rcor=7; rNcor=28; rlogoDP=40; rNIcor=48; rNsEucl=7; rSSD=9; rNSW=9; rank_mean=21.143; match_rank=16 a 0 0 0 0 0 35 52 68 67 19 98 1 2 17 0 0 0 0 c 0 0 0 0 0 16 9 9 8 2 0 1 92 19 0 0 0 0 g 0 0 0 0 0 20 15 9 18 7 1 0 1 12 0 0 0 0 t 0 0 0 0 0 29 24 14 7 72 1 98 5 52 0 0 0 0

PK08316.1_M1306_1.02_CISBP_shift5 (PK08316.1_M1306_1.02_CISBP) 0.883 0.631 2.053 0.602 0.919 1.326 0.934 19 19 43 22 21 34 27 26.429 22
; oligos_5-7nt_m1 versus PK08316.1_M1306_1.02_CISBP; m=7/12; ncol2=10; w=10; offset=1; strand=D; shift=5; score=26.4286; -----wwaawATCtw--- ; cor=0.883; Ncor=0.631; logoDP=2.053; NIcor=0.602; NsEucl=0.919; SSD=1.326; NSW=0.934; rcor=19; rNcor=19; rlogoDP=43; rNIcor=22; rNsEucl=21; rSSD=34; rNSW=27; rank_mean=26.429; match_rank=22 a 0 0 0 0 0 29 42 52 56 26 88 10 9 20 26 0 0 0 c 0 0 0 0 0 20 15 17 12 4 0 5 80 21 22 0 0 0 g 0 0 0 0 0 23 17 16 20 12 5 5 7 18 24 0 0 0 t 0 0 0 0 0 28 26 15 12 58 7 80 4 41 28 0 0 0

LOC_Os08g06110_M1365_1.02_CISBP_rc_shift6 (LOC_Os08g06110_M1365_1.02_CISBP_rc) 0.898 0.578 0.593 -0.048 0.924 0.924 0.949 11 31 53 52 12 15 14 26.857 23
; oligos_5-7nt_m1 versus LOC_Os08g06110_M1365_1.02_CISBP_rc; m=8/12; ncol2=9; w=9; offset=2; strand=R; shift=6; score=26.8571; ------aaaTATCtw--- ; cor=0.898; Ncor=0.578; logoDP=0.593; NIcor=-0.048; NsEucl=0.924; SSD=0.924; NSW=0.949; rcor=11; rNcor=31; rlogoDP=53; rNIcor=52; rNsEucl=12; rSSD=15; rNSW=14; rank_mean=26.857; match_rank=23 a 0 0 0 0 0 0 45 57 62 19 99 0 1 13 25 0 0 0 c 0 0 0 0 0 0 12 16 9 1 0 1 96 19 24 0 0 0 g 0 0 0 0 0 0 21 13 22 8 0 0 0 12 23 0 0 0 t 0 0 0 0 0 0 22 14 7 72 1 99 3 56 28 0 0 0

ARR11_ARR11_3_ArabidopsisPBM_shift6 (ARR11_ARR11_3_ArabidopsisPBM) 0.796 0.569 3.823 0.532 0.908 1.699 0.915 36 33 30 32 33 46 37 35.286 33
; oligos_5-7nt_m1 versus ARR11_ARR11_3_ArabidopsisPBM; m=9/12; ncol2=10; w=10; offset=2; strand=D; shift=6; score=35.2857; ------wAAGATCTTk-- ; cor=0.796; Ncor=0.569; logoDP=3.823; NIcor=0.532; NsEucl=0.908; SSD=1.699; NSW=0.915; rcor=36; rNcor=33; rlogoDP=30; rNIcor=32; rNsEucl=33; rSSD=46; rNSW=37; rank_mean=35.286; match_rank=33 a 0 0 0 0 0 0 35 68 84 5 95 2 20 8 14 22 0 0 c 0 0 0 0 0 0 13 7 2 2 1 2 73 7 12 20 0 0 g 0 0 0 0 0 0 22 11 6 73 2 1 2 2 6 30 0 0 t 0 0 0 0 0 0 30 14 8 20 2 95 5 83 68 28 0 0

RVE1_RVE1_2_ArabidopsisPBM_shift6 (RVE1_RVE1_2_ArabidopsisPBM) 0.773 0.552 2.891 0.534 0.904 1.845 0.908 41 37 35 30 38 49 41 38.714 41
; oligos_5-7nt_m1 versus RVE1_RVE1_2_ArabidopsisPBM; m=10/12; ncol2=10; w=10; offset=2; strand=D; shift=6; score=38.7143; ------smatATCwaw-- ; cor=0.773; Ncor=0.552; logoDP=2.891; NIcor=0.534; NsEucl=0.904; SSD=1.845; NSW=0.908; rcor=41; rNcor=37; rlogoDP=35; rNIcor=30; rNsEucl=38; rSSD=49; rNSW=41; rank_mean=38.714; match_rank=41 a 0 0 0 0 0 0 20 54 65 23 91 3 6 29 61 50 0 0 c 0 0 0 0 0 0 31 31 9 3 4 3 89 20 16 16 0 0 g 0 0 0 0 0 0 29 4 16 15 3 3 4 5 13 6 0 0 t 0 0 0 0 0 0 20 11 10 59 2 91 1 46 10 28 0 0

AHL20_AHL20_ArabidopsisPBM_shift6 (AHL20_AHL20_ArabidopsisPBM) 0.768 0.548 5.407 0.522 0.896 2.163 0.892 45 39 20 33 42 58 50 41.000 47
; oligos_5-7nt_m1 versus AHL20_AHL20_ArabidopsisPBM; m=11/12; ncol2=10; w=10; offset=2; strand=D; shift=6; score= 41; ------wAATATATTw-- ; cor=0.768; Ncor=0.548; logoDP=5.407; NIcor=0.522; NsEucl=0.896; SSD=2.163; NSW=0.892; rcor=45; rNcor=39; rlogoDP=20; rNIcor=33; rNsEucl=42; rSSD=58; rNSW=50; rank_mean=41.000; match_rank=47 a 0 0 0 0 0 0 44 95 88 8 87 13 91 11 3 44 0 0 c 0 0 0 0 0 0 16 1 0 1 0 0 1 1 1 10 0 0 g 0 0 0 0 0 0 11 1 1 0 0 0 1 0 1 21 0 0 t 0 0 0 0 0 0 29 3 11 91 13 87 7 88 95 25 0 0

PRH_M1167_1.02_CISBP_shift8 (PRH_M1167_1.02_CISBP) 0.756 0.432 5.785 0.430 0.871 2.132 0.867 52 55 18 41 58 57 59 48.571 58
; oligos_5-7nt_m1 versus PRH_M1167_1.02_CISBP; m=12/12; ncol2=8; w=8; offset=4; strand=D; shift=8; score=48.5714; --------ATATATwA-- ; cor=0.756; Ncor=0.432; logoDP=5.785; NIcor=0.430; NsEucl=0.871; SSD=2.132; NSW=0.867; rcor=52; rNcor=55; rlogoDP=18; rNIcor=41; rNsEucl=58; rSSD=57; rNSW=59; rank_mean=48.571; match_rank=58 a 0 0 0 0 0 0 0 0 100 0 100 0 100 14 50 80 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 100 0 100 0 86 50 20 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_m1_shift4 (oligos_5-7nt_m1)																	; oligos_5-7nt_m1; m=0 (reference); ncol1=14; shift=4; ncol=18; ----vrAAATATCTycwd ; Alignment reference a 0 0 0 0 17 23 49 52 50 1 47 4 7 3 12 13 15 14 c 0 0 0 0 16 8 0 0 1 1 1 1 44 6 15 15 13 10 g 0 0 0 0 15 15 2 0 1 3 3 0 0 1 5 12 10 14 t 0 0 0 0 5 7 2 1 1 48 2 48 2 43 21 13 15 15
CCA1_CCA1_ArabidopsisPBM_shift5 (CCA1_CCA1_ArabidopsisPBM)	0.987	0.705	8.672	0.704	0.969	0.191	0.990	2	13	6	11	2	2	2	5.429	1	; oligos_5-7nt_m1 versus CCA1_CCA1_ArabidopsisPBM; m=1/12; ncol2=10; w=10; offset=1; strand=D; shift=5; score= 5.4286; -----aAAATATCTt--- ; cor=0.987; Ncor=0.705; logoDP=8.672; NIcor=0.704; NsEucl=0.969; SSD=0.191; NSW=0.990; rcor=2; rNcor=13; rlogoDP=6; rNIcor=11; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=5.429; match_rank=1 a 0 0 0 0 0 60 93 96 98 4 100 0 0 3 17 0 0 0 c 0 0 0 0 0 8 0 0 0 0 0 1 100 9 21 0 0 0 g 0 0 0 0 0 10 1 4 2 0 0 0 0 1 11 0 0 0 t 0 0 0 0 0 22 6 0 0 96 0 99 0 87 51 0 0 0
RVE1_RVE1_ArabidopsisPBM_shift5 (RVE1_RVE1_ArabidopsisPBM)	0.976	0.697	7.901	0.701	0.963	0.268	0.987	3	14	10	12	3	3	3	6.857	2	; oligos_5-7nt_m1 versus RVE1_RVE1_ArabidopsisPBM; m=2/12; ncol2=10; w=10; offset=1; strand=D; shift=5; score= 6.8571; -----wAAATATCTk--- ; cor=0.976; Ncor=0.697; logoDP=7.901; NIcor=0.701; NsEucl=0.963; SSD=0.268; NSW=0.987; rcor=3; rNcor=14; rlogoDP=10; rNIcor=12; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=6.857; match_rank=2 a 0 0 0 0 0 65 92 92 98 7 99 0 1 2 9 0 0 0 c 0 0 0 0 0 4 0 0 0 0 1 1 98 10 20 0 0 0 g 0 0 0 0 0 6 2 7 1 4 0 0 0 4 28 0 0 0 t 0 0 0 0 0 25 6 1 1 89 0 99 1 84 43 0 0 0
CCA1_MA0972.1_JASPAR_shift6 (CCA1_MA0972.1_JASPAR)	0.995	0.569	8.536	0.567	0.974	0.088	0.994	1	34	7	27	1	1	1	10.286	6	; oligos_5-7nt_m1 versus CCA1_MA0972.1_JASPAR; m=3/12; ncol2=8; w=8; offset=2; strand=D; shift=6; score=10.2857; ------AAATATCT---- ; cor=0.995; Ncor=0.569; logoDP=8.536; NIcor=0.567; NsEucl=0.974; SSD=0.088; NSW=0.994; rcor=1; rNcor=34; rlogoDP=7; rNIcor=27; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=10.286; match_rank=6 a 0 0 0 0 0 0 934 960 985 35 992 1 5 21 0 0 0 0 c 0 0 0 0 0 0 1 1 4 0 5 12 991 91 0 0 0 0 g 0 0 0 0 0 0 10 37 10 5 1 1 0 14 0 0 0 0 t 0 0 0 0 0 0 54 2 1 960 2 986 4 874 0 0 0 0
CCA1_M01819_TRANSFAC_shift0 (CCA1_M01819_TRANSFAC)	0.873	0.631	8.927	0.624	0.931	1.613	0.938	20	20	5	18	9	40	21	19.000	13	; oligos_5-7nt_m1 versus CCA1_M01819_TRANSFAC; m=4/12; ncol2=17; w=13; offset=-4; strand=D; shift=0; score= 19; smharAAAAwATCTAar- ; cor=0.873; Ncor=0.631; logoDP=8.927; NIcor=0.624; NsEucl=0.931; SSD=1.613; NSW=0.938; rcor=20; rNcor=20; rlogoDP=5; rNIcor=18; rNsEucl=9; rSSD=40; rNSW=21; rank_mean=19.000; match_rank=13 a 0 3 2 3 3 6 7 7 7 3 7 0 0 1 5 3 2 0 c 4 3 2 1 0 0 0 0 0 0 0 0 7 0 0 1 1 0 g 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 1 2 0 t 0 0 2 1 1 0 0 0 0 4 0 7 0 6 1 1 1 0
PK02532.1_M1303_1.02_CISBP_rc_shift6 (PK02532.1_M1303_1.02_CISBP_rc)	0.945	0.608	2.859	0.029	0.940	0.593	0.967	4	27	38	49	5	8	6	19.571	15	; oligos_5-7nt_m1 versus PK02532.1_M1303_1.02_CISBP_rc; m=5/12; ncol2=9; w=9; offset=2; strand=R; shift=6; score=19.5714; ------wAATATCTn--- ; cor=0.945; Ncor=0.608; logoDP=2.859; NIcor=0.029; NsEucl=0.940; SSD=0.593; NSW=0.967; rcor=4; rNcor=27; rlogoDP=38; rNIcor=49; rNsEucl=5; rSSD=8; rNSW=6; rank_mean=19.571; match_rank=15 a 0 0 0 0 0 0 50 100 100 0 100 0 0 0 25 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 100 0 25 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 t 0 0 0 0 0 0 50 0 0 100 0 100 0 100 25 0 0 0
EPR1_M1317_1.02_CISBP_rc_shift5 (EPR1_M1317_1.02_CISBP_rc)	0.926	0.595	2.171	0.086	0.934	0.713	0.960	7	28	40	48	7	9	9	21.143	16	; oligos_5-7nt_m1 versus EPR1_M1317_1.02_CISBP_rc; m=6/12; ncol2=9; w=9; offset=1; strand=R; shift=5; score=21.1429; -----waAaTATCt---- ; cor=0.926; Ncor=0.595; logoDP=2.171; NIcor=0.086; NsEucl=0.934; SSD=0.713; NSW=0.960; rcor=7; rNcor=28; rlogoDP=40; rNIcor=48; rNsEucl=7; rSSD=9; rNSW=9; rank_mean=21.143; match_rank=16 a 0 0 0 0 0 35 52 68 67 19 98 1 2 17 0 0 0 0 c 0 0 0 0 0 16 9 9 8 2 0 1 92 19 0 0 0 0 g 0 0 0 0 0 20 15 9 18 7 1 0 1 12 0 0 0 0 t 0 0 0 0 0 29 24 14 7 72 1 98 5 52 0 0 0 0
PK08316.1_M1306_1.02_CISBP_shift5 (PK08316.1_M1306_1.02_CISBP)	0.883	0.631	2.053	0.602	0.919	1.326	0.934	19	19	43	22	21	34	27	26.429	22	; oligos_5-7nt_m1 versus PK08316.1_M1306_1.02_CISBP; m=7/12; ncol2=10; w=10; offset=1; strand=D; shift=5; score=26.4286; -----wwaawATCtw--- ; cor=0.883; Ncor=0.631; logoDP=2.053; NIcor=0.602; NsEucl=0.919; SSD=1.326; NSW=0.934; rcor=19; rNcor=19; rlogoDP=43; rNIcor=22; rNsEucl=21; rSSD=34; rNSW=27; rank_mean=26.429; match_rank=22 a 0 0 0 0 0 29 42 52 56 26 88 10 9 20 26 0 0 0 c 0 0 0 0 0 20 15 17 12 4 0 5 80 21 22 0 0 0 g 0 0 0 0 0 23 17 16 20 12 5 5 7 18 24 0 0 0 t 0 0 0 0 0 28 26 15 12 58 7 80 4 41 28 0 0 0
LOC_Os08g06110_M1365_1.02_CISBP_rc_shift6 (LOC_Os08g06110_M1365_1.02_CISBP_rc)	0.898	0.578	0.593	-0.048	0.924	0.924	0.949	11	31	53	52	12	15	14	26.857	23	; oligos_5-7nt_m1 versus LOC_Os08g06110_M1365_1.02_CISBP_rc; m=8/12; ncol2=9; w=9; offset=2; strand=R; shift=6; score=26.8571; ------aaaTATCtw--- ; cor=0.898; Ncor=0.578; logoDP=0.593; NIcor=-0.048; NsEucl=0.924; SSD=0.924; NSW=0.949; rcor=11; rNcor=31; rlogoDP=53; rNIcor=52; rNsEucl=12; rSSD=15; rNSW=14; rank_mean=26.857; match_rank=23 a 0 0 0 0 0 0 45 57 62 19 99 0 1 13 25 0 0 0 c 0 0 0 0 0 0 12 16 9 1 0 1 96 19 24 0 0 0 g 0 0 0 0 0 0 21 13 22 8 0 0 0 12 23 0 0 0 t 0 0 0 0 0 0 22 14 7 72 1 99 3 56 28 0 0 0
ARR11_ARR11_3_ArabidopsisPBM_shift6 (ARR11_ARR11_3_ArabidopsisPBM)	0.796	0.569	3.823	0.532	0.908	1.699	0.915	36	33	30	32	33	46	37	35.286	33	; oligos_5-7nt_m1 versus ARR11_ARR11_3_ArabidopsisPBM; m=9/12; ncol2=10; w=10; offset=2; strand=D; shift=6; score=35.2857; ------wAAGATCTTk-- ; cor=0.796; Ncor=0.569; logoDP=3.823; NIcor=0.532; NsEucl=0.908; SSD=1.699; NSW=0.915; rcor=36; rNcor=33; rlogoDP=30; rNIcor=32; rNsEucl=33; rSSD=46; rNSW=37; rank_mean=35.286; match_rank=33 a 0 0 0 0 0 0 35 68 84 5 95 2 20 8 14 22 0 0 c 0 0 0 0 0 0 13 7 2 2 1 2 73 7 12 20 0 0 g 0 0 0 0 0 0 22 11 6 73 2 1 2 2 6 30 0 0 t 0 0 0 0 0 0 30 14 8 20 2 95 5 83 68 28 0 0
RVE1_RVE1_2_ArabidopsisPBM_shift6 (RVE1_RVE1_2_ArabidopsisPBM)	0.773	0.552	2.891	0.534	0.904	1.845	0.908	41	37	35	30	38	49	41	38.714	41	; oligos_5-7nt_m1 versus RVE1_RVE1_2_ArabidopsisPBM; m=10/12; ncol2=10; w=10; offset=2; strand=D; shift=6; score=38.7143; ------smatATCwaw-- ; cor=0.773; Ncor=0.552; logoDP=2.891; NIcor=0.534; NsEucl=0.904; SSD=1.845; NSW=0.908; rcor=41; rNcor=37; rlogoDP=35; rNIcor=30; rNsEucl=38; rSSD=49; rNSW=41; rank_mean=38.714; match_rank=41 a 0 0 0 0 0 0 20 54 65 23 91 3 6 29 61 50 0 0 c 0 0 0 0 0 0 31 31 9 3 4 3 89 20 16 16 0 0 g 0 0 0 0 0 0 29 4 16 15 3 3 4 5 13 6 0 0 t 0 0 0 0 0 0 20 11 10 59 2 91 1 46 10 28 0 0
AHL20_AHL20_ArabidopsisPBM_shift6 (AHL20_AHL20_ArabidopsisPBM)	0.768	0.548	5.407	0.522	0.896	2.163	0.892	45	39	20	33	42	58	50	41.000	47	; oligos_5-7nt_m1 versus AHL20_AHL20_ArabidopsisPBM; m=11/12; ncol2=10; w=10; offset=2; strand=D; shift=6; score= 41; ------wAATATATTw-- ; cor=0.768; Ncor=0.548; logoDP=5.407; NIcor=0.522; NsEucl=0.896; SSD=2.163; NSW=0.892; rcor=45; rNcor=39; rlogoDP=20; rNIcor=33; rNsEucl=42; rSSD=58; rNSW=50; rank_mean=41.000; match_rank=47 a 0 0 0 0 0 0 44 95 88 8 87 13 91 11 3 44 0 0 c 0 0 0 0 0 0 16 1 0 1 0 0 1 1 1 10 0 0 g 0 0 0 0 0 0 11 1 1 0 0 0 1 0 1 21 0 0 t 0 0 0 0 0 0 29 3 11 91 13 87 7 88 95 25 0 0
PRH_M1167_1.02_CISBP_shift8 (PRH_M1167_1.02_CISBP)	0.756	0.432	5.785	0.430	0.871	2.132	0.867	52	55	18	41	58	57	59	48.571	58	; oligos_5-7nt_m1 versus PRH_M1167_1.02_CISBP; m=12/12; ncol2=8; w=8; offset=4; strand=D; shift=8; score=48.5714; --------ATATATwA-- ; cor=0.756; Ncor=0.432; logoDP=5.785; NIcor=0.430; NsEucl=0.871; SSD=2.132; NSW=0.867; rcor=52; rNcor=55; rlogoDP=18; rNIcor=41; rNsEucl=58; rSSD=57; rNSW=59; rank_mean=48.571; match_rank=58 a 0 0 0 0 0 0 0 0 100 0 100 0 100 14 50 80 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 100 0 100 0 86 50 20 0 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m3_shift2 ; 20 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_shift2 (oligos_5-7nt_m3)
; oligos_5-7nt_m3; m=0 (reference); ncol1=9; shift=2; ncol=11; --waAATCAwa ; Alignment reference a 0 0 30 32 83 83 0 0 83 34 32 c 0 0 20 20 0 0 0 83 0 11 17 g 0 0 12 13 0 0 0 0 0 13 19 t 0 0 21 18 0 0 83 0 0 25 15

HAT3_M0848_1.02_CISBP_shift2 (HAT3_M0848_1.02_CISBP) 0.929 0.826 4.614 0.844 0.933 0.571 0.964 6 1 26 1 8 7 7 8.000 3
; oligos_5-7nt_m3 versus HAT3_M0848_1.02_CISBP; m=1/19; ncol2=8; w=8; offset=0; strand=D; shift=2; score= 8; --syAATCAw- ; cor=0.929; Ncor=0.826; logoDP=4.614; NIcor=0.844; NsEucl=0.933; SSD=0.571; NSW=0.964; rcor=6; rNcor=1; rlogoDP=26; rNIcor=1; rNsEucl=8; rSSD=7; rNSW=7; rank_mean=8.000; match_rank=3 a 0 0 12 6 85 86 5 11 82 33 0 c 0 0 35 54 7 6 6 76 3 15 0 g 0 0 35 3 1 3 0 6 6 12 0 t 0 0 18 37 7 5 89 7 9 40 0

LOC_Os09g35910_M1108_1.02_CISBP_shift0 (LOC_Os09g35910_M1108_1.02_CISBP) 0.936 0.681 6.767 0.688 0.939 0.476 0.970 5 15 14 13 6 5 5 9.000 4
; oligos_5-7nt_m3 versus LOC_Os09g35910_M1108_1.02_CISBP; m=2/19; ncol2=10; w=8; offset=-2; strand=D; shift=0; score= 9; rwyyAATCAw- ; cor=0.936; Ncor=0.681; logoDP=6.767; NIcor=0.688; NsEucl=0.939; SSD=0.476; NSW=0.970; rcor=5; rNcor=15; rlogoDP=14; rNIcor=13; rNsEucl=6; rSSD=5; rNSW=5; rank_mean=9.000; match_rank=4 a 30 28 11 5 87 96 1 1 79 40 0 c 22 23 37 64 5 3 0 96 3 17 0 g 25 23 19 2 2 0 0 1 10 12 0 t 23 26 33 29 6 1 99 2 8 31 0

ATHB-7_MA0954.1_JASPAR_shift2 (ATHB-7_MA0954.1_JASPAR) 0.892 0.803 9.649 0.808 0.923 0.961 0.947 14 5 4 3 14 16 15 10.143 5
; oligos_5-7nt_m3 versus ATHB-7_MA0954.1_JASPAR; m=3/19; ncol2=10; w=9; offset=0; strand=D; shift=2; score=10.1429; --yCAATCAWt ; cor=0.892; Ncor=0.803; logoDP=9.649; NIcor=0.808; NsEucl=0.923; SSD=0.961; NSW=0.947; rcor=14; rNcor=5; rlogoDP=4; rNIcor=3; rNsEucl=14; rSSD=16; rNSW=15; rank_mean=10.143; match_rank=5 a 0 0 152 27 1000 1000 0 0 1000 291 183 c 0 0 338 828 0 0 0 1000 0 0 98 g 0 0 152 27 0 0 0 0 0 0 190 t 0 0 358 118 0 0 1000 0 0 709 528

GRMZM2G038252_M1209_1.02_CISBP_shift2 (GRMZM2G038252_M1209_1.02_CISBP) 0.898 0.799 7.704 0.800 0.922 0.772 0.952 10 7 11 9 16 11 11 10.714 7
; oligos_5-7nt_m3 versus GRMZM2G038252_M1209_1.02_CISBP; m=4/19; ncol2=8; w=8; offset=0; strand=D; shift=2; score=10.7143; --tCAATYAa- ; cor=0.898; Ncor=0.799; logoDP=7.704; NIcor=0.800; NsEucl=0.922; SSD=0.772; NSW=0.952; rcor=10; rNcor=7; rlogoDP=11; rNIcor=9; rNsEucl=16; rSSD=11; rNSW=11; rank_mean=10.714; match_rank=7 a 0 0 11 6 99 98 1 0 95 55 0 c 0 0 23 77 1 0 0 70 1 10 0 g 0 0 16 0 0 2 0 0 0 21 0 t 0 0 50 17 0 0 99 30 4 14 0

ATHB7_M0846_1.02_CISBP_shift2 (ATHB7_M0846_1.02_CISBP) 0.891 0.802 9.649 0.807 0.923 0.967 0.946 15 6 3 6 15 17 16 11.143 8
; oligos_5-7nt_m3 versus ATHB7_M0846_1.02_CISBP; m=5/19; ncol2=10; w=9; offset=0; strand=D; shift=2; score=11.1429; --yCAATCAWt ; cor=0.891; Ncor=0.802; logoDP=9.649; NIcor=0.807; NsEucl=0.923; SSD=0.967; NSW=0.946; rcor=15; rNcor=6; rlogoDP=3; rNIcor=6; rNsEucl=15; rSSD=17; rNSW=16; rank_mean=11.143; match_rank=8 a 0 0 15 3 100 100 0 0 100 29 18 c 0 0 34 83 0 0 0 100 0 0 10 g 0 0 15 3 0 0 0 0 0 0 19 t 0 0 36 11 0 0 100 0 0 71 53

HAT1_MA1024.1_JASPAR_shift2 (HAT1_MA1024.1_JASPAR) 0.885 0.796 9.650 0.807 0.921 1.010 0.944 17 8 2 5 18 19 18 12.429 9
; oligos_5-7nt_m3 versus HAT1_MA1024.1_JASPAR; m=6/19; ncol2=10; w=9; offset=0; strand=D; shift=2; score=12.4286; --syAATCATk ; cor=0.885; Ncor=0.796; logoDP=9.650; NIcor=0.807; NsEucl=0.921; SSD=1.010; NSW=0.944; rcor=17; rNcor=8; rlogoDP=2; rNIcor=5; rNsEucl=18; rSSD=19; rNSW=18; rank_mean=12.429; match_rank=9 a 0 0 149 69 1000 1000 0 0 1000 98 101 c 0 0 374 506 0 0 0 1000 0 0 101 g 0 0 328 69 0 0 0 0 0 0 286 t 0 0 149 356 0 0 1000 0 0 902 512

HAT1_M0851_1.02_CISBP_shift2 (HAT1_M0851_1.02_CISBP) 0.884 0.796 9.650 0.807 0.921 1.014 0.944 18 9 1 4 19 20 19 12.857 10
; oligos_5-7nt_m3 versus HAT1_M0851_1.02_CISBP; m=7/19; ncol2=10; w=9; offset=0; strand=D; shift=2; score=12.8571; --syAATCATk ; cor=0.884; Ncor=0.796; logoDP=9.650; NIcor=0.807; NsEucl=0.921; SSD=1.014; NSW=0.944; rcor=18; rNcor=9; rlogoDP=1; rNIcor=4; rNsEucl=19; rSSD=20; rNSW=19; rank_mean=12.857; match_rank=10 a 0 0 15 6 100 100 0 0 100 10 10 c 0 0 37 51 0 0 0 100 0 0 10 g 0 0 33 7 0 0 0 0 0 0 29 t 0 0 15 36 0 0 100 0 0 90 51

ATHB-4_M0845_1.02_CISBP_shift2 (ATHB-4_M0845_1.02_CISBP) 0.898 0.808 2.868 0.816 0.925 0.902 0.950 12 4 37 2 11 13 12 13.000 11
; oligos_5-7nt_m3 versus ATHB-4_M0845_1.02_CISBP; m=8/19; ncol2=10; w=9; offset=0; strand=D; shift=2; score= 13; --syAATcAtt ; cor=0.898; Ncor=0.808; logoDP=2.868; NIcor=0.816; NsEucl=0.925; SSD=0.902; NSW=0.950; rcor=12; rNcor=4; rlogoDP=37; rNIcor=2; rNsEucl=11; rSSD=13; rNSW=12; rank_mean=13.000; match_rank=11 a 0 0 17 11 77 79 11 13 75 23 22 c 0 0 35 48 7 9 4 59 6 13 20 g 0 0 27 4 3 5 7 14 8 11 20 t 0 0 21 37 13 7 78 14 11 53 38

ATWOX13_M0853_1.02_CISBP_shift2 (ATWOX13_M0853_1.02_CISBP) 0.859 0.763 8.096 0.757 0.904 1.178 0.926 24 11 8 10 37 28 33 21.571 17
; oligos_5-7nt_m3 versus ATWOX13_M0853_1.02_CISBP; m=9/19; ncol2=8; w=8; offset=0; strand=D; shift=2; score=21.5714; --TCAATCAa- ; cor=0.859; Ncor=0.763; logoDP=8.096; NIcor=0.757; NsEucl=0.904; SSD=1.178; NSW=0.926; rcor=24; rNcor=11; rlogoDP=8; rNIcor=10; rNsEucl=37; rSSD=28; rNSW=33; rank_mean=21.571; match_rank=17 a 0 0 0 0 100 100 0 7 93 60 0 c 0 0 9 85 0 0 0 80 0 10 0 g 0 0 9 0 0 0 0 0 0 20 0 t 0 0 82 15 0 0 100 13 7 10 0

ATHB6_M0843_1.02_CISBP_shift2 (ATHB6_M0843_1.02_CISBP) 0.816 0.816 4.783 0.806 0.911 1.295 0.928 29 2 25 7 29 31 30 21.857 18
; oligos_5-7nt_m3 versus ATHB6_M0843_1.02_CISBP; m=10/19; ncol2=9; w=9; offset=0; strand=D; shift=2; score=21.8571; --byAATmATk ; cor=0.816; Ncor=0.816; logoDP=4.783; NIcor=0.806; NsEucl=0.911; SSD=1.295; NSW=0.928; rcor=29; rNcor=2; rlogoDP=25; rNIcor=7; rNsEucl=29; rSSD=31; rNSW=30; rank_mean=21.857; match_rank=18 a 0 0 18 15 75 89 2 36 92 11 23 c 0 0 25 52 9 7 1 31 1 7 11 g 0 0 29 8 7 0 0 13 4 13 27 t 0 0 28 25 9 4 97 20 3 69 39

WOX13_WOX13_ArabidopsisPBM_shift0 (WOX13_WOX13_ArabidopsisPBM) 0.865 0.629 7.009 0.619 0.909 1.064 0.933 21 21 12 19 32 24 28 22.429 19
; oligos_5-7nt_m3 versus WOX13_WOX13_ArabidopsisPBM; m=11/19; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=22.4286; wrTCAATCAa- ; cor=0.865; Ncor=0.629; logoDP=7.009; NIcor=0.619; NsEucl=0.909; SSD=1.064; NSW=0.933; rcor=21; rNcor=21; rlogoDP=12; rNIcor=19; rNsEucl=32; rSSD=24; rNSW=28; rank_mean=22.429; match_rank=19 a 32 54 3 2 95 96 1 1 90 40 0 c 16 3 13 93 1 1 1 86 3 15 0 g 15 31 12 1 1 1 1 1 2 21 0 t 37 12 72 4 3 2 97 12 5 24 0

ATHB-6_MA0953.1_JASPAR_shift2 (ATHB-6_MA0953.1_JASPAR) 0.815 0.815 4.801 0.803 0.910 1.305 0.927 30 3 24 8 30 33 31 22.714 20
; oligos_5-7nt_m3 versus ATHB-6_MA0953.1_JASPAR; m=12/19; ncol2=9; w=9; offset=0; strand=D; shift=2; score=22.7143; --bcAATmATk ; cor=0.815; Ncor=0.815; logoDP=4.801; NIcor=0.803; NsEucl=0.910; SSD=1.305; NSW=0.927; rcor=30; rNcor=3; rlogoDP=24; rNIcor=8; rNsEucl=30; rSSD=33; rNSW=31; rank_mean=22.714; match_rank=20 a 0 0 177 149 745 886 20 356 924 106 234 c 0 0 252 524 89 71 6 310 5 66 111 g 0 0 287 85 73 1 1 128 38 130 266 t 0 0 284 243 92 42 972 206 32 698 389

estExt_gwp_gw1.C_70211_M1195_1.02_CISBP_shift3 (estExt_gwp_gw1.C_70211_M1195_1.02_CISBP) 0.836 0.608 5.162 0.596 0.905 1.166 0.927 26 26 21 24 36 27 32 27.429 25
; oligos_5-7nt_m3 versus estExt_gwp_gw1.C_70211_M1195_1.02_CISBP; m=13/19; ncol2=10; w=8; offset=1; strand=D; shift=3; score=27.4286; ---yaATmAtk ; cor=0.836; Ncor=0.608; logoDP=5.162; NIcor=0.596; NsEucl=0.905; SSD=1.166; NSW=0.927; rcor=26; rNcor=26; rlogoDP=21; rNIcor=24; rNsEucl=36; rSSD=27; rNSW=32; rank_mean=27.429; match_rank=25 a 0 0 0 15 66 89 0.0000 31 93 13 22 c 0 0 0 45 19 11 0.0000 33 0 14 11 g 0 0 0 12 15 0 0.0000 18 7 13 31 t 0 0 0 28 0 0 1.0000 18 0 60 36

ATHB-12_MA0950.1_JASPAR_rc_shift3 (ATHB-12_MA0950.1_JASPAR_rc) 0.864 0.768 0.605 -0.075 0.911 1.018 0.936 23 10 52 55 27 22 24 30.429 27
; oligos_5-7nt_m3 versus ATHB-12_MA0950.1_JASPAR_rc; m=14/19; ncol2=8; w=8; offset=1; strand=R; shift=3; score=30.4286; ---CAATcAtt ; cor=0.864; Ncor=0.768; logoDP=0.605; NIcor=-0.075; NsEucl=0.911; SSD=1.018; NSW=0.936; rcor=23; rNcor=10; rlogoDP=52; rNIcor=55; rNsEucl=27; rSSD=22; rNSW=24; rank_mean=30.429; match_rank=27 a 0 0 0 88 940 966 13 118 941 233 124 c 0 0 0 766 19 17 15 633 6 53 107 g 0 0 0 18 10 8 7 201 35 46 191 t 0 0 0 128 30 9 965 48 18 668 579

ATHB12_ATHB12_ArabidopsisPBM_rc_shift2 (ATHB12_ATHB12_ArabidopsisPBM_rc) 0.839 0.755 0.617 -0.059 0.913 1.232 0.932 25 12 51 53 25 30 29 32.143 28
; oligos_5-7nt_m3 versus ATHB12_ATHB12_ArabidopsisPBM_rc; m=15/19; ncol2=10; w=9; offset=0; strand=R; shift=2; score=32.1429; --yCAATcAtt ; cor=0.839; Ncor=0.755; logoDP=0.617; NIcor=-0.059; NsEucl=0.913; SSD=1.232; NSW=0.932; rcor=25; rNcor=12; rlogoDP=51; rNIcor=53; rNsEucl=25; rSSD=30; rNSW=29; rank_mean=32.143; match_rank=28 a 0 0 5 8 94 96 1 12 94 23 12 c 0 0 56 77 2 2 1 63 1 5 11 g 0 0 14 2 1 1 1 20 3 5 19 t 0 0 25 13 3 1 97 5 2 67 58

YAB1_YAB1_ArabidopsisPBM_shift3 (YAB1_YAB1_ArabidopsisPBM) 0.782 0.569 4.031 0.533 0.891 1.524 0.905 40 32 29 31 46 36 42 36.571 37
; oligos_5-7nt_m3 versus YAB1_YAB1_ArabidopsisPBM; m=16/19; ncol2=10; w=8; offset=1; strand=D; shift=3; score=36.5714; ---ywATmATA ; cor=0.782; Ncor=0.569; logoDP=4.031; NIcor=0.533; NsEucl=0.891; SSD=1.524; NSW=0.905; rcor=40; rNcor=32; rlogoDP=29; rNIcor=31; rNsEucl=46; rSSD=36; rNSW=42; rank_mean=36.571; match_rank=37 a 0 0 0 9 64 86 4 29 91 5 73 c 0 0 0 47 3 3 2 43 1 3 8 g 0 0 0 10 4 2 4 13 5 4 12 t 0 0 0 34 29 9 90 15 3 88 7

APRR2_M1332_1.02_CISBP_shift0 (APRR2_M1332_1.02_CISBP) 0.767 0.558 2.954 0.571 0.887 1.629 0.898 46 36 34 26 49 41 47 39.857 44
; oligos_5-7nt_m3 versus APRR2_M1332_1.02_CISBP; m=17/19; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=39.8571; rsrwaATCya- ; cor=0.767; Ncor=0.558; logoDP=2.954; NIcor=0.571; NsEucl=0.887; SSD=1.629; NSW=0.898; rcor=46; rNcor=36; rlogoDP=34; rNIcor=26; rNsEucl=49; rSSD=41; rNSW=47; rank_mean=39.857; match_rank=44 a 30 15 27 30 63 87 11 14 15 34 0 c 18 38 12 22 5 2 4 71 28 22 0 g 30 25 53 20 12 1 0 7 13 24 0 t 22 22 8 28 20 10 85 8 44 20 0

e_gw1.362.4.1_M1384_1.02_CISBP_shift0 (e_gw1.362.4.1_M1384_1.02_CISBP) 0.754 0.548 5.091 0.541 0.886 1.667 0.896 55 40 23 29 51 44 49 41.571 49
; oligos_5-7nt_m3 versus e_gw1.362.4.1_M1384_1.02_CISBP; m=18/19; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=41.5714; asmrdATCtw- ; cor=0.754; Ncor=0.548; logoDP=5.091; NIcor=0.541; NsEucl=0.886; SSD=1.667; NSW=0.896; rcor=55; rNcor=40; rlogoDP=23; rNIcor=29; rNsEucl=51; rSSD=44; rNSW=49; rank_mean=41.571; match_rank=49 a 35 18 29 35 42 100 1 7 19 26 0 c 19 29 38 12 4 0 0 89 18 23 0 g 24 32 20 47 25 0 0 0 14 20 0 t 22 21 13 6 29 0 99 4 49 31 0

estExt_fgenesh1_pg.C_Chr_16.00010090_M1397_1.02_CISBP_shift1 (estExt_fgenesh1_pg.C_Chr_16.00010090_M1397_1.02_CISBP) 0.756 0.529 3.196 0.509 0.869 1.685 0.880 53 42 31 36 59 45 53 45.571 53
; oligos_5-7nt_m3 versus estExt_fgenesh1_pg.C_Chr_16.00010090_M1397_1.02_CISBP; m=19/19; ncol2=8; w=7; offset=-1; strand=D; shift=1; score=45.5714; -smrdATct-- ; cor=0.756; Ncor=0.529; logoDP=3.196; NIcor=0.509; NsEucl=0.869; SSD=1.685; NSW=0.880; rcor=53; rNcor=42; rlogoDP=31; rNIcor=36; rNsEucl=59; rSSD=45; rNSW=53; rank_mean=45.571; match_rank=53 a 0 20 27 28 33 98 9 13 24 0 0 c 0 29 33 20 10 0 3 66 23 0 0 g 0 29 23 39 27 1 1 10 21 0 0 t 0 22 17 13 30 1 87 11 32 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_shift2 (oligos_5-7nt_m3)																	; oligos_5-7nt_m3; m=0 (reference); ncol1=9; shift=2; ncol=11; --waAATCAwa ; Alignment reference a 0 0 30 32 83 83 0 0 83 34 32 c 0 0 20 20 0 0 0 83 0 11 17 g 0 0 12 13 0 0 0 0 0 13 19 t 0 0 21 18 0 0 83 0 0 25 15
HAT3_M0848_1.02_CISBP_shift2 (HAT3_M0848_1.02_CISBP)	0.929	0.826	4.614	0.844	0.933	0.571	0.964	6	1	26	1	8	7	7	8.000	3	; oligos_5-7nt_m3 versus HAT3_M0848_1.02_CISBP; m=1/19; ncol2=8; w=8; offset=0; strand=D; shift=2; score= 8; --syAATCAw- ; cor=0.929; Ncor=0.826; logoDP=4.614; NIcor=0.844; NsEucl=0.933; SSD=0.571; NSW=0.964; rcor=6; rNcor=1; rlogoDP=26; rNIcor=1; rNsEucl=8; rSSD=7; rNSW=7; rank_mean=8.000; match_rank=3 a 0 0 12 6 85 86 5 11 82 33 0 c 0 0 35 54 7 6 6 76 3 15 0 g 0 0 35 3 1 3 0 6 6 12 0 t 0 0 18 37 7 5 89 7 9 40 0
LOC_Os09g35910_M1108_1.02_CISBP_shift0 (LOC_Os09g35910_M1108_1.02_CISBP)	0.936	0.681	6.767	0.688	0.939	0.476	0.970	5	15	14	13	6	5	5	9.000	4	; oligos_5-7nt_m3 versus LOC_Os09g35910_M1108_1.02_CISBP; m=2/19; ncol2=10; w=8; offset=-2; strand=D; shift=0; score= 9; rwyyAATCAw- ; cor=0.936; Ncor=0.681; logoDP=6.767; NIcor=0.688; NsEucl=0.939; SSD=0.476; NSW=0.970; rcor=5; rNcor=15; rlogoDP=14; rNIcor=13; rNsEucl=6; rSSD=5; rNSW=5; rank_mean=9.000; match_rank=4 a 30 28 11 5 87 96 1 1 79 40 0 c 22 23 37 64 5 3 0 96 3 17 0 g 25 23 19 2 2 0 0 1 10 12 0 t 23 26 33 29 6 1 99 2 8 31 0
ATHB-7_MA0954.1_JASPAR_shift2 (ATHB-7_MA0954.1_JASPAR)	0.892	0.803	9.649	0.808	0.923	0.961	0.947	14	5	4	3	14	16	15	10.143	5	; oligos_5-7nt_m3 versus ATHB-7_MA0954.1_JASPAR; m=3/19; ncol2=10; w=9; offset=0; strand=D; shift=2; score=10.1429; --yCAATCAWt ; cor=0.892; Ncor=0.803; logoDP=9.649; NIcor=0.808; NsEucl=0.923; SSD=0.961; NSW=0.947; rcor=14; rNcor=5; rlogoDP=4; rNIcor=3; rNsEucl=14; rSSD=16; rNSW=15; rank_mean=10.143; match_rank=5 a 0 0 152 27 1000 1000 0 0 1000 291 183 c 0 0 338 828 0 0 0 1000 0 0 98 g 0 0 152 27 0 0 0 0 0 0 190 t 0 0 358 118 0 0 1000 0 0 709 528
GRMZM2G038252_M1209_1.02_CISBP_shift2 (GRMZM2G038252_M1209_1.02_CISBP)	0.898	0.799	7.704	0.800	0.922	0.772	0.952	10	7	11	9	16	11	11	10.714	7	; oligos_5-7nt_m3 versus GRMZM2G038252_M1209_1.02_CISBP; m=4/19; ncol2=8; w=8; offset=0; strand=D; shift=2; score=10.7143; --tCAATYAa- ; cor=0.898; Ncor=0.799; logoDP=7.704; NIcor=0.800; NsEucl=0.922; SSD=0.772; NSW=0.952; rcor=10; rNcor=7; rlogoDP=11; rNIcor=9; rNsEucl=16; rSSD=11; rNSW=11; rank_mean=10.714; match_rank=7 a 0 0 11 6 99 98 1 0 95 55 0 c 0 0 23 77 1 0 0 70 1 10 0 g 0 0 16 0 0 2 0 0 0 21 0 t 0 0 50 17 0 0 99 30 4 14 0
ATHB7_M0846_1.02_CISBP_shift2 (ATHB7_M0846_1.02_CISBP)	0.891	0.802	9.649	0.807	0.923	0.967	0.946	15	6	3	6	15	17	16	11.143	8	; oligos_5-7nt_m3 versus ATHB7_M0846_1.02_CISBP; m=5/19; ncol2=10; w=9; offset=0; strand=D; shift=2; score=11.1429; --yCAATCAWt ; cor=0.891; Ncor=0.802; logoDP=9.649; NIcor=0.807; NsEucl=0.923; SSD=0.967; NSW=0.946; rcor=15; rNcor=6; rlogoDP=3; rNIcor=6; rNsEucl=15; rSSD=17; rNSW=16; rank_mean=11.143; match_rank=8 a 0 0 15 3 100 100 0 0 100 29 18 c 0 0 34 83 0 0 0 100 0 0 10 g 0 0 15 3 0 0 0 0 0 0 19 t 0 0 36 11 0 0 100 0 0 71 53
HAT1_MA1024.1_JASPAR_shift2 (HAT1_MA1024.1_JASPAR)	0.885	0.796	9.650	0.807	0.921	1.010	0.944	17	8	2	5	18	19	18	12.429	9	; oligos_5-7nt_m3 versus HAT1_MA1024.1_JASPAR; m=6/19; ncol2=10; w=9; offset=0; strand=D; shift=2; score=12.4286; --syAATCATk ; cor=0.885; Ncor=0.796; logoDP=9.650; NIcor=0.807; NsEucl=0.921; SSD=1.010; NSW=0.944; rcor=17; rNcor=8; rlogoDP=2; rNIcor=5; rNsEucl=18; rSSD=19; rNSW=18; rank_mean=12.429; match_rank=9 a 0 0 149 69 1000 1000 0 0 1000 98 101 c 0 0 374 506 0 0 0 1000 0 0 101 g 0 0 328 69 0 0 0 0 0 0 286 t 0 0 149 356 0 0 1000 0 0 902 512
HAT1_M0851_1.02_CISBP_shift2 (HAT1_M0851_1.02_CISBP)	0.884	0.796	9.650	0.807	0.921	1.014	0.944	18	9	1	4	19	20	19	12.857	10	; oligos_5-7nt_m3 versus HAT1_M0851_1.02_CISBP; m=7/19; ncol2=10; w=9; offset=0; strand=D; shift=2; score=12.8571; --syAATCATk ; cor=0.884; Ncor=0.796; logoDP=9.650; NIcor=0.807; NsEucl=0.921; SSD=1.014; NSW=0.944; rcor=18; rNcor=9; rlogoDP=1; rNIcor=4; rNsEucl=19; rSSD=20; rNSW=19; rank_mean=12.857; match_rank=10 a 0 0 15 6 100 100 0 0 100 10 10 c 0 0 37 51 0 0 0 100 0 0 10 g 0 0 33 7 0 0 0 0 0 0 29 t 0 0 15 36 0 0 100 0 0 90 51
ATHB-4_M0845_1.02_CISBP_shift2 (ATHB-4_M0845_1.02_CISBP)	0.898	0.808	2.868	0.816	0.925	0.902	0.950	12	4	37	2	11	13	12	13.000	11	; oligos_5-7nt_m3 versus ATHB-4_M0845_1.02_CISBP; m=8/19; ncol2=10; w=9; offset=0; strand=D; shift=2; score= 13; --syAATcAtt ; cor=0.898; Ncor=0.808; logoDP=2.868; NIcor=0.816; NsEucl=0.925; SSD=0.902; NSW=0.950; rcor=12; rNcor=4; rlogoDP=37; rNIcor=2; rNsEucl=11; rSSD=13; rNSW=12; rank_mean=13.000; match_rank=11 a 0 0 17 11 77 79 11 13 75 23 22 c 0 0 35 48 7 9 4 59 6 13 20 g 0 0 27 4 3 5 7 14 8 11 20 t 0 0 21 37 13 7 78 14 11 53 38
ATWOX13_M0853_1.02_CISBP_shift2 (ATWOX13_M0853_1.02_CISBP)	0.859	0.763	8.096	0.757	0.904	1.178	0.926	24	11	8	10	37	28	33	21.571	17	; oligos_5-7nt_m3 versus ATWOX13_M0853_1.02_CISBP; m=9/19; ncol2=8; w=8; offset=0; strand=D; shift=2; score=21.5714; --TCAATCAa- ; cor=0.859; Ncor=0.763; logoDP=8.096; NIcor=0.757; NsEucl=0.904; SSD=1.178; NSW=0.926; rcor=24; rNcor=11; rlogoDP=8; rNIcor=10; rNsEucl=37; rSSD=28; rNSW=33; rank_mean=21.571; match_rank=17 a 0 0 0 0 100 100 0 7 93 60 0 c 0 0 9 85 0 0 0 80 0 10 0 g 0 0 9 0 0 0 0 0 0 20 0 t 0 0 82 15 0 0 100 13 7 10 0
ATHB6_M0843_1.02_CISBP_shift2 (ATHB6_M0843_1.02_CISBP)	0.816	0.816	4.783	0.806	0.911	1.295	0.928	29	2	25	7	29	31	30	21.857	18	; oligos_5-7nt_m3 versus ATHB6_M0843_1.02_CISBP; m=10/19; ncol2=9; w=9; offset=0; strand=D; shift=2; score=21.8571; --byAATmATk ; cor=0.816; Ncor=0.816; logoDP=4.783; NIcor=0.806; NsEucl=0.911; SSD=1.295; NSW=0.928; rcor=29; rNcor=2; rlogoDP=25; rNIcor=7; rNsEucl=29; rSSD=31; rNSW=30; rank_mean=21.857; match_rank=18 a 0 0 18 15 75 89 2 36 92 11 23 c 0 0 25 52 9 7 1 31 1 7 11 g 0 0 29 8 7 0 0 13 4 13 27 t 0 0 28 25 9 4 97 20 3 69 39
WOX13_WOX13_ArabidopsisPBM_shift0 (WOX13_WOX13_ArabidopsisPBM)	0.865	0.629	7.009	0.619	0.909	1.064	0.933	21	21	12	19	32	24	28	22.429	19	; oligos_5-7nt_m3 versus WOX13_WOX13_ArabidopsisPBM; m=11/19; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=22.4286; wrTCAATCAa- ; cor=0.865; Ncor=0.629; logoDP=7.009; NIcor=0.619; NsEucl=0.909; SSD=1.064; NSW=0.933; rcor=21; rNcor=21; rlogoDP=12; rNIcor=19; rNsEucl=32; rSSD=24; rNSW=28; rank_mean=22.429; match_rank=19 a 32 54 3 2 95 96 1 1 90 40 0 c 16 3 13 93 1 1 1 86 3 15 0 g 15 31 12 1 1 1 1 1 2 21 0 t 37 12 72 4 3 2 97 12 5 24 0
ATHB-6_MA0953.1_JASPAR_shift2 (ATHB-6_MA0953.1_JASPAR)	0.815	0.815	4.801	0.803	0.910	1.305	0.927	30	3	24	8	30	33	31	22.714	20	; oligos_5-7nt_m3 versus ATHB-6_MA0953.1_JASPAR; m=12/19; ncol2=9; w=9; offset=0; strand=D; shift=2; score=22.7143; --bcAATmATk ; cor=0.815; Ncor=0.815; logoDP=4.801; NIcor=0.803; NsEucl=0.910; SSD=1.305; NSW=0.927; rcor=30; rNcor=3; rlogoDP=24; rNIcor=8; rNsEucl=30; rSSD=33; rNSW=31; rank_mean=22.714; match_rank=20 a 0 0 177 149 745 886 20 356 924 106 234 c 0 0 252 524 89 71 6 310 5 66 111 g 0 0 287 85 73 1 1 128 38 130 266 t 0 0 284 243 92 42 972 206 32 698 389
estExt_gwp_gw1.C_70211_M1195_1.02_CISBP_shift3 (estExt_gwp_gw1.C_70211_M1195_1.02_CISBP)	0.836	0.608	5.162	0.596	0.905	1.166	0.927	26	26	21	24	36	27	32	27.429	25	; oligos_5-7nt_m3 versus estExt_gwp_gw1.C_70211_M1195_1.02_CISBP; m=13/19; ncol2=10; w=8; offset=1; strand=D; shift=3; score=27.4286; ---yaATmAtk ; cor=0.836; Ncor=0.608; logoDP=5.162; NIcor=0.596; NsEucl=0.905; SSD=1.166; NSW=0.927; rcor=26; rNcor=26; rlogoDP=21; rNIcor=24; rNsEucl=36; rSSD=27; rNSW=32; rank_mean=27.429; match_rank=25 a 0 0 0 15 66 89 0.0000 31 93 13 22 c 0 0 0 45 19 11 0.0000 33 0 14 11 g 0 0 0 12 15 0 0.0000 18 7 13 31 t 0 0 0 28 0 0 1.0000 18 0 60 36
ATHB-12_MA0950.1_JASPAR_rc_shift3 (ATHB-12_MA0950.1_JASPAR_rc)	0.864	0.768	0.605	-0.075	0.911	1.018	0.936	23	10	52	55	27	22	24	30.429	27	; oligos_5-7nt_m3 versus ATHB-12_MA0950.1_JASPAR_rc; m=14/19; ncol2=8; w=8; offset=1; strand=R; shift=3; score=30.4286; ---CAATcAtt ; cor=0.864; Ncor=0.768; logoDP=0.605; NIcor=-0.075; NsEucl=0.911; SSD=1.018; NSW=0.936; rcor=23; rNcor=10; rlogoDP=52; rNIcor=55; rNsEucl=27; rSSD=22; rNSW=24; rank_mean=30.429; match_rank=27 a 0 0 0 88 940 966 13 118 941 233 124 c 0 0 0 766 19 17 15 633 6 53 107 g 0 0 0 18 10 8 7 201 35 46 191 t 0 0 0 128 30 9 965 48 18 668 579
ATHB12_ATHB12_ArabidopsisPBM_rc_shift2 (ATHB12_ATHB12_ArabidopsisPBM_rc)	0.839	0.755	0.617	-0.059	0.913	1.232	0.932	25	12	51	53	25	30	29	32.143	28	; oligos_5-7nt_m3 versus ATHB12_ATHB12_ArabidopsisPBM_rc; m=15/19; ncol2=10; w=9; offset=0; strand=R; shift=2; score=32.1429; --yCAATcAtt ; cor=0.839; Ncor=0.755; logoDP=0.617; NIcor=-0.059; NsEucl=0.913; SSD=1.232; NSW=0.932; rcor=25; rNcor=12; rlogoDP=51; rNIcor=53; rNsEucl=25; rSSD=30; rNSW=29; rank_mean=32.143; match_rank=28 a 0 0 5 8 94 96 1 12 94 23 12 c 0 0 56 77 2 2 1 63 1 5 11 g 0 0 14 2 1 1 1 20 3 5 19 t 0 0 25 13 3 1 97 5 2 67 58
YAB1_YAB1_ArabidopsisPBM_shift3 (YAB1_YAB1_ArabidopsisPBM)	0.782	0.569	4.031	0.533	0.891	1.524	0.905	40	32	29	31	46	36	42	36.571	37	; oligos_5-7nt_m3 versus YAB1_YAB1_ArabidopsisPBM; m=16/19; ncol2=10; w=8; offset=1; strand=D; shift=3; score=36.5714; ---ywATmATA ; cor=0.782; Ncor=0.569; logoDP=4.031; NIcor=0.533; NsEucl=0.891; SSD=1.524; NSW=0.905; rcor=40; rNcor=32; rlogoDP=29; rNIcor=31; rNsEucl=46; rSSD=36; rNSW=42; rank_mean=36.571; match_rank=37 a 0 0 0 9 64 86 4 29 91 5 73 c 0 0 0 47 3 3 2 43 1 3 8 g 0 0 0 10 4 2 4 13 5 4 12 t 0 0 0 34 29 9 90 15 3 88 7
APRR2_M1332_1.02_CISBP_shift0 (APRR2_M1332_1.02_CISBP)	0.767	0.558	2.954	0.571	0.887	1.629	0.898	46	36	34	26	49	41	47	39.857	44	; oligos_5-7nt_m3 versus APRR2_M1332_1.02_CISBP; m=17/19; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=39.8571; rsrwaATCya- ; cor=0.767; Ncor=0.558; logoDP=2.954; NIcor=0.571; NsEucl=0.887; SSD=1.629; NSW=0.898; rcor=46; rNcor=36; rlogoDP=34; rNIcor=26; rNsEucl=49; rSSD=41; rNSW=47; rank_mean=39.857; match_rank=44 a 30 15 27 30 63 87 11 14 15 34 0 c 18 38 12 22 5 2 4 71 28 22 0 g 30 25 53 20 12 1 0 7 13 24 0 t 22 22 8 28 20 10 85 8 44 20 0
e_gw1.362.4.1_M1384_1.02_CISBP_shift0 (e_gw1.362.4.1_M1384_1.02_CISBP)	0.754	0.548	5.091	0.541	0.886	1.667	0.896	55	40	23	29	51	44	49	41.571	49	; oligos_5-7nt_m3 versus e_gw1.362.4.1_M1384_1.02_CISBP; m=18/19; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=41.5714; asmrdATCtw- ; cor=0.754; Ncor=0.548; logoDP=5.091; NIcor=0.541; NsEucl=0.886; SSD=1.667; NSW=0.896; rcor=55; rNcor=40; rlogoDP=23; rNIcor=29; rNsEucl=51; rSSD=44; rNSW=49; rank_mean=41.571; match_rank=49 a 35 18 29 35 42 100 1 7 19 26 0 c 19 29 38 12 4 0 0 89 18 23 0 g 24 32 20 47 25 0 0 0 14 20 0 t 22 21 13 6 29 0 99 4 49 31 0
estExt_fgenesh1_pg.C_Chr_16.00010090_M1397_1.02_CISBP_shift1 (estExt_fgenesh1_pg.C_Chr_16.00010090_M1397_1.02_CISBP)	0.756	0.529	3.196	0.509	0.869	1.685	0.880	53	42	31	36	59	45	53	45.571	53	; oligos_5-7nt_m3 versus estExt_fgenesh1_pg.C_Chr_16.00010090_M1397_1.02_CISBP; m=19/19; ncol2=8; w=7; offset=-1; strand=D; shift=1; score=45.5714; -smrdATct-- ; cor=0.756; Ncor=0.529; logoDP=3.196; NIcor=0.509; NsEucl=0.869; SSD=1.685; NSW=0.880; rcor=53; rNcor=42; rlogoDP=31; rNIcor=36; rNsEucl=59; rSSD=45; rNSW=53; rank_mean=45.571; match_rank=53 a 0 20 27 28 33 98 9 13 24 0 0 c 0 29 33 20 10 0 3 66 23 0 0 g 0 29 23 39 27 1 1 10 21 0 0 t 0 22 17 13 30 1 87 11 32 0 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m5_shift0 ; 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
oligos_5-7nt_m5_shift0 (oligos_5-7nt_m5)
; oligos_5-7nt_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; hwtaTTTAAACtt ; Alignment reference a 10 9 8 19 1 1 0 30 27 30 2 7 6 c 9 6 2 6 1 3 1 3 1 0 30 7 7 g 3 7 3 4 2 1 0 0 3 1 1 8 6 t 11 11 20 4 29 28 32 0 2 2 0 11 14

AT2G20110_M0588_1.02_CISBP_rc_shift3 (AT2G20110_M0588_1.02_CISBP_rc) 0.909 0.559 5.836 0.522 0.924 0.741 0.954 9 35 17 34 13 10 10 18.286 12
; oligos_5-7nt_m5 versus AT2G20110_M0588_1.02_CISBP_rc; m=1/6; ncol2=8; w=8; offset=3; strand=R; shift=3; score=18.2857; ---dTTTAAAy-- ; cor=0.909; Ncor=0.559; logoDP=5.836; NIcor=0.522; NsEucl=0.924; SSD=0.741; NSW=0.954; rcor=9; rNcor=35; rlogoDP=17; rNIcor=34; rNsEucl=13; rSSD=10; rNSW=10; rank_mean=18.286; match_rank=12 a 0 0 0 50 0 0 0 80 100 100 20 0 0 c 0 0 0 0 0 0 20 0 0 0 40 0 0 g 0 0 0 25 0 0 0 20 0 0 0 0 0 t 0 0 0 25 100 100 80 0 0 0 40 0 0

BRADI1G55710_M0592_1.02_CISBP_shift2 (BRADI1G55710_M0592_1.02_CISBP) 0.813 0.625 1.370 0.629 0.909 1.649 0.918 32 24 49 16 31 43 36 33.000 30
; oligos_5-7nt_m5 versus BRADI1G55710_M0592_1.02_CISBP; m=2/6; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 33; --mrTtyraAyk- ; cor=0.813; Ncor=0.625; logoDP=1.370; NIcor=0.629; NsEucl=0.909; SSD=1.649; NSW=0.918; rcor=32; rNcor=24; rlogoDP=49; rNIcor=16; rNsEucl=31; rSSD=43; rNSW=36; rank_mean=33.000; match_rank=30 a 0 0 29 46 6 11 6 51 60 76 12 24 0 c 0 0 27 14 12 16 33 11 13 6 28 20 0 g 0 0 20 28 6 13 10 33 16 12 14 27 0 t 0 0 24 12 76 60 51 5 11 6 46 29 0

SOL1_M0590_1.02_CISBP_rc_shift3 (SOL1_M0590_1.02_CISBP_rc) 0.832 0.512 4.548 0.440 0.899 1.298 0.919 28 45 28 40 41 32 35 35.571 36
; oligos_5-7nt_m5 versus SOL1_M0590_1.02_CISBP_rc; m=3/6; ncol2=8; w=8; offset=3; strand=R; shift=3; score=35.5714; ---wTTyAAAy-- ; cor=0.832; Ncor=0.512; logoDP=4.548; NIcor=0.440; NsEucl=0.899; SSD=1.298; NSW=0.919; rcor=28; rNcor=45; rlogoDP=28; rNIcor=40; rNsEucl=41; rSSD=32; rNSW=35; rank_mean=35.571; match_rank=36 a 0 0 0 62 7 0 7 80 100 96 23 0 0 c 0 0 0 0 0 2 61 2 0 0 41 0 0 g 0 0 0 10 0 0 0 15 0 2 10 0 0 t 0 0 0 28 93 98 32 3 0 2 26 0 0

fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP_shift3 (fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP) 0.771 0.593 1.419 0.597 0.905 1.797 0.910 42 30 48 23 34 47 38 37.429 38
; oligos_5-7nt_m5 versus fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP; m=4/6; ncol2=10; w=10; offset=3; strand=D; shift=3; score=37.4286; ---dTTTraawww ; cor=0.771; Ncor=0.593; logoDP=1.419; NIcor=0.597; NsEucl=0.905; SSD=1.797; NSW=0.910; rcor=42; rNcor=30; rlogoDP=48; rNIcor=23; rNsEucl=34; rSSD=47; rNSW=38; rank_mean=37.429; match_rank=38 a 0 0 0 34 9 12 6 34 56 52 26 25 26 c 0 0 0 10 10 8 24 14 13 14 22 20 19 g 0 0 0 26 6 5 0 45 11 16 15 19 22 t 0 0 0 30 75 75 70 7 20 18 37 36 33

TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_shift2 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint) 0.760 0.468 5.152 0.472 0.876 1.973 0.877 49 48 22 39 52 52 54 45.143 52
; oligos_5-7nt_m5 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint; m=5/6; ncol2=8; w=8; offset=2; strand=D; shift=2; score=45.1429; --CTTTTAAA--- ; cor=0.760; Ncor=0.468; logoDP=5.152; NIcor=0.472; NsEucl=0.876; SSD=1.973; NSW=0.877; rcor=49; rNcor=48; rlogoDP=22; rNIcor=39; rNsEucl=52; rSSD=52; rNSW=54; rank_mean=45.143; match_rank=52 a 0 0 11 0 8 2 0 87 96 87 0 0 0 c 0 0 69 0 8 8 0 0 0 1 0 0 0 g 0 0 8 0 8 8 0 0 0 8 0 0 0 t 0 0 8 96 72 78 96 9 0 0 0 0 0

TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn3_B_3D-footprint_rc_shift4 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn3_B_3D-footprint_rc) 0.755 0.465 1.703 0.027 0.874 2.037 0.873 54 49 44 50 54 54 56 51.571 60
; oligos_5-7nt_m5 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn3_B_3D-footprint_rc; m=6/6; ncol2=8; w=8; offset=4; strand=R; shift=4; score=51.5714; ----TATAAACG- ; cor=0.755; Ncor=0.465; logoDP=1.703; NIcor=0.027; NsEucl=0.874; SSD=2.037; NSW=0.873; rcor=54; rNcor=49; rlogoDP=44; rNIcor=50; rNsEucl=54; rSSD=54; rNSW=56; rank_mean=51.571; match_rank=60 a 0 0 0 0 7 96 0 96 88 73 7 9 0 c 0 0 0 0 8 0 7 0 7 7 88 14 0 g 0 0 0 0 0 0 0 0 0 7 0 66 0 t 0 0 0 0 81 0 89 0 1 9 1 7 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=13; shift=0; ncol=13; hwtaTTTAAACtt ; Alignment reference a 10 9 8 19 1 1 0 30 27 30 2 7 6 c 9 6 2 6 1 3 1 3 1 0 30 7 7 g 3 7 3 4 2 1 0 0 3 1 1 8 6 t 11 11 20 4 29 28 32 0 2 2 0 11 14
AT2G20110_M0588_1.02_CISBP_rc_shift3 (AT2G20110_M0588_1.02_CISBP_rc)	0.909	0.559	5.836	0.522	0.924	0.741	0.954	9	35	17	34	13	10	10	18.286	12	; oligos_5-7nt_m5 versus AT2G20110_M0588_1.02_CISBP_rc; m=1/6; ncol2=8; w=8; offset=3; strand=R; shift=3; score=18.2857; ---dTTTAAAy-- ; cor=0.909; Ncor=0.559; logoDP=5.836; NIcor=0.522; NsEucl=0.924; SSD=0.741; NSW=0.954; rcor=9; rNcor=35; rlogoDP=17; rNIcor=34; rNsEucl=13; rSSD=10; rNSW=10; rank_mean=18.286; match_rank=12 a 0 0 0 50 0 0 0 80 100 100 20 0 0 c 0 0 0 0 0 0 20 0 0 0 40 0 0 g 0 0 0 25 0 0 0 20 0 0 0 0 0 t 0 0 0 25 100 100 80 0 0 0 40 0 0
BRADI1G55710_M0592_1.02_CISBP_shift2 (BRADI1G55710_M0592_1.02_CISBP)	0.813	0.625	1.370	0.629	0.909	1.649	0.918	32	24	49	16	31	43	36	33.000	30	; oligos_5-7nt_m5 versus BRADI1G55710_M0592_1.02_CISBP; m=2/6; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 33; --mrTtyraAyk- ; cor=0.813; Ncor=0.625; logoDP=1.370; NIcor=0.629; NsEucl=0.909; SSD=1.649; NSW=0.918; rcor=32; rNcor=24; rlogoDP=49; rNIcor=16; rNsEucl=31; rSSD=43; rNSW=36; rank_mean=33.000; match_rank=30 a 0 0 29 46 6 11 6 51 60 76 12 24 0 c 0 0 27 14 12 16 33 11 13 6 28 20 0 g 0 0 20 28 6 13 10 33 16 12 14 27 0 t 0 0 24 12 76 60 51 5 11 6 46 29 0
SOL1_M0590_1.02_CISBP_rc_shift3 (SOL1_M0590_1.02_CISBP_rc)	0.832	0.512	4.548	0.440	0.899	1.298	0.919	28	45	28	40	41	32	35	35.571	36	; oligos_5-7nt_m5 versus SOL1_M0590_1.02_CISBP_rc; m=3/6; ncol2=8; w=8; offset=3; strand=R; shift=3; score=35.5714; ---wTTyAAAy-- ; cor=0.832; Ncor=0.512; logoDP=4.548; NIcor=0.440; NsEucl=0.899; SSD=1.298; NSW=0.919; rcor=28; rNcor=45; rlogoDP=28; rNIcor=40; rNsEucl=41; rSSD=32; rNSW=35; rank_mean=35.571; match_rank=36 a 0 0 0 62 7 0 7 80 100 96 23 0 0 c 0 0 0 0 0 2 61 2 0 0 41 0 0 g 0 0 0 10 0 0 0 15 0 2 10 0 0 t 0 0 0 28 93 98 32 3 0 2 26 0 0
fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP_shift3 (fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP)	0.771	0.593	1.419	0.597	0.905	1.797	0.910	42	30	48	23	34	47	38	37.429	38	; oligos_5-7nt_m5 versus fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP; m=4/6; ncol2=10; w=10; offset=3; strand=D; shift=3; score=37.4286; ---dTTTraawww ; cor=0.771; Ncor=0.593; logoDP=1.419; NIcor=0.597; NsEucl=0.905; SSD=1.797; NSW=0.910; rcor=42; rNcor=30; rlogoDP=48; rNIcor=23; rNsEucl=34; rSSD=47; rNSW=38; rank_mean=37.429; match_rank=38 a 0 0 0 34 9 12 6 34 56 52 26 25 26 c 0 0 0 10 10 8 24 14 13 14 22 20 19 g 0 0 0 26 6 5 0 45 11 16 15 19 22 t 0 0 0 30 75 75 70 7 20 18 37 36 33
TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_shift2 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint)	0.760	0.468	5.152	0.472	0.876	1.973	0.877	49	48	22	39	52	52	54	45.143	52	; oligos_5-7nt_m5 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint; m=5/6; ncol2=8; w=8; offset=2; strand=D; shift=2; score=45.1429; --CTTTTAAA--- ; cor=0.760; Ncor=0.468; logoDP=5.152; NIcor=0.472; NsEucl=0.876; SSD=1.973; NSW=0.877; rcor=49; rNcor=48; rlogoDP=22; rNIcor=39; rNsEucl=52; rSSD=52; rNSW=54; rank_mean=45.143; match_rank=52 a 0 0 11 0 8 2 0 87 96 87 0 0 0 c 0 0 69 0 8 8 0 0 0 1 0 0 0 g 0 0 8 0 8 8 0 0 0 8 0 0 0 t 0 0 8 96 72 78 96 9 0 0 0 0 0
TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn3_B_3D-footprint_rc_shift4 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn3_B_3D-footprint_rc)	0.755	0.465	1.703	0.027	0.874	2.037	0.873	54	49	44	50	54	54	56	51.571	60	; oligos_5-7nt_m5 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn3_B_3D-footprint_rc; m=6/6; ncol2=8; w=8; offset=4; strand=R; shift=4; score=51.5714; ----TATAAACG- ; cor=0.755; Ncor=0.465; logoDP=1.703; NIcor=0.027; NsEucl=0.874; SSD=2.037; NSW=0.873; rcor=54; rNcor=49; rlogoDP=44; rNIcor=50; rNsEucl=54; rSSD=54; rNSW=56; rank_mean=51.571; match_rank=60 a 0 0 0 0 7 96 0 96 88 73 7 9 0 c 0 0 0 0 8 0 7 0 7 7 88 14 0 g 0 0 0 0 0 0 0 0 0 7 0 66 0 t 0 0 0 0 81 0 89 0 1 9 1 7 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m2_shift0 ; 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
oligos_5-7nt_m2_shift0 (oligos_5-7nt_m2)
; oligos_5-7nt_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; dwGTTTAAACwh ; Alignment reference a 11 16 3 3 1 0 30 34 33 2 11 12 c 3 1 1 0 1 5 1 0 0 30 8 10 g 10 8 30 0 0 1 5 1 0 1 1 3 t 12 11 2 33 34 30 0 1 3 3 16 11

AT2G20110_M0588_1.02_CISBP_shift2 (AT2G20110_M0588_1.02_CISBP) 0.892 0.595 6.987 0.578 0.916 0.910 0.943 13 29 13 25 23 14 20 19.571 14
; oligos_5-7nt_m2 versus AT2G20110_M0588_1.02_CISBP; m=1/6; ncol2=8; w=8; offset=2; strand=D; shift=2; score=19.5714; --rTTTAAAh-- ; cor=0.892; Ncor=0.595; logoDP=6.987; NIcor=0.578; NsEucl=0.916; SSD=0.910; NSW=0.943; rcor=13; rNcor=29; rlogoDP=13; rNIcor=25; rNsEucl=23; rSSD=14; rNSW=20; rank_mean=19.571; match_rank=14 a 0 0 40 0 0 0 80 100 100 25 0 0 c 0 0 0 0 0 20 0 0 0 25 0 0 g 0 0 40 0 0 0 20 0 0 0 0 0 t 0 0 20 100 100 80 0 0 0 50 0 0

BRADI1G55710_M0592_1.02_CISBP_shift1 (BRADI1G55710_M0592_1.02_CISBP) 0.811 0.675 1.558 0.664 0.905 1.810 0.909 33 16 45 14 35 48 39 32.857 29
; oligos_5-7nt_m2 versus BRADI1G55710_M0592_1.02_CISBP; m=2/6; ncol2=10; w=10; offset=1; strand=D; shift=1; score=32.8571; -mrTtyraAyk- ; cor=0.811; Ncor=0.675; logoDP=1.558; NIcor=0.664; NsEucl=0.905; SSD=1.810; NSW=0.909; rcor=33; rNcor=16; rlogoDP=45; rNIcor=14; rNsEucl=35; rSSD=48; rNSW=39; rank_mean=32.857; match_rank=29 a 0 29 46 6 11 6 51 60 76 12 24 0 c 0 27 14 12 16 33 11 13 6 28 20 0 g 0 20 28 6 13 10 33 16 12 14 27 0 t 0 24 12 76 60 51 5 11 6 46 29 0

fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP_shift2 (fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP) 0.785 0.654 1.532 0.630 0.902 1.940 0.903 37 18 46 15 39 50 43 35.429 35
; oligos_5-7nt_m2 versus fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP; m=3/6; ncol2=10; w=10; offset=2; strand=D; shift=2; score=35.4286; --dTTTraawww ; cor=0.785; Ncor=0.654; logoDP=1.532; NIcor=0.630; NsEucl=0.902; SSD=1.940; NSW=0.903; rcor=37; rNcor=18; rlogoDP=46; rNIcor=15; rNsEucl=39; rSSD=50; rNSW=43; rank_mean=35.429; match_rank=35 a 0 0 34 9 12 6 34 56 52 26 25 26 c 0 0 10 10 8 24 14 13 14 22 20 19 g 0 0 26 6 5 0 45 11 16 15 19 22 t 0 0 30 75 75 70 7 20 18 37 36 33

AT3G04850_M0589_1.02_CISBP_rc_shift1 (AT3G04850_M0589_1.02_CISBP_rc) 0.751 0.626 2.991 0.617 0.901 1.965 0.902 59 22 33 20 40 51 44 38.429 39
; oligos_5-7nt_m2 versus AT3G04850_M0589_1.02_CISBP_rc; m=4/6; ncol2=10; w=10; offset=1; strand=R; shift=1; score=38.4286; -awTTyrAAwt- ; cor=0.751; Ncor=0.626; logoDP=2.991; NIcor=0.617; NsEucl=0.901; SSD=1.965; NSW=0.902; rcor=59; rNcor=22; rlogoDP=33; rNIcor=20; rNsEucl=40; rSSD=51; rNSW=44; rank_mean=38.429; match_rank=39 a 0 52 50 12 6 3 52 88 74 30 18 0 c 0 12 7 9 4 42 4 2 5 13 18 0 g 0 18 14 5 2 4 42 4 9 7 12 0 t 0 18 29 74 88 51 2 6 12 50 52 0

SOL1_M0590_1.02_CISBP_rc_shift2 (SOL1_M0590_1.02_CISBP_rc) 0.799 0.532 5.746 0.511 0.887 1.630 0.898 35 41 19 35 50 42 48 38.571 40
; oligos_5-7nt_m2 versus SOL1_M0590_1.02_CISBP_rc; m=5/6; ncol2=8; w=8; offset=2; strand=R; shift=2; score=38.5714; --wTTyAAAy-- ; cor=0.799; Ncor=0.532; logoDP=5.746; NIcor=0.511; NsEucl=0.887; SSD=1.630; NSW=0.898; rcor=35; rNcor=41; rlogoDP=19; rNIcor=35; rNsEucl=50; rSSD=42; rNSW=48; rank_mean=38.571; match_rank=40 a 0 0 62 7 0 7 80 100 96 23 0 0 c 0 0 0 0 2 61 2 0 0 41 0 0 g 0 0 10 0 0 0 15 0 2 10 0 0 t 0 0 28 93 98 32 3 0 2 26 0 0

gw1.20.00.89.1_M0601_1.02_CISBP_shift1 (gw1.20.00.89.1_M0601_1.02_CISBP) 0.750 0.625 0.878 0.611 0.894 2.264 0.887 60 23 50 21 44 59 51 44.000 51
; oligos_5-7nt_m2 versus gw1.20.00.89.1_M0601_1.02_CISBP; m=6/6; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 44; -awttyraawt- ; cor=0.750; Ncor=0.625; logoDP=0.878; NIcor=0.611; NsEucl=0.894; SSD=2.264; NSW=0.887; rcor=60; rNcor=23; rlogoDP=50; rNIcor=21; rNsEucl=44; rSSD=59; rNSW=51; rank_mean=44.000; match_rank=51 a 0 54 28 10 20 8 43 59 61 38 23 0 c 0 12 14 18 12 28 21 9 12 20 11 0 g 0 11 20 12 9 21 28 12 18 14 12 0 t 0 23 38 60 59 43 8 20 9 28 54 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_m2_shift0 (oligos_5-7nt_m2)																	; oligos_5-7nt_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; dwGTTTAAACwh ; Alignment reference a 11 16 3 3 1 0 30 34 33 2 11 12 c 3 1 1 0 1 5 1 0 0 30 8 10 g 10 8 30 0 0 1 5 1 0 1 1 3 t 12 11 2 33 34 30 0 1 3 3 16 11
AT2G20110_M0588_1.02_CISBP_shift2 (AT2G20110_M0588_1.02_CISBP)	0.892	0.595	6.987	0.578	0.916	0.910	0.943	13	29	13	25	23	14	20	19.571	14	; oligos_5-7nt_m2 versus AT2G20110_M0588_1.02_CISBP; m=1/6; ncol2=8; w=8; offset=2; strand=D; shift=2; score=19.5714; --rTTTAAAh-- ; cor=0.892; Ncor=0.595; logoDP=6.987; NIcor=0.578; NsEucl=0.916; SSD=0.910; NSW=0.943; rcor=13; rNcor=29; rlogoDP=13; rNIcor=25; rNsEucl=23; rSSD=14; rNSW=20; rank_mean=19.571; match_rank=14 a 0 0 40 0 0 0 80 100 100 25 0 0 c 0 0 0 0 0 20 0 0 0 25 0 0 g 0 0 40 0 0 0 20 0 0 0 0 0 t 0 0 20 100 100 80 0 0 0 50 0 0
BRADI1G55710_M0592_1.02_CISBP_shift1 (BRADI1G55710_M0592_1.02_CISBP)	0.811	0.675	1.558	0.664	0.905	1.810	0.909	33	16	45	14	35	48	39	32.857	29	; oligos_5-7nt_m2 versus BRADI1G55710_M0592_1.02_CISBP; m=2/6; ncol2=10; w=10; offset=1; strand=D; shift=1; score=32.8571; -mrTtyraAyk- ; cor=0.811; Ncor=0.675; logoDP=1.558; NIcor=0.664; NsEucl=0.905; SSD=1.810; NSW=0.909; rcor=33; rNcor=16; rlogoDP=45; rNIcor=14; rNsEucl=35; rSSD=48; rNSW=39; rank_mean=32.857; match_rank=29 a 0 29 46 6 11 6 51 60 76 12 24 0 c 0 27 14 12 16 33 11 13 6 28 20 0 g 0 20 28 6 13 10 33 16 12 14 27 0 t 0 24 12 76 60 51 5 11 6 46 29 0
fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP_shift2 (fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP)	0.785	0.654	1.532	0.630	0.902	1.940	0.903	37	18	46	15	39	50	43	35.429	35	; oligos_5-7nt_m2 versus fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP; m=3/6; ncol2=10; w=10; offset=2; strand=D; shift=2; score=35.4286; --dTTTraawww ; cor=0.785; Ncor=0.654; logoDP=1.532; NIcor=0.630; NsEucl=0.902; SSD=1.940; NSW=0.903; rcor=37; rNcor=18; rlogoDP=46; rNIcor=15; rNsEucl=39; rSSD=50; rNSW=43; rank_mean=35.429; match_rank=35 a 0 0 34 9 12 6 34 56 52 26 25 26 c 0 0 10 10 8 24 14 13 14 22 20 19 g 0 0 26 6 5 0 45 11 16 15 19 22 t 0 0 30 75 75 70 7 20 18 37 36 33
AT3G04850_M0589_1.02_CISBP_rc_shift1 (AT3G04850_M0589_1.02_CISBP_rc)	0.751	0.626	2.991	0.617	0.901	1.965	0.902	59	22	33	20	40	51	44	38.429	39	; oligos_5-7nt_m2 versus AT3G04850_M0589_1.02_CISBP_rc; m=4/6; ncol2=10; w=10; offset=1; strand=R; shift=1; score=38.4286; -awTTyrAAwt- ; cor=0.751; Ncor=0.626; logoDP=2.991; NIcor=0.617; NsEucl=0.901; SSD=1.965; NSW=0.902; rcor=59; rNcor=22; rlogoDP=33; rNIcor=20; rNsEucl=40; rSSD=51; rNSW=44; rank_mean=38.429; match_rank=39 a 0 52 50 12 6 3 52 88 74 30 18 0 c 0 12 7 9 4 42 4 2 5 13 18 0 g 0 18 14 5 2 4 42 4 9 7 12 0 t 0 18 29 74 88 51 2 6 12 50 52 0
SOL1_M0590_1.02_CISBP_rc_shift2 (SOL1_M0590_1.02_CISBP_rc)	0.799	0.532	5.746	0.511	0.887	1.630	0.898	35	41	19	35	50	42	48	38.571	40	; oligos_5-7nt_m2 versus SOL1_M0590_1.02_CISBP_rc; m=5/6; ncol2=8; w=8; offset=2; strand=R; shift=2; score=38.5714; --wTTyAAAy-- ; cor=0.799; Ncor=0.532; logoDP=5.746; NIcor=0.511; NsEucl=0.887; SSD=1.630; NSW=0.898; rcor=35; rNcor=41; rlogoDP=19; rNIcor=35; rNsEucl=50; rSSD=42; rNSW=48; rank_mean=38.571; match_rank=40 a 0 0 62 7 0 7 80 100 96 23 0 0 c 0 0 0 0 2 61 2 0 0 41 0 0 g 0 0 10 0 0 0 15 0 2 10 0 0 t 0 0 28 93 98 32 3 0 2 26 0 0
gw1.20.00.89.1_M0601_1.02_CISBP_shift1 (gw1.20.00.89.1_M0601_1.02_CISBP)	0.750	0.625	0.878	0.611	0.894	2.264	0.887	60	23	50	21	44	59	51	44.000	51	; oligos_5-7nt_m2 versus gw1.20.00.89.1_M0601_1.02_CISBP; m=6/6; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 44; -awttyraawt- ; cor=0.750; Ncor=0.625; logoDP=0.878; NIcor=0.611; NsEucl=0.894; SSD=2.264; NSW=0.887; rcor=60; rNcor=23; rlogoDP=50; rNIcor=21; rNsEucl=44; rSSD=59; rNSW=51; rank_mean=44.000; match_rank=51 a 0 54 28 10 20 8 43 59 61 38 23 0 c 0 12 14 18 12 28 21 9 12 20 11 0 g 0 11 20 12 9 21 28 12 18 14 12 0 t 0 23 38 60 59 43 8 20 9 28 54 0

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift0 ; 12 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=14; shift=0; ncol=16; wsAAATawmATCtw-- ; Alignment reference a 13 5 39 37 39 3 26 13 14 36 1 1 10 11 0 0 c 7 18 2 2 1 8 7 1 18 2 0 39 9 8 0 0 g 6 11 1 3 2 1 2 2 6 0 1 0 5 6 0 0 t 16 8 0 0 0 30 7 26 4 4 40 2 18 17 0 0

TIFY2A_M0760_1.02_CISBP_rc_shift7 (TIFY2A_M0760_1.02_CISBP_rc) 0.917 0.458 0.240 -0.099 0.941 0.347 0.975 8 50 56 57 4 4 4 26.143 21
; dyads_test_vs_ctrl_m1 versus TIFY2A_M0760_1.02_CISBP_rc; m=1/11; ncol2=7; w=7; offset=7; strand=R; shift=7; score=26.1429; -------hsATCtd-- ; cor=0.917; Ncor=0.458; logoDP=0.240; NIcor=-0.099; NsEucl=0.941; SSD=0.347; NSW=0.975; rcor=8; rNcor=50; rlogoDP=56; rNIcor=57; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=26.143; match_rank=21 a 0 0 0 0 0 0 0 28 24 99 7 5 23 26 0 0 c 0 0 0 0 0 0 0 25 31 0 1 86 13 23 0 0 g 0 0 0 0 0 0 0 20 32 0 0 1 24 25 0 0 t 0 0 0 0 0 0 0 27 13 1 92 8 40 26 0 0

TIFY2B_M0762_1.02_CISBP_rc_shift6 (TIFY2B_M0762_1.02_CISBP_rc) 0.888 0.444 0.270 -0.073 0.928 0.510 0.964 16 52 54 54 10 6 8 28.571 26
; dyads_test_vs_ctrl_m1 versus TIFY2B_M0762_1.02_CISBP_rc; m=2/11; ncol2=7; w=7; offset=6; strand=R; shift=6; score=28.5714; ------hwsATCt--- ; cor=0.888; Ncor=0.444; logoDP=0.270; NIcor=-0.073; NsEucl=0.928; SSD=0.510; NSW=0.964; rcor=16; rNcor=52; rlogoDP=54; rNIcor=54; rNsEucl=10; rSSD=6; rNSW=8; rank_mean=28.571; match_rank=26 a 0 0 0 0 0 0 26 28 24 100 3 4 21 0 0 0 c 0 0 0 0 0 0 26 24 27 0 0 96 11 0 0 0 g 0 0 0 0 0 0 17 19 40 0 0 0 23 0 0 0 t 0 0 0 0 0 0 31 29 9 0 97 0 45 0 0 0

GATA27_M0771_1.02_CISBP_rc_shift5 (GATA27_M0771_1.02_CISBP_rc) 0.802 0.516 0.191 -0.094 0.922 0.983 0.945 34 43 58 56 17 18 17 34.714 31
; dyads_test_vs_ctrl_m1 versus GATA27_M0771_1.02_CISBP_rc; m=3/11; ncol2=9; w=9; offset=5; strand=R; shift=5; score=34.7143; -----wwygATCkr-- ; cor=0.802; Ncor=0.516; logoDP=0.191; NIcor=-0.094; NsEucl=0.922; SSD=0.983; NSW=0.945; rcor=34; rNcor=43; rlogoDP=58; rNIcor=56; rNsEucl=17; rSSD=18; rNSW=17; rank_mean=34.714; match_rank=31 a 0 0 0 0 0 26 27 23 23 73 14 16 18 26 0 0 c 0 0 0 0 0 24 22 27 24 4 0 73 14 20 0 0 g 0 0 0 0 0 21 23 17 42 18 0 3 37 30 0 0 t 0 0 0 0 0 29 28 33 11 5 86 8 31 24 0 0

PK27213.1_M1312_1.02_CISBP_rc_shift6 (PK27213.1_M1312_1.02_CISBP_rc) 0.813 0.407 0.195 -0.042 0.921 0.804 0.950 31 60 57 51 20 12 13 34.857 32
; dyads_test_vs_ctrl_m1 versus PK27213.1_M1312_1.02_CISBP_rc; m=4/11; ncol2=10; w=8; offset=6; strand=R; shift=6; score=34.8571; ------sttATCywkw ; cor=0.813; Ncor=0.407; logoDP=0.195; NIcor=-0.042; NsEucl=0.921; SSD=0.804; NSW=0.950; rcor=31; rNcor=60; rlogoDP=57; rNIcor=51; rNsEucl=20; rSSD=12; rNSW=13; rank_mean=34.857; match_rank=32 a 0 0 0 0 0 0 20 17 18 91 5 6 16 27 24 35 c 0 0 0 0 0 0 35 23 12 0 9 85 37 21 23 19 g 0 0 0 0 0 0 25 8 12 4 6 4 17 24 25 18 t 0 0 0 0 0 0 20 52 58 5 80 5 30 28 28 28

PK29550.1_M1314_1.02_CISBP_rc_shift5 (PK29550.1_M1314_1.02_CISBP_rc) 0.751 0.451 1.501 0.240 0.914 1.190 0.934 56 51 47 46 24 29 26 39.857 43
; dyads_test_vs_ctrl_m1 versus PK29550.1_M1314_1.02_CISBP_rc; m=5/11; ncol2=10; w=9; offset=5; strand=R; shift=5; score=39.8571; -----ycttATCyrw- ; cor=0.751; Ncor=0.451; logoDP=1.501; NIcor=0.240; NsEucl=0.914; SSD=1.190; NSW=0.934; rcor=56; rNcor=51; rlogoDP=47; rNIcor=46; rNsEucl=24; rSSD=29; rNSW=26; rank_mean=39.857; match_rank=43 a 0 0 0 0 0 19 20 17 18 89 4 4 7 34 27 0 c 0 0 0 0 0 36 35 24 12 3 7 86 54 14 24 0 g 0 0 0 0 0 20 24 5 13 3 5 3 9 28 22 0 t 0 0 0 0 0 25 21 54 57 5 84 7 30 24 27 0

AT5G08520_M1339_1.02_CISBP_rc_shift5 (AT5G08520_M1339_1.02_CISBP_rc) 0.760 0.489 0.256 -0.127 0.916 1.144 0.936 48 47 55 60 22 26 23 40.143 45
; dyads_test_vs_ctrl_m1 versus AT5G08520_M1339_1.02_CISBP_rc; m=6/11; ncol2=9; w=9; offset=5; strand=R; shift=5; score=40.1429; -----ccytATCyd-- ; cor=0.760; Ncor=0.489; logoDP=0.256; NIcor=-0.127; NsEucl=0.916; SSD=1.144; NSW=0.936; rcor=48; rNcor=47; rlogoDP=55; rNIcor=60; rNsEucl=22; rSSD=26; rNSW=23; rank_mean=40.143; match_rank=45 a 0 0 0 0 0 20 18 17 18 98 2 4 15 29 0 0 c 0 0 0 0 0 35 37 25 15 0 12 89 42 21 0 0 g 0 0 0 0 0 21 24 8 13 1 8 3 15 25 0 0 t 0 0 0 0 0 24 21 50 54 1 78 4 28 25 0 0

GATA15_MA1016.1_JASPAR_rc_shift6 (GATA15_MA1016.1_JASPAR_rc) 0.785 0.418 0.185 -0.110 0.911 1.016 0.936 38 57 60 59 26 21 22 40.429 46
; dyads_test_vs_ctrl_m1 versus GATA15_MA1016.1_JASPAR_rc; m=7/11; ncol2=9; w=8; offset=6; strand=R; shift=6; score=40.4286; ------yygATCryr- ; cor=0.785; Ncor=0.418; logoDP=0.185; NIcor=-0.110; NsEucl=0.911; SSD=1.016; NSW=0.936; rcor=38; rNcor=57; rlogoDP=60; rNIcor=59; rNsEucl=26; rSSD=21; rNSW=22; rank_mean=40.429; match_rank=46 a 0 0 0 0 0 0 212 207 126 996 19 19 465 208 296 0 c 0 0 0 0 0 0 280 268 156 0 0 903 66 284 217 0 g 0 0 0 0 0 0 239 201 663 1 0 38 288 200 281 0 t 0 0 0 0 0 0 269 324 55 3 980 40 182 308 206 0

GATA15_M0761_1.02_CISBP_rc_shift6 (GATA15_M0761_1.02_CISBP_rc) 0.784 0.418 0.186 -0.109 0.911 1.018 0.936 39 58 59 58 28 23 25 41.429 48
; dyads_test_vs_ctrl_m1 versus GATA15_M0761_1.02_CISBP_rc; m=8/11; ncol2=9; w=8; offset=6; strand=R; shift=6; score=41.4286; ------yygATCryr- ; cor=0.784; Ncor=0.418; logoDP=0.186; NIcor=-0.109; NsEucl=0.911; SSD=1.018; NSW=0.936; rcor=39; rNcor=58; rlogoDP=59; rNIcor=58; rNsEucl=28; rSSD=23; rNSW=25; rank_mean=41.429; match_rank=48 a 0 0 0 0 0 0 21 21 13 100 2 2 46 21 30 0 c 0 0 0 0 0 0 28 27 15 0 0 90 7 28 22 0 g 0 0 0 0 0 0 24 20 66 0 0 4 29 20 27 0 t 0 0 0 0 0 0 27 32 6 0 98 4 18 31 21 0

Medtr8g106590.1_M0145_1.02_CISBP_shift3 (Medtr8g106590.1_M0145_1.02_CISBP) 0.758 0.433 3.107 0.413 0.888 1.601 0.900 50 53 32 42 47 38 45 43.857 50
; dyads_test_vs_ctrl_m1 versus Medtr8g106590.1_M0145_1.02_CISBP; m=9/11; ncol2=8; w=8; offset=3; strand=D; shift=3; score=43.8571; ---AAAWTAAT----- ; cor=0.758; Ncor=0.433; logoDP=3.107; NIcor=0.413; NsEucl=0.888; SSD=1.601; NSW=0.900; rcor=50; rNcor=53; rlogoDP=32; rNIcor=42; rNsEucl=47; rSSD=38; rNSW=45; rank_mean=43.857; match_rank=50 a 0 0 0 84 88 83 69 17 83 76 19 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 3 4 0 0 0 0 0 g 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 4 12 17 31 83 17 21 77 0 0 0 0 0

AHL20_MA0933.1_JASPAR_shift3 (AHL20_MA0933.1_JASPAR) 0.751 0.429 2.873 0.392 0.888 1.604 0.900 57 56 36 44 48 39 46 46.571 54
; dyads_test_vs_ctrl_m1 versus AHL20_MA0933.1_JASPAR; m=10/11; ncol2=8; w=8; offset=3; strand=D; shift=3; score=46.5714; ---AATWAAwT----- ; cor=0.751; Ncor=0.429; logoDP=2.873; NIcor=0.392; NsEucl=0.888; SSD=1.604; NSW=0.900; rcor=57; rNcor=56; rlogoDP=36; rNIcor=44; rNsEucl=48; rSSD=39; rNSW=46; rank_mean=46.571; match_rank=54 a 0 0 0 774 753 120 250 774 843 648 54 0 0 0 0 0 c 0 0 0 66 6 4 6 4 8 12 28 0 0 0 0 0 g 0 0 0 73 5 13 6 4 1 3 18 0 0 0 0 0 t 0 0 0 88 235 862 738 218 148 337 900 0 0 0 0 0

CCA1_MA0972.1_JASPAR_shift2 (CCA1_MA0972.1_JASPAR) 0.757 0.433 4.603 0.411 0.866 2.305 0.856 51 54 27 43 60 60 60 50.714 59
; dyads_test_vs_ctrl_m1 versus CCA1_MA0972.1_JASPAR; m=11/11; ncol2=8; w=8; offset=2; strand=D; shift=2; score=50.7143; --AAATATCT------ ; cor=0.757; Ncor=0.433; logoDP=4.603; NIcor=0.411; NsEucl=0.866; SSD=2.305; NSW=0.856; rcor=51; rNcor=54; rlogoDP=27; rNIcor=43; rNsEucl=60; rSSD=60; rNSW=60; rank_mean=50.714; match_rank=59 a 0 0 934 960 985 35 992 1 5 21 0 0 0 0 0 0 c 0 0 1 1 4 0 5 12 991 91 0 0 0 0 0 0 g 0 0 10 37 10 5 1 1 0 14 0 0 0 0 0 0 t 0 0 54 2 1 960 2 986 4 874 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_m1_shift0 (dyads_test_vs_ctrl_m1)																	; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=0; ncol=16; wsAAATawmATCtw-- ; Alignment reference a 13 5 39 37 39 3 26 13 14 36 1 1 10 11 0 0 c 7 18 2 2 1 8 7 1 18 2 0 39 9 8 0 0 g 6 11 1 3 2 1 2 2 6 0 1 0 5 6 0 0 t 16 8 0 0 0 30 7 26 4 4 40 2 18 17 0 0
TIFY2A_M0760_1.02_CISBP_rc_shift7 (TIFY2A_M0760_1.02_CISBP_rc)	0.917	0.458	0.240	-0.099	0.941	0.347	0.975	8	50	56	57	4	4	4	26.143	21	; dyads_test_vs_ctrl_m1 versus TIFY2A_M0760_1.02_CISBP_rc; m=1/11; ncol2=7; w=7; offset=7; strand=R; shift=7; score=26.1429; -------hsATCtd-- ; cor=0.917; Ncor=0.458; logoDP=0.240; NIcor=-0.099; NsEucl=0.941; SSD=0.347; NSW=0.975; rcor=8; rNcor=50; rlogoDP=56; rNIcor=57; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=26.143; match_rank=21 a 0 0 0 0 0 0 0 28 24 99 7 5 23 26 0 0 c 0 0 0 0 0 0 0 25 31 0 1 86 13 23 0 0 g 0 0 0 0 0 0 0 20 32 0 0 1 24 25 0 0 t 0 0 0 0 0 0 0 27 13 1 92 8 40 26 0 0
TIFY2B_M0762_1.02_CISBP_rc_shift6 (TIFY2B_M0762_1.02_CISBP_rc)	0.888	0.444	0.270	-0.073	0.928	0.510	0.964	16	52	54	54	10	6	8	28.571	26	; dyads_test_vs_ctrl_m1 versus TIFY2B_M0762_1.02_CISBP_rc; m=2/11; ncol2=7; w=7; offset=6; strand=R; shift=6; score=28.5714; ------hwsATCt--- ; cor=0.888; Ncor=0.444; logoDP=0.270; NIcor=-0.073; NsEucl=0.928; SSD=0.510; NSW=0.964; rcor=16; rNcor=52; rlogoDP=54; rNIcor=54; rNsEucl=10; rSSD=6; rNSW=8; rank_mean=28.571; match_rank=26 a 0 0 0 0 0 0 26 28 24 100 3 4 21 0 0 0 c 0 0 0 0 0 0 26 24 27 0 0 96 11 0 0 0 g 0 0 0 0 0 0 17 19 40 0 0 0 23 0 0 0 t 0 0 0 0 0 0 31 29 9 0 97 0 45 0 0 0
GATA27_M0771_1.02_CISBP_rc_shift5 (GATA27_M0771_1.02_CISBP_rc)	0.802	0.516	0.191	-0.094	0.922	0.983	0.945	34	43	58	56	17	18	17	34.714	31	; dyads_test_vs_ctrl_m1 versus GATA27_M0771_1.02_CISBP_rc; m=3/11; ncol2=9; w=9; offset=5; strand=R; shift=5; score=34.7143; -----wwygATCkr-- ; cor=0.802; Ncor=0.516; logoDP=0.191; NIcor=-0.094; NsEucl=0.922; SSD=0.983; NSW=0.945; rcor=34; rNcor=43; rlogoDP=58; rNIcor=56; rNsEucl=17; rSSD=18; rNSW=17; rank_mean=34.714; match_rank=31 a 0 0 0 0 0 26 27 23 23 73 14 16 18 26 0 0 c 0 0 0 0 0 24 22 27 24 4 0 73 14 20 0 0 g 0 0 0 0 0 21 23 17 42 18 0 3 37 30 0 0 t 0 0 0 0 0 29 28 33 11 5 86 8 31 24 0 0
PK27213.1_M1312_1.02_CISBP_rc_shift6 (PK27213.1_M1312_1.02_CISBP_rc)	0.813	0.407	0.195	-0.042	0.921	0.804	0.950	31	60	57	51	20	12	13	34.857	32	; dyads_test_vs_ctrl_m1 versus PK27213.1_M1312_1.02_CISBP_rc; m=4/11; ncol2=10; w=8; offset=6; strand=R; shift=6; score=34.8571; ------sttATCywkw ; cor=0.813; Ncor=0.407; logoDP=0.195; NIcor=-0.042; NsEucl=0.921; SSD=0.804; NSW=0.950; rcor=31; rNcor=60; rlogoDP=57; rNIcor=51; rNsEucl=20; rSSD=12; rNSW=13; rank_mean=34.857; match_rank=32 a 0 0 0 0 0 0 20 17 18 91 5 6 16 27 24 35 c 0 0 0 0 0 0 35 23 12 0 9 85 37 21 23 19 g 0 0 0 0 0 0 25 8 12 4 6 4 17 24 25 18 t 0 0 0 0 0 0 20 52 58 5 80 5 30 28 28 28
PK29550.1_M1314_1.02_CISBP_rc_shift5 (PK29550.1_M1314_1.02_CISBP_rc)	0.751	0.451	1.501	0.240	0.914	1.190	0.934	56	51	47	46	24	29	26	39.857	43	; dyads_test_vs_ctrl_m1 versus PK29550.1_M1314_1.02_CISBP_rc; m=5/11; ncol2=10; w=9; offset=5; strand=R; shift=5; score=39.8571; -----ycttATCyrw- ; cor=0.751; Ncor=0.451; logoDP=1.501; NIcor=0.240; NsEucl=0.914; SSD=1.190; NSW=0.934; rcor=56; rNcor=51; rlogoDP=47; rNIcor=46; rNsEucl=24; rSSD=29; rNSW=26; rank_mean=39.857; match_rank=43 a 0 0 0 0 0 19 20 17 18 89 4 4 7 34 27 0 c 0 0 0 0 0 36 35 24 12 3 7 86 54 14 24 0 g 0 0 0 0 0 20 24 5 13 3 5 3 9 28 22 0 t 0 0 0 0 0 25 21 54 57 5 84 7 30 24 27 0
AT5G08520_M1339_1.02_CISBP_rc_shift5 (AT5G08520_M1339_1.02_CISBP_rc)	0.760	0.489	0.256	-0.127	0.916	1.144	0.936	48	47	55	60	22	26	23	40.143	45	; dyads_test_vs_ctrl_m1 versus AT5G08520_M1339_1.02_CISBP_rc; m=6/11; ncol2=9; w=9; offset=5; strand=R; shift=5; score=40.1429; -----ccytATCyd-- ; cor=0.760; Ncor=0.489; logoDP=0.256; NIcor=-0.127; NsEucl=0.916; SSD=1.144; NSW=0.936; rcor=48; rNcor=47; rlogoDP=55; rNIcor=60; rNsEucl=22; rSSD=26; rNSW=23; rank_mean=40.143; match_rank=45 a 0 0 0 0 0 20 18 17 18 98 2 4 15 29 0 0 c 0 0 0 0 0 35 37 25 15 0 12 89 42 21 0 0 g 0 0 0 0 0 21 24 8 13 1 8 3 15 25 0 0 t 0 0 0 0 0 24 21 50 54 1 78 4 28 25 0 0
GATA15_MA1016.1_JASPAR_rc_shift6 (GATA15_MA1016.1_JASPAR_rc)	0.785	0.418	0.185	-0.110	0.911	1.016	0.936	38	57	60	59	26	21	22	40.429	46	; dyads_test_vs_ctrl_m1 versus GATA15_MA1016.1_JASPAR_rc; m=7/11; ncol2=9; w=8; offset=6; strand=R; shift=6; score=40.4286; ------yygATCryr- ; cor=0.785; Ncor=0.418; logoDP=0.185; NIcor=-0.110; NsEucl=0.911; SSD=1.016; NSW=0.936; rcor=38; rNcor=57; rlogoDP=60; rNIcor=59; rNsEucl=26; rSSD=21; rNSW=22; rank_mean=40.429; match_rank=46 a 0 0 0 0 0 0 212 207 126 996 19 19 465 208 296 0 c 0 0 0 0 0 0 280 268 156 0 0 903 66 284 217 0 g 0 0 0 0 0 0 239 201 663 1 0 38 288 200 281 0 t 0 0 0 0 0 0 269 324 55 3 980 40 182 308 206 0
GATA15_M0761_1.02_CISBP_rc_shift6 (GATA15_M0761_1.02_CISBP_rc)	0.784	0.418	0.186	-0.109	0.911	1.018	0.936	39	58	59	58	28	23	25	41.429	48	; dyads_test_vs_ctrl_m1 versus GATA15_M0761_1.02_CISBP_rc; m=8/11; ncol2=9; w=8; offset=6; strand=R; shift=6; score=41.4286; ------yygATCryr- ; cor=0.784; Ncor=0.418; logoDP=0.186; NIcor=-0.109; NsEucl=0.911; SSD=1.018; NSW=0.936; rcor=39; rNcor=58; rlogoDP=59; rNIcor=58; rNsEucl=28; rSSD=23; rNSW=25; rank_mean=41.429; match_rank=48 a 0 0 0 0 0 0 21 21 13 100 2 2 46 21 30 0 c 0 0 0 0 0 0 28 27 15 0 0 90 7 28 22 0 g 0 0 0 0 0 0 24 20 66 0 0 4 29 20 27 0 t 0 0 0 0 0 0 27 32 6 0 98 4 18 31 21 0
Medtr8g106590.1_M0145_1.02_CISBP_shift3 (Medtr8g106590.1_M0145_1.02_CISBP)	0.758	0.433	3.107	0.413	0.888	1.601	0.900	50	53	32	42	47	38	45	43.857	50	; dyads_test_vs_ctrl_m1 versus Medtr8g106590.1_M0145_1.02_CISBP; m=9/11; ncol2=8; w=8; offset=3; strand=D; shift=3; score=43.8571; ---AAAWTAAT----- ; cor=0.758; Ncor=0.433; logoDP=3.107; NIcor=0.413; NsEucl=0.888; SSD=1.601; NSW=0.900; rcor=50; rNcor=53; rlogoDP=32; rNIcor=42; rNsEucl=47; rSSD=38; rNSW=45; rank_mean=43.857; match_rank=50 a 0 0 0 84 88 83 69 17 83 76 19 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 3 4 0 0 0 0 0 g 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 4 12 17 31 83 17 21 77 0 0 0 0 0
AHL20_MA0933.1_JASPAR_shift3 (AHL20_MA0933.1_JASPAR)	0.751	0.429	2.873	0.392	0.888	1.604	0.900	57	56	36	44	48	39	46	46.571	54	; dyads_test_vs_ctrl_m1 versus AHL20_MA0933.1_JASPAR; m=10/11; ncol2=8; w=8; offset=3; strand=D; shift=3; score=46.5714; ---AATWAAwT----- ; cor=0.751; Ncor=0.429; logoDP=2.873; NIcor=0.392; NsEucl=0.888; SSD=1.604; NSW=0.900; rcor=57; rNcor=56; rlogoDP=36; rNIcor=44; rNsEucl=48; rSSD=39; rNSW=46; rank_mean=46.571; match_rank=54 a 0 0 0 774 753 120 250 774 843 648 54 0 0 0 0 0 c 0 0 0 66 6 4 6 4 8 12 28 0 0 0 0 0 g 0 0 0 73 5 13 6 4 1 3 18 0 0 0 0 0 t 0 0 0 88 235 862 738 218 148 337 900 0 0 0 0 0
CCA1_MA0972.1_JASPAR_shift2 (CCA1_MA0972.1_JASPAR)	0.757	0.433	4.603	0.411	0.866	2.305	0.856	51	54	27	43	60	60	60	50.714	59	; dyads_test_vs_ctrl_m1 versus CCA1_MA0972.1_JASPAR; m=11/11; ncol2=8; w=8; offset=2; strand=D; shift=2; score=50.7143; --AAATATCT------ ; cor=0.757; Ncor=0.433; logoDP=4.603; NIcor=0.411; NsEucl=0.866; SSD=2.305; NSW=0.856; rcor=51; rNcor=54; rlogoDP=27; rNIcor=43; rNsEucl=60; rSSD=60; rNSW=60; rank_mean=50.714; match_rank=59 a 0 0 934 960 985 35 992 1 5 21 0 0 0 0 0 0 c 0 0 1 1 4 0 5 12 991 91 0 0 0 0 0 0 g 0 0 10 37 10 5 1 1 0 14 0 0 0 0 0 0 t 0 0 54 2 1 960 2 986 4 874 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m2_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_m2_shift0 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=10; shift=0; ncol=13; wdGTTTAAww--- ; Alignment reference a 12 9 0 0 0 0 28 28 8 9 0 0 0 c 2 1 0 0 0 0 0 0 4 5 0 0 0 g 6 7 28 0 0 0 0 0 5 2 0 0 0 t 8 11 0 28 28 28 0 0 11 12 0 0 0

AT2G20110_M0588_1.02_CISBP_shift2 (AT2G20110_M0588_1.02_CISBP) 0.834 0.667 7.963 0.625 0.893 1.457 0.909 27 17 9 17 45 35 40 27.143 24
; dyads_test_vs_ctrl_m2 versus AT2G20110_M0588_1.02_CISBP; m=1/5; ncol2=8; w=8; offset=2; strand=D; shift=2; score=27.1429; --rTTTAAAh--- ; cor=0.834; Ncor=0.667; logoDP=7.963; NIcor=0.625; NsEucl=0.893; SSD=1.457; NSW=0.909; rcor=27; rNcor=17; rlogoDP=9; rNIcor=17; rNsEucl=45; rSSD=35; rNSW=40; rank_mean=27.143; match_rank=24 a 0 0 40 0 0 0 80 100 100 25 0 0 0 c 0 0 0 0 0 20 0 0 0 25 0 0 0 g 0 0 40 0 0 0 20 0 0 0 0 0 0 t 0 0 20 100 100 80 0 0 0 50 0 0 0

TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc_shift3 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc) 0.865 0.551 2.666 0.100 0.895 1.088 0.922 22 38 39 47 43 25 34 35.429 34
; dyads_test_vs_ctrl_m2 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc; m=2/5; ncol2=8; w=7; offset=3; strand=R; shift=3; score=35.4286; ---TTTAAAAG-- ; cor=0.865; Ncor=0.551; logoDP=2.666; NIcor=0.100; NsEucl=0.895; SSD=1.088; NSW=0.922; rcor=22; rNcor=38; rlogoDP=39; rNIcor=47; rNsEucl=43; rSSD=25; rNSW=34; rank_mean=35.429; match_rank=34 a 0 0 0 0 0 9 96 78 72 96 8 0 0 c 0 0 0 8 0 0 0 8 8 0 8 0 0 g 0 0 0 1 0 0 0 8 8 0 69 0 0 t 0 0 0 87 96 87 0 2 8 0 11 0 0

SOL1_M0590_1.02_CISBP_shift2 (SOL1_M0590_1.02_CISBP) 0.763 0.610 6.428 0.552 0.875 2.006 0.875 47 25 15 28 53 53 55 39.429 42
; dyads_test_vs_ctrl_m2 versus SOL1_M0590_1.02_CISBP; m=3/5; ncol2=8; w=8; offset=2; strand=D; shift=2; score=39.4286; --rTTTrAAw--- ; cor=0.763; Ncor=0.610; logoDP=6.428; NIcor=0.552; NsEucl=0.875; SSD=2.006; NSW=0.875; rcor=47; rNcor=25; rlogoDP=15; rNIcor=28; rNsEucl=53; rSSD=53; rNSW=55; rank_mean=39.429; match_rank=42 a 0 0 26 2 0 3 32 98 93 28 0 0 0 c 0 0 10 2 0 15 0 0 0 10 0 0 0 g 0 0 41 0 0 2 61 2 0 0 0 0 0 t 0 0 23 96 100 80 7 0 7 62 0 0 0

WOX13_WOX13_2_ArabidopsisPBM_shift3 (WOX13_WOX13_2_ArabidopsisPBM) 0.769 0.414 2.144 0.364 0.873 1.586 0.887 43 59 41 45 55 37 52 47.429 56
; dyads_test_vs_ctrl_m2 versus WOX13_WOX13_2_ArabidopsisPBM; m=4/5; ncol2=10; w=7; offset=3; strand=D; shift=3; score=47.4286; ---tttAATTaam ; cor=0.769; Ncor=0.414; logoDP=2.144; NIcor=0.364; NsEucl=0.873; SSD=1.586; NSW=0.887; rcor=43; rNcor=59; rlogoDP=41; rNIcor=45; rNsEucl=55; rSSD=37; rNSW=52; rank_mean=47.429; match_rank=56 a 0 0 0 22 17 20 81 81 8 11 59 57 27 c 0 0 0 23 15 17 5 2 9 3 4 12 34 g 0 0 0 19 11 4 3 9 2 6 17 15 20 t 0 0 0 36 57 59 11 8 81 80 20 16 19

fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP_shift2 (fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP) 0.769 0.512 2.078 0.502 0.871 2.125 0.867 44 44 42 37 57 56 58 48.286 57
; dyads_test_vs_ctrl_m2 versus fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP; m=5/5; ncol2=10; w=8; offset=2; strand=D; shift=2; score=48.2857; --dTTTraawww- ; cor=0.769; Ncor=0.512; logoDP=2.078; NIcor=0.502; NsEucl=0.871; SSD=2.125; NSW=0.867; rcor=44; rNcor=44; rlogoDP=42; rNIcor=37; rNsEucl=57; rSSD=56; rNSW=58; rank_mean=48.286; match_rank=57 a 0 0 34 9 12 6 34 56 52 26 25 26 0 c 0 0 10 10 8 24 14 13 14 22 20 19 0 g 0 0 26 6 5 0 45 11 16 15 19 22 0 t 0 0 30 75 75 70 7 20 18 37 36 33 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_m2_shift0 (dyads_test_vs_ctrl_m2)																	; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=10; shift=0; ncol=13; wdGTTTAAww--- ; Alignment reference a 12 9 0 0 0 0 28 28 8 9 0 0 0 c 2 1 0 0 0 0 0 0 4 5 0 0 0 g 6 7 28 0 0 0 0 0 5 2 0 0 0 t 8 11 0 28 28 28 0 0 11 12 0 0 0
AT2G20110_M0588_1.02_CISBP_shift2 (AT2G20110_M0588_1.02_CISBP)	0.834	0.667	7.963	0.625	0.893	1.457	0.909	27	17	9	17	45	35	40	27.143	24	; dyads_test_vs_ctrl_m2 versus AT2G20110_M0588_1.02_CISBP; m=1/5; ncol2=8; w=8; offset=2; strand=D; shift=2; score=27.1429; --rTTTAAAh--- ; cor=0.834; Ncor=0.667; logoDP=7.963; NIcor=0.625; NsEucl=0.893; SSD=1.457; NSW=0.909; rcor=27; rNcor=17; rlogoDP=9; rNIcor=17; rNsEucl=45; rSSD=35; rNSW=40; rank_mean=27.143; match_rank=24 a 0 0 40 0 0 0 80 100 100 25 0 0 0 c 0 0 0 0 0 20 0 0 0 25 0 0 0 g 0 0 40 0 0 0 20 0 0 0 0 0 0 t 0 0 20 100 100 80 0 0 0 50 0 0 0
TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc_shift3 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc)	0.865	0.551	2.666	0.100	0.895	1.088	0.922	22	38	39	47	43	25	34	35.429	34	; dyads_test_vs_ctrl_m2 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc; m=2/5; ncol2=8; w=7; offset=3; strand=R; shift=3; score=35.4286; ---TTTAAAAG-- ; cor=0.865; Ncor=0.551; logoDP=2.666; NIcor=0.100; NsEucl=0.895; SSD=1.088; NSW=0.922; rcor=22; rNcor=38; rlogoDP=39; rNIcor=47; rNsEucl=43; rSSD=25; rNSW=34; rank_mean=35.429; match_rank=34 a 0 0 0 0 0 9 96 78 72 96 8 0 0 c 0 0 0 8 0 0 0 8 8 0 8 0 0 g 0 0 0 1 0 0 0 8 8 0 69 0 0 t 0 0 0 87 96 87 0 2 8 0 11 0 0
SOL1_M0590_1.02_CISBP_shift2 (SOL1_M0590_1.02_CISBP)	0.763	0.610	6.428	0.552	0.875	2.006	0.875	47	25	15	28	53	53	55	39.429	42	; dyads_test_vs_ctrl_m2 versus SOL1_M0590_1.02_CISBP; m=3/5; ncol2=8; w=8; offset=2; strand=D; shift=2; score=39.4286; --rTTTrAAw--- ; cor=0.763; Ncor=0.610; logoDP=6.428; NIcor=0.552; NsEucl=0.875; SSD=2.006; NSW=0.875; rcor=47; rNcor=25; rlogoDP=15; rNIcor=28; rNsEucl=53; rSSD=53; rNSW=55; rank_mean=39.429; match_rank=42 a 0 0 26 2 0 3 32 98 93 28 0 0 0 c 0 0 10 2 0 15 0 0 0 10 0 0 0 g 0 0 41 0 0 2 61 2 0 0 0 0 0 t 0 0 23 96 100 80 7 0 7 62 0 0 0
WOX13_WOX13_2_ArabidopsisPBM_shift3 (WOX13_WOX13_2_ArabidopsisPBM)	0.769	0.414	2.144	0.364	0.873	1.586	0.887	43	59	41	45	55	37	52	47.429	56	; dyads_test_vs_ctrl_m2 versus WOX13_WOX13_2_ArabidopsisPBM; m=4/5; ncol2=10; w=7; offset=3; strand=D; shift=3; score=47.4286; ---tttAATTaam ; cor=0.769; Ncor=0.414; logoDP=2.144; NIcor=0.364; NsEucl=0.873; SSD=1.586; NSW=0.887; rcor=43; rNcor=59; rlogoDP=41; rNIcor=45; rNsEucl=55; rSSD=37; rNSW=52; rank_mean=47.429; match_rank=56 a 0 0 0 22 17 20 81 81 8 11 59 57 27 c 0 0 0 23 15 17 5 2 9 3 4 12 34 g 0 0 0 19 11 4 3 9 2 6 17 15 20 t 0 0 0 36 57 59 11 8 81 80 20 16 19
fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP_shift2 (fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP)	0.769	0.512	2.078	0.502	0.871	2.125	0.867	44	44	42	37	57	56	58	48.286	57	; dyads_test_vs_ctrl_m2 versus fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP; m=5/5; ncol2=10; w=8; offset=2; strand=D; shift=2; score=48.2857; --dTTTraawww- ; cor=0.769; Ncor=0.512; logoDP=2.078; NIcor=0.502; NsEucl=0.871; SSD=2.125; NSW=0.867; rcor=44; rNcor=44; rlogoDP=42; rNIcor=37; rNsEucl=57; rSSD=56; rNSW=58; rank_mean=48.286; match_rank=57 a 0 0 34 9 12 6 34 56 52 26 25 26 0 c 0 0 10 10 8 24 14 13 14 22 20 19 0 g 0 0 26 6 5 0 45 11 16 15 19 22 0 t 0 0 30 75 75 70 7 20 18 37 36 33 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m4_shift0 ; 2 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=12; shift=0; ncol=12; tyAGTCTCAamy ; Alignment reference a 11 12 36 1 2 0 3 1 39 21 16 10 c 12 14 5 2 1 47 1 46 5 12 17 17 g 10 10 3 46 1 0 0 0 3 10 8 6 t 17 14 6 1 46 3 46 3 3 7 9 17

ARF_M00438_TRANSFAC_shift0 (ARF_M00438_TRANSFAC) 0.751 0.501 5.913 0.494 0.872 2.104 0.869 58 46 16 38 56 55 57 46.571 55
; oligos_5-7nt_m4 versus ARF_M00438_TRANSFAC; m=1/1; ncol2=8; w=8; offset=0; strand=D; shift=0; score=46.5714; yTTGTCtC---- ; cor=0.751; Ncor=0.501; logoDP=5.913; NIcor=0.494; NsEucl=0.872; SSD=2.104; NSW=0.869; rcor=58; rNcor=46; rlogoDP=16; rNIcor=38; rNsEucl=56; rSSD=55; rNSW=57; rank_mean=46.571; match_rank=55 a 0 0 0 0 0 0 1 0 0 0 0 0 c 3 0 0 0 0 6 1 6 0 0 0 0 g 0 1 0 6 0 0 0 0 0 0 0 0 t 2 5 6 0 6 0 4 0 0 0 0 0