One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 6/regulon6.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 6/regulon6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m2_shift3 ; 14 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_shift3 (oligos_5-7nt_m2)
; oligos_5-7nt_m2; m=0 (reference); ncol1=12; shift=3; ncol=17; ---waAAAATATCww-- ; Alignment reference a 0 0 0 30 24 63 69 71 71 2 66 4 5 20 22 0 0 c 0 0 0 8 17 3 0 0 1 2 2 2 54 12 14 0 0 g 0 0 0 12 18 5 2 2 1 1 1 2 4 14 16 0 0 t 0 0 0 24 15 3 3 1 1 69 5 66 11 28 22 0 0

RVE1_RVE1_ArabidopsisPBM_shift5 (RVE1_RVE1_ArabidopsisPBM) 0.946 0.788 7.322 0.778 0.946 0.577 0.971 2 1 8 1 1 3 1 2.429 1
; oligos_5-7nt_m2 versus RVE1_RVE1_ArabidopsisPBM; m=1/13; ncol2=10; w=10; offset=2; strand=D; shift=5; score= 2.4286; -----wAAATATCTk-- ; cor=0.946; Ncor=0.788; logoDP=7.322; NIcor=0.778; NsEucl=0.946; SSD=0.577; NSW=0.971; rcor=2; rNcor=1; rlogoDP=8; rNIcor=1; rNsEucl=1; rSSD=3; rNSW=1; rank_mean=2.429; match_rank=1 a 0 0 0 0 0 65 92 92 98 7 99 0 1 2 9 0 0 c 0 0 0 0 0 4 0 0 0 0 1 1 98 10 20 0 0 g 0 0 0 0 0 6 2 7 1 4 0 0 0 4 28 0 0 t 0 0 0 0 0 25 6 1 1 89 0 99 1 84 43 0 0

CCA1_CCA1_ArabidopsisPBM_shift5 (CCA1_CCA1_ArabidopsisPBM) 0.943 0.786 7.931 0.771 0.943 0.645 0.968 3 2 5 2 2 5 3 3.143 2
; oligos_5-7nt_m2 versus CCA1_CCA1_ArabidopsisPBM; m=2/13; ncol2=10; w=10; offset=2; strand=D; shift=5; score= 3.1429; -----aAAATATCTt-- ; cor=0.943; Ncor=0.786; logoDP=7.931; NIcor=0.771; NsEucl=0.943; SSD=0.645; NSW=0.968; rcor=3; rNcor=2; rlogoDP=5; rNIcor=2; rNsEucl=2; rSSD=5; rNSW=3; rank_mean=3.143; match_rank=2 a 0 0 0 0 0 60 93 96 98 4 100 0 0 3 17 0 0 c 0 0 0 0 0 8 0 0 0 0 0 1 100 9 21 0 0 g 0 0 0 0 0 10 1 4 2 0 0 0 0 1 11 0 0 t 0 0 0 0 0 22 6 0 0 96 0 99 0 87 51 0 0

CCA1_MA0972.1_JASPAR_shift6 (CCA1_MA0972.1_JASPAR) 0.960 0.640 7.692 0.631 0.939 0.470 0.971 1 8 6 5 3 1 2 3.714 3
; oligos_5-7nt_m2 versus CCA1_MA0972.1_JASPAR; m=3/13; ncol2=8; w=8; offset=3; strand=D; shift=6; score= 3.7143; ------AAATATCT--- ; cor=0.960; Ncor=0.640; logoDP=7.692; NIcor=0.631; NsEucl=0.939; SSD=0.470; NSW=0.971; rcor=1; rNcor=8; rlogoDP=6; rNIcor=5; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=3.714; match_rank=3 a 0 0 0 0 0 0 934 960 985 35 992 1 5 21 0 0 0 c 0 0 0 0 0 0 1 1 4 0 5 12 991 91 0 0 0 g 0 0 0 0 0 0 10 37 10 5 1 1 0 14 0 0 0 t 0 0 0 0 0 0 54 2 1 960 2 986 4 874 0 0 0

CCA1_M01819_TRANSFAC_shift0 (CCA1_M01819_TRANSFAC) 0.901 0.636 8.811 0.624 0.933 1.295 0.946 5 9 1 6 4 17 6 6.857 4
; oligos_5-7nt_m2 versus CCA1_M01819_TRANSFAC; m=4/13; ncol2=17; w=12; offset=-3; strand=D; shift=0; score= 6.8571; smharAAAAwATCTAar ; cor=0.901; Ncor=0.636; logoDP=8.811; NIcor=0.624; NsEucl=0.933; SSD=1.295; NSW=0.946; rcor=5; rNcor=9; rlogoDP=1; rNIcor=6; rNsEucl=4; rSSD=17; rNSW=6; rank_mean=6.857; match_rank=4 a 0 3 2 3 3 6 7 7 7 3 7 0 0 1 5 3 2 c 4 3 2 1 0 0 0 0 0 0 0 0 7 0 0 1 1 g 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 1 2 t 0 0 2 1 1 0 0 0 0 4 0 7 0 6 1 1 1

EPR1_M1317_1.02_CISBP_rc_shift5 (EPR1_M1317_1.02_CISBP_rc) 0.886 0.665 2.039 0.120 0.922 0.987 0.945 7 5 29 33 6 8 7 13.571 8
; oligos_5-7nt_m2 versus EPR1_M1317_1.02_CISBP_rc; m=5/13; ncol2=9; w=9; offset=2; strand=R; shift=5; score=13.5714; -----waAaTATCt--- ; cor=0.886; Ncor=0.665; logoDP=2.039; NIcor=0.120; NsEucl=0.922; SSD=0.987; NSW=0.945; rcor=7; rNcor=5; rlogoDP=29; rNIcor=33; rNsEucl=6; rSSD=8; rNSW=7; rank_mean=13.571; match_rank=8 a 0 0 0 0 0 35 52 68 67 19 98 1 2 17 0 0 0 c 0 0 0 0 0 16 9 9 8 2 0 1 92 19 0 0 0 g 0 0 0 0 0 20 15 9 18 7 1 0 1 12 0 0 0 t 0 0 0 0 0 29 24 14 7 72 1 98 5 52 0 0 0

PK08316.1_M1306_1.02_CISBP_shift5 (PK08316.1_M1306_1.02_CISBP) 0.846 0.705 1.861 0.662 0.914 1.486 0.926 14 3 35 3 9 26 11 14.429 10
; oligos_5-7nt_m2 versus PK08316.1_M1306_1.02_CISBP; m=6/13; ncol2=10; w=10; offset=2; strand=D; shift=5; score=14.4286; -----wwaawATCtw-- ; cor=0.846; Ncor=0.705; logoDP=1.861; NIcor=0.662; NsEucl=0.914; SSD=1.486; NSW=0.926; rcor=14; rNcor=3; rlogoDP=35; rNIcor=3; rNsEucl=9; rSSD=26; rNSW=11; rank_mean=14.429; match_rank=10 a 0 0 0 0 0 29 42 52 56 26 88 10 9 20 26 0 0 c 0 0 0 0 0 20 15 17 12 4 0 5 80 21 22 0 0 g 0 0 0 0 0 23 17 16 20 12 5 5 7 18 24 0 0 t 0 0 0 0 0 28 26 15 12 58 7 80 4 41 28 0 0

PK02532.1_M1303_1.02_CISBP_rc_shift6 (PK02532.1_M1303_1.02_CISBP_rc) 0.898 0.673 1.947 -0.037 0.918 1.077 0.940 6 4 31 39 7 9 8 14.857 12
; oligos_5-7nt_m2 versus PK02532.1_M1303_1.02_CISBP_rc; m=7/13; ncol2=9; w=9; offset=3; strand=R; shift=6; score=14.8571; ------wAATATCTn-- ; cor=0.898; Ncor=0.673; logoDP=1.947; NIcor=-0.037; NsEucl=0.918; SSD=1.077; NSW=0.940; rcor=6; rNcor=4; rlogoDP=31; rNIcor=39; rNsEucl=7; rSSD=9; rNSW=8; rank_mean=14.857; match_rank=12 a 0 0 0 0 0 0 50 100 100 0 100 0 0 0 25 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 100 0 25 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 t 0 0 0 0 0 0 50 0 0 100 0 100 0 100 25 0 0

LOC_Os08g06110_M1365_1.02_CISBP_rc_shift6 (LOC_Os08g06110_M1365_1.02_CISBP_rc) 0.878 0.659 0.509 -0.090 0.924 0.924 0.949 8 7 39 40 5 7 5 15.857 13
; oligos_5-7nt_m2 versus LOC_Os08g06110_M1365_1.02_CISBP_rc; m=8/13; ncol2=9; w=9; offset=3; strand=R; shift=6; score=15.8571; ------aaaTATCtw-- ; cor=0.878; Ncor=0.659; logoDP=0.509; NIcor=-0.090; NsEucl=0.924; SSD=0.924; NSW=0.949; rcor=8; rNcor=7; rlogoDP=39; rNIcor=40; rNsEucl=5; rSSD=7; rNSW=5; rank_mean=15.857; match_rank=13 a 0 0 0 0 0 0 45 57 62 19 99 0 1 13 25 0 0 c 0 0 0 0 0 0 12 16 9 1 0 1 96 19 24 0 0 g 0 0 0 0 0 0 21 13 22 8 0 0 0 12 23 0 0 t 0 0 0 0 0 0 22 14 7 72 1 99 3 56 28 0 0

RVE1_RVE1_2_ArabidopsisPBM_shift6 (RVE1_RVE1_2_ArabidopsisPBM) 0.787 0.545 2.522 0.520 0.903 1.538 0.915 28 12 26 9 10 28 14 18.143 16
; oligos_5-7nt_m2 versus RVE1_RVE1_2_ArabidopsisPBM; m=9/13; ncol2=10; w=9; offset=3; strand=D; shift=6; score=18.1429; ------smatATCwaw- ; cor=0.787; Ncor=0.545; logoDP=2.522; NIcor=0.520; NsEucl=0.903; SSD=1.538; NSW=0.915; rcor=28; rNcor=12; rlogoDP=26; rNIcor=9; rNsEucl=10; rSSD=28; rNSW=14; rank_mean=18.143; match_rank=16 a 0 0 0 0 0 0 20 54 65 23 91 3 6 29 61 50 0 c 0 0 0 0 0 0 31 31 9 3 4 3 89 20 16 16 0 g 0 0 0 0 0 0 29 4 16 15 3 3 4 5 13 6 0 t 0 0 0 0 0 0 20 11 10 59 2 91 1 46 10 28 0

HMGIY_M01800_TRANSFAC_rc_shift5 (HMGIY_M01800_TRANSFAC_rc) 0.878 0.439 2.003 0.049 0.890 0.875 0.927 9 32 30 35 17 6 10 19.857 19
; oligos_5-7nt_m2 versus HMGIY_M01800_TRANSFAC_rc; m=10/13; ncol2=6; w=6; offset=2; strand=R; shift=5; score=19.8571; -----AAAWww------ ; cor=0.878; Ncor=0.439; logoDP=2.003; NIcor=0.049; NsEucl=0.890; SSD=0.875; NSW=0.927; rcor=9; rNcor=32; rlogoDP=30; rNIcor=35; rNsEucl=17; rSSD=6; rNSW=10; rank_mean=19.857; match_rank=19 a 0 0 0 0 0 9 13 11 10 7 9 0 0 0 0 0 0 c 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 t 0 0 0 0 0 1 1 3 4 6 5 0 0 0 0 0 0

HMGA_M0118_1.02_CISBP_shift1 (HMGA_M0118_1.02_CISBP) 0.802 0.401 1.878 0.399 0.889 1.200 0.914 23 41 33 21 18 13 15 23.429 25
; oligos_5-7nt_m2 versus HMGA_M0118_1.02_CISBP; m=11/13; ncol2=9; w=7; offset=-2; strand=D; shift=1; score=23.4286; -ssrrwAAwt------- ; cor=0.802; Ncor=0.401; logoDP=1.878; NIcor=0.399; NsEucl=0.889; SSD=1.200; NSW=0.914; rcor=23; rNcor=41; rlogoDP=33; rNIcor=21; rNsEucl=18; rSSD=13; rNSW=15; rank_mean=23.429; match_rank=25 a 0 24 21 35 33 41 71 89 45 21 0 0 0 0 0 0 0 c 0 27 31 18 18 4 5 0 1 18 0 0 0 0 0 0 0 g 0 26 25 30 25 21 0 4 4 10 0 0 0 0 0 0 0 t 0 23 23 17 24 34 24 7 50 51 0 0 0 0 0 0 0

PRH_M1167_1.02_CISBP_shift8 (PRH_M1167_1.02_CISBP) 0.755 0.406 5.334 0.412 0.859 1.944 0.861 40 40 15 17 39 39 40 32.857 38
; oligos_5-7nt_m2 versus PRH_M1167_1.02_CISBP; m=12/13; ncol2=8; w=7; offset=5; strand=D; shift=8; score=32.8571; --------ATATATwA- ; cor=0.755; Ncor=0.406; logoDP=5.334; NIcor=0.412; NsEucl=0.859; SSD=1.944; NSW=0.861; rcor=40; rNcor=40; rlogoDP=15; rNIcor=17; rNsEucl=39; rSSD=39; rNSW=40; rank_mean=32.857; match_rank=38 a 0 0 0 0 0 0 0 0 100 0 100 0 100 14 50 80 0 c 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 t 0 0 0 0 0 0 0 0 0 100 0 100 0 86 50 20 0

TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn4_B_3D-footprint_rc_shift2 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn4_B_3D-footprint_rc) 0.756 0.407 1.807 -0.009 0.865 1.783 0.873 37 38 36 36 33 33 35 35.429 41
; oligos_5-7nt_m2 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn4_B_3D-footprint_rc; m=13/13; ncol2=8; w=7; offset=-1; strand=R; shift=2; score=35.4286; --TATAAaAt------- ; cor=0.756; Ncor=0.407; logoDP=1.807; NIcor=-0.009; NsEucl=0.865; SSD=1.783; NSW=0.873; rcor=37; rNcor=38; rlogoDP=36; rNIcor=36; rNsEucl=33; rSSD=33; rNSW=35; rank_mean=35.429; match_rank=41 a 0 0 0 96 0 96 96 54 96 13 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 13 0 16 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 13 0 13 0 0 0 0 0 0 0 t 0 0 96 0 96 0 0 16 0 54 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_m2_shift3 (oligos_5-7nt_m2)																	; oligos_5-7nt_m2; m=0 (reference); ncol1=12; shift=3; ncol=17; ---waAAAATATCww-- ; Alignment reference a 0 0 0 30 24 63 69 71 71 2 66 4 5 20 22 0 0 c 0 0 0 8 17 3 0 0 1 2 2 2 54 12 14 0 0 g 0 0 0 12 18 5 2 2 1 1 1 2 4 14 16 0 0 t 0 0 0 24 15 3 3 1 1 69 5 66 11 28 22 0 0
RVE1_RVE1_ArabidopsisPBM_shift5 (RVE1_RVE1_ArabidopsisPBM)	0.946	0.788	7.322	0.778	0.946	0.577	0.971	2	1	8	1	1	3	1	2.429	1	; oligos_5-7nt_m2 versus RVE1_RVE1_ArabidopsisPBM; m=1/13; ncol2=10; w=10; offset=2; strand=D; shift=5; score= 2.4286; -----wAAATATCTk-- ; cor=0.946; Ncor=0.788; logoDP=7.322; NIcor=0.778; NsEucl=0.946; SSD=0.577; NSW=0.971; rcor=2; rNcor=1; rlogoDP=8; rNIcor=1; rNsEucl=1; rSSD=3; rNSW=1; rank_mean=2.429; match_rank=1 a 0 0 0 0 0 65 92 92 98 7 99 0 1 2 9 0 0 c 0 0 0 0 0 4 0 0 0 0 1 1 98 10 20 0 0 g 0 0 0 0 0 6 2 7 1 4 0 0 0 4 28 0 0 t 0 0 0 0 0 25 6 1 1 89 0 99 1 84 43 0 0
CCA1_CCA1_ArabidopsisPBM_shift5 (CCA1_CCA1_ArabidopsisPBM)	0.943	0.786	7.931	0.771	0.943	0.645	0.968	3	2	5	2	2	5	3	3.143	2	; oligos_5-7nt_m2 versus CCA1_CCA1_ArabidopsisPBM; m=2/13; ncol2=10; w=10; offset=2; strand=D; shift=5; score= 3.1429; -----aAAATATCTt-- ; cor=0.943; Ncor=0.786; logoDP=7.931; NIcor=0.771; NsEucl=0.943; SSD=0.645; NSW=0.968; rcor=3; rNcor=2; rlogoDP=5; rNIcor=2; rNsEucl=2; rSSD=5; rNSW=3; rank_mean=3.143; match_rank=2 a 0 0 0 0 0 60 93 96 98 4 100 0 0 3 17 0 0 c 0 0 0 0 0 8 0 0 0 0 0 1 100 9 21 0 0 g 0 0 0 0 0 10 1 4 2 0 0 0 0 1 11 0 0 t 0 0 0 0 0 22 6 0 0 96 0 99 0 87 51 0 0
CCA1_MA0972.1_JASPAR_shift6 (CCA1_MA0972.1_JASPAR)	0.960	0.640	7.692	0.631	0.939	0.470	0.971	1	8	6	5	3	1	2	3.714	3	; oligos_5-7nt_m2 versus CCA1_MA0972.1_JASPAR; m=3/13; ncol2=8; w=8; offset=3; strand=D; shift=6; score= 3.7143; ------AAATATCT--- ; cor=0.960; Ncor=0.640; logoDP=7.692; NIcor=0.631; NsEucl=0.939; SSD=0.470; NSW=0.971; rcor=1; rNcor=8; rlogoDP=6; rNIcor=5; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=3.714; match_rank=3 a 0 0 0 0 0 0 934 960 985 35 992 1 5 21 0 0 0 c 0 0 0 0 0 0 1 1 4 0 5 12 991 91 0 0 0 g 0 0 0 0 0 0 10 37 10 5 1 1 0 14 0 0 0 t 0 0 0 0 0 0 54 2 1 960 2 986 4 874 0 0 0
CCA1_M01819_TRANSFAC_shift0 (CCA1_M01819_TRANSFAC)	0.901	0.636	8.811	0.624	0.933	1.295	0.946	5	9	1	6	4	17	6	6.857	4	; oligos_5-7nt_m2 versus CCA1_M01819_TRANSFAC; m=4/13; ncol2=17; w=12; offset=-3; strand=D; shift=0; score= 6.8571; smharAAAAwATCTAar ; cor=0.901; Ncor=0.636; logoDP=8.811; NIcor=0.624; NsEucl=0.933; SSD=1.295; NSW=0.946; rcor=5; rNcor=9; rlogoDP=1; rNIcor=6; rNsEucl=4; rSSD=17; rNSW=6; rank_mean=6.857; match_rank=4 a 0 3 2 3 3 6 7 7 7 3 7 0 0 1 5 3 2 c 4 3 2 1 0 0 0 0 0 0 0 0 7 0 0 1 1 g 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 1 2 t 0 0 2 1 1 0 0 0 0 4 0 7 0 6 1 1 1
EPR1_M1317_1.02_CISBP_rc_shift5 (EPR1_M1317_1.02_CISBP_rc)	0.886	0.665	2.039	0.120	0.922	0.987	0.945	7	5	29	33	6	8	7	13.571	8	; oligos_5-7nt_m2 versus EPR1_M1317_1.02_CISBP_rc; m=5/13; ncol2=9; w=9; offset=2; strand=R; shift=5; score=13.5714; -----waAaTATCt--- ; cor=0.886; Ncor=0.665; logoDP=2.039; NIcor=0.120; NsEucl=0.922; SSD=0.987; NSW=0.945; rcor=7; rNcor=5; rlogoDP=29; rNIcor=33; rNsEucl=6; rSSD=8; rNSW=7; rank_mean=13.571; match_rank=8 a 0 0 0 0 0 35 52 68 67 19 98 1 2 17 0 0 0 c 0 0 0 0 0 16 9 9 8 2 0 1 92 19 0 0 0 g 0 0 0 0 0 20 15 9 18 7 1 0 1 12 0 0 0 t 0 0 0 0 0 29 24 14 7 72 1 98 5 52 0 0 0
PK08316.1_M1306_1.02_CISBP_shift5 (PK08316.1_M1306_1.02_CISBP)	0.846	0.705	1.861	0.662	0.914	1.486	0.926	14	3	35	3	9	26	11	14.429	10	; oligos_5-7nt_m2 versus PK08316.1_M1306_1.02_CISBP; m=6/13; ncol2=10; w=10; offset=2; strand=D; shift=5; score=14.4286; -----wwaawATCtw-- ; cor=0.846; Ncor=0.705; logoDP=1.861; NIcor=0.662; NsEucl=0.914; SSD=1.486; NSW=0.926; rcor=14; rNcor=3; rlogoDP=35; rNIcor=3; rNsEucl=9; rSSD=26; rNSW=11; rank_mean=14.429; match_rank=10 a 0 0 0 0 0 29 42 52 56 26 88 10 9 20 26 0 0 c 0 0 0 0 0 20 15 17 12 4 0 5 80 21 22 0 0 g 0 0 0 0 0 23 17 16 20 12 5 5 7 18 24 0 0 t 0 0 0 0 0 28 26 15 12 58 7 80 4 41 28 0 0
PK02532.1_M1303_1.02_CISBP_rc_shift6 (PK02532.1_M1303_1.02_CISBP_rc)	0.898	0.673	1.947	-0.037	0.918	1.077	0.940	6	4	31	39	7	9	8	14.857	12	; oligos_5-7nt_m2 versus PK02532.1_M1303_1.02_CISBP_rc; m=7/13; ncol2=9; w=9; offset=3; strand=R; shift=6; score=14.8571; ------wAATATCTn-- ; cor=0.898; Ncor=0.673; logoDP=1.947; NIcor=-0.037; NsEucl=0.918; SSD=1.077; NSW=0.940; rcor=6; rNcor=4; rlogoDP=31; rNIcor=39; rNsEucl=7; rSSD=9; rNSW=8; rank_mean=14.857; match_rank=12 a 0 0 0 0 0 0 50 100 100 0 100 0 0 0 25 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 100 0 25 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 t 0 0 0 0 0 0 50 0 0 100 0 100 0 100 25 0 0
LOC_Os08g06110_M1365_1.02_CISBP_rc_shift6 (LOC_Os08g06110_M1365_1.02_CISBP_rc)	0.878	0.659	0.509	-0.090	0.924	0.924	0.949	8	7	39	40	5	7	5	15.857	13	; oligos_5-7nt_m2 versus LOC_Os08g06110_M1365_1.02_CISBP_rc; m=8/13; ncol2=9; w=9; offset=3; strand=R; shift=6; score=15.8571; ------aaaTATCtw-- ; cor=0.878; Ncor=0.659; logoDP=0.509; NIcor=-0.090; NsEucl=0.924; SSD=0.924; NSW=0.949; rcor=8; rNcor=7; rlogoDP=39; rNIcor=40; rNsEucl=5; rSSD=7; rNSW=5; rank_mean=15.857; match_rank=13 a 0 0 0 0 0 0 45 57 62 19 99 0 1 13 25 0 0 c 0 0 0 0 0 0 12 16 9 1 0 1 96 19 24 0 0 g 0 0 0 0 0 0 21 13 22 8 0 0 0 12 23 0 0 t 0 0 0 0 0 0 22 14 7 72 1 99 3 56 28 0 0
RVE1_RVE1_2_ArabidopsisPBM_shift6 (RVE1_RVE1_2_ArabidopsisPBM)	0.787	0.545	2.522	0.520	0.903	1.538	0.915	28	12	26	9	10	28	14	18.143	16	; oligos_5-7nt_m2 versus RVE1_RVE1_2_ArabidopsisPBM; m=9/13; ncol2=10; w=9; offset=3; strand=D; shift=6; score=18.1429; ------smatATCwaw- ; cor=0.787; Ncor=0.545; logoDP=2.522; NIcor=0.520; NsEucl=0.903; SSD=1.538; NSW=0.915; rcor=28; rNcor=12; rlogoDP=26; rNIcor=9; rNsEucl=10; rSSD=28; rNSW=14; rank_mean=18.143; match_rank=16 a 0 0 0 0 0 0 20 54 65 23 91 3 6 29 61 50 0 c 0 0 0 0 0 0 31 31 9 3 4 3 89 20 16 16 0 g 0 0 0 0 0 0 29 4 16 15 3 3 4 5 13 6 0 t 0 0 0 0 0 0 20 11 10 59 2 91 1 46 10 28 0
HMGIY_M01800_TRANSFAC_rc_shift5 (HMGIY_M01800_TRANSFAC_rc)	0.878	0.439	2.003	0.049	0.890	0.875	0.927	9	32	30	35	17	6	10	19.857	19	; oligos_5-7nt_m2 versus HMGIY_M01800_TRANSFAC_rc; m=10/13; ncol2=6; w=6; offset=2; strand=R; shift=5; score=19.8571; -----AAAWww------ ; cor=0.878; Ncor=0.439; logoDP=2.003; NIcor=0.049; NsEucl=0.890; SSD=0.875; NSW=0.927; rcor=9; rNcor=32; rlogoDP=30; rNIcor=35; rNsEucl=17; rSSD=6; rNSW=10; rank_mean=19.857; match_rank=19 a 0 0 0 0 0 9 13 11 10 7 9 0 0 0 0 0 0 c 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 t 0 0 0 0 0 1 1 3 4 6 5 0 0 0 0 0 0
HMGA_M0118_1.02_CISBP_shift1 (HMGA_M0118_1.02_CISBP)	0.802	0.401	1.878	0.399	0.889	1.200	0.914	23	41	33	21	18	13	15	23.429	25	; oligos_5-7nt_m2 versus HMGA_M0118_1.02_CISBP; m=11/13; ncol2=9; w=7; offset=-2; strand=D; shift=1; score=23.4286; -ssrrwAAwt------- ; cor=0.802; Ncor=0.401; logoDP=1.878; NIcor=0.399; NsEucl=0.889; SSD=1.200; NSW=0.914; rcor=23; rNcor=41; rlogoDP=33; rNIcor=21; rNsEucl=18; rSSD=13; rNSW=15; rank_mean=23.429; match_rank=25 a 0 24 21 35 33 41 71 89 45 21 0 0 0 0 0 0 0 c 0 27 31 18 18 4 5 0 1 18 0 0 0 0 0 0 0 g 0 26 25 30 25 21 0 4 4 10 0 0 0 0 0 0 0 t 0 23 23 17 24 34 24 7 50 51 0 0 0 0 0 0 0
PRH_M1167_1.02_CISBP_shift8 (PRH_M1167_1.02_CISBP)	0.755	0.406	5.334	0.412	0.859	1.944	0.861	40	40	15	17	39	39	40	32.857	38	; oligos_5-7nt_m2 versus PRH_M1167_1.02_CISBP; m=12/13; ncol2=8; w=7; offset=5; strand=D; shift=8; score=32.8571; --------ATATATwA- ; cor=0.755; Ncor=0.406; logoDP=5.334; NIcor=0.412; NsEucl=0.859; SSD=1.944; NSW=0.861; rcor=40; rNcor=40; rlogoDP=15; rNIcor=17; rNsEucl=39; rSSD=39; rNSW=40; rank_mean=32.857; match_rank=38 a 0 0 0 0 0 0 0 0 100 0 100 0 100 14 50 80 0 c 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 t 0 0 0 0 0 0 0 0 0 100 0 100 0 86 50 20 0
TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn4_B_3D-footprint_rc_shift2 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn4_B_3D-footprint_rc)	0.756	0.407	1.807	-0.009	0.865	1.783	0.873	37	38	36	36	33	33	35	35.429	41	; oligos_5-7nt_m2 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn4_B_3D-footprint_rc; m=13/13; ncol2=8; w=7; offset=-1; strand=R; shift=2; score=35.4286; --TATAAaAt------- ; cor=0.756; Ncor=0.407; logoDP=1.807; NIcor=-0.009; NsEucl=0.865; SSD=1.783; NSW=0.873; rcor=37; rNcor=38; rlogoDP=36; rNIcor=36; rNsEucl=33; rSSD=33; rNSW=35; rank_mean=35.429; match_rank=41 a 0 0 0 96 0 96 96 54 96 13 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 13 0 16 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 13 0 13 0 0 0 0 0 0 0 t 0 0 96 0 96 0 0 16 0 54 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m1_shift3 ; 15 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_shift3 (oligos_5-7nt_m1)
; oligos_5-7nt_m1; m=0 (reference); ncol1=10; shift=3; ncol=17; ---waaAAATAtw---- ; Alignment reference a 0 0 0 52 55 79 163 163 163 0 163 38 54 0 0 0 0 c 0 0 0 36 36 30 0 0 0 0 0 33 35 0 0 0 0 g 0 0 0 21 35 25 0 0 0 0 0 33 31 0 0 0 0 t 0 0 0 54 37 29 0 0 0 163 0 59 43 0 0 0 0

CCA1_CCA1_ArabidopsisPBM_shift5 (CCA1_CCA1_ArabidopsisPBM) 0.851 0.567 8.375 0.540 0.895 1.404 0.912 12 10 2 7 12 21 16 11.429 5
; oligos_5-7nt_m1 versus CCA1_CCA1_ArabidopsisPBM; m=1/14; ncol2=10; w=8; offset=2; strand=D; shift=5; score=11.4286; -----aAAATATCTt-- ; cor=0.851; Ncor=0.567; logoDP=8.375; NIcor=0.540; NsEucl=0.895; SSD=1.404; NSW=0.912; rcor=12; rNcor=10; rlogoDP=2; rNIcor=7; rNsEucl=12; rSSD=21; rNSW=16; rank_mean=11.429; match_rank=5 a 0 0 0 0 0 60 93 96 98 4 100 0 0 3 17 0 0 c 0 0 0 0 0 8 0 0 0 0 0 1 100 9 21 0 0 g 0 0 0 0 0 10 1 4 2 0 0 0 0 1 11 0 0 t 0 0 0 0 0 22 6 0 0 96 0 99 0 87 51 0 0

Medtr8g106590.1_M0145_1.02_CISBP_shift5 (Medtr8g106590.1_M0145_1.02_CISBP) 0.825 0.660 5.248 0.635 0.900 1.289 0.919 18 6 16 4 11 16 12 11.857 6
; oligos_5-7nt_m1 versus Medtr8g106590.1_M0145_1.02_CISBP; m=2/14; ncol2=8; w=8; offset=2; strand=D; shift=5; score=11.8571; -----AAAWTAAT---- ; cor=0.825; Ncor=0.660; logoDP=5.248; NIcor=0.635; NsEucl=0.900; SSD=1.289; NSW=0.919; rcor=18; rNcor=6; rlogoDP=16; rNIcor=4; rNsEucl=11; rSSD=16; rNSW=12; rank_mean=11.857; match_rank=6 a 0 0 0 0 0 84 88 83 69 17 83 76 19 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 3 4 0 0 0 0 g 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 4 12 17 31 83 17 21 77 0 0 0 0

RVE1_RVE1_ArabidopsisPBM_shift5 (RVE1_RVE1_ArabidopsisPBM) 0.843 0.562 7.524 0.532 0.895 1.419 0.911 15 11 7 8 13 22 17 13.286 7
; oligos_5-7nt_m1 versus RVE1_RVE1_ArabidopsisPBM; m=3/14; ncol2=10; w=8; offset=2; strand=D; shift=5; score=13.2857; -----wAAATATCTk-- ; cor=0.843; Ncor=0.562; logoDP=7.524; NIcor=0.532; NsEucl=0.895; SSD=1.419; NSW=0.911; rcor=15; rNcor=11; rlogoDP=7; rNIcor=8; rNsEucl=13; rSSD=22; rNSW=17; rank_mean=13.286; match_rank=7 a 0 0 0 0 0 65 92 92 98 7 99 0 1 2 9 0 0 c 0 0 0 0 0 4 0 0 0 0 1 1 98 10 20 0 0 g 0 0 0 0 0 6 2 7 1 4 0 0 0 4 28 0 0 t 0 0 0 0 0 25 6 1 1 89 0 99 1 84 43 0 0

CCA1_MA0972.1_JASPAR_shift6 (CCA1_MA0972.1_JASPAR) 0.851 0.542 8.273 0.514 0.883 1.346 0.904 11 13 4 10 20 19 20 13.857 9
; oligos_5-7nt_m1 versus CCA1_MA0972.1_JASPAR; m=4/14; ncol2=8; w=7; offset=3; strand=D; shift=6; score=13.8571; ------AAATATCT--- ; cor=0.851; Ncor=0.542; logoDP=8.273; NIcor=0.514; NsEucl=0.883; SSD=1.346; NSW=0.904; rcor=11; rNcor=13; rlogoDP=4; rNIcor=10; rNsEucl=20; rSSD=19; rNSW=20; rank_mean=13.857; match_rank=9 a 0 0 0 0 0 0 934 960 985 35 992 1 5 21 0 0 0 c 0 0 0 0 0 0 1 1 4 0 5 12 991 91 0 0 0 g 0 0 0 0 0 0 10 37 10 5 1 1 0 14 0 0 0 t 0 0 0 0 0 0 54 2 1 960 2 986 4 874 0 0 0

TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qnc_B_3D-footprint_rc_shift7 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qnc_B_3D-footprint_rc) 0.923 0.462 0.203 -0.034 0.915 0.517 0.957 4 21 40 38 8 2 4 16.714 14
; oligos_5-7nt_m1 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qnc_B_3D-footprint_rc; m=5/14; ncol2=8; w=6; offset=4; strand=R; shift=7; score=16.7143; -------AATAAaAG-- ; cor=0.923; Ncor=0.462; logoDP=0.203; NIcor=-0.034; NsEucl=0.915; SSD=0.517; NSW=0.957; rcor=4; rNcor=21; rlogoDP=40; rNIcor=38; rNsEucl=8; rSSD=2; rNSW=4; rank_mean=16.714; match_rank=14 a 0 0 0 0 0 0 0 96 96 0 96 74 53 96 10 0 0 c 0 0 0 0 0 0 0 0 0 0 0 10 10 0 12 0 0 g 0 0 0 0 0 0 0 0 0 0 0 12 21 0 74 0 0 t 0 0 0 0 0 0 0 0 0 96 0 0 12 0 0 0 0

HMGA_M0118_1.02_CISBP_shift1 (HMGA_M0118_1.02_CISBP) 0.810 0.472 2.283 0.476 0.891 1.160 0.917 22 19 28 12 15 11 13 17.143 15
; oligos_5-7nt_m1 versus HMGA_M0118_1.02_CISBP; m=6/14; ncol2=9; w=7; offset=-2; strand=D; shift=1; score=17.1429; -ssrrwAAwt------- ; cor=0.810; Ncor=0.472; logoDP=2.283; NIcor=0.476; NsEucl=0.891; SSD=1.160; NSW=0.917; rcor=22; rNcor=19; rlogoDP=28; rNIcor=12; rNsEucl=15; rSSD=11; rNSW=13; rank_mean=17.143; match_rank=15 a 0 24 21 35 33 41 71 89 45 21 0 0 0 0 0 0 0 c 0 27 31 18 18 4 5 0 1 18 0 0 0 0 0 0 0 g 0 26 25 30 25 21 0 4 4 10 0 0 0 0 0 0 0 t 0 23 23 17 24 34 24 7 50 51 0 0 0 0 0 0 0

AHL20_AHL20_ArabidopsisPBM_shift6 (AHL20_AHL20_ArabidopsisPBM) 0.820 0.441 5.335 0.405 0.884 1.312 0.906 20 30 14 20 19 18 18 19.857 18
; oligos_5-7nt_m1 versus AHL20_AHL20_ArabidopsisPBM; m=7/14; ncol2=10; w=7; offset=3; strand=D; shift=6; score=19.8571; ------wAATATATTw- ; cor=0.820; Ncor=0.441; logoDP=5.335; NIcor=0.405; NsEucl=0.884; SSD=1.312; NSW=0.906; rcor=20; rNcor=30; rlogoDP=14; rNIcor=20; rNsEucl=19; rSSD=18; rNSW=18; rank_mean=19.857; match_rank=18 a 0 0 0 0 0 0 44 95 88 8 87 13 91 11 3 44 0 c 0 0 0 0 0 0 16 1 0 1 0 0 1 1 1 10 0 g 0 0 0 0 0 0 11 1 1 0 0 0 1 0 1 21 0 t 0 0 0 0 0 0 29 3 11 91 13 87 7 88 95 25 0

CCA1_M01819_TRANSFAC_shift0 (CCA1_M01819_TRANSFAC) 0.780 0.459 8.358 0.427 0.894 2.255 0.887 31 22 3 14 14 41 27 21.714 22
; oligos_5-7nt_m1 versus CCA1_M01819_TRANSFAC; m=8/14; ncol2=17; w=10; offset=-3; strand=D; shift=0; score=21.7143; smharAAAAwATCTAar ; cor=0.780; Ncor=0.459; logoDP=8.358; NIcor=0.427; NsEucl=0.894; SSD=2.255; NSW=0.887; rcor=31; rNcor=22; rlogoDP=3; rNIcor=14; rNsEucl=14; rSSD=41; rNSW=27; rank_mean=21.714; match_rank=22 a 0 3 2 3 3 6 7 7 7 3 7 0 0 1 5 3 2 c 4 3 2 1 0 0 0 0 0 0 0 0 7 0 0 1 1 g 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 1 2 t 0 0 2 1 1 0 0 0 0 4 0 7 0 6 1 1 1

HMGIY_M01800_TRANSFAC_rc_shift5 (HMGIY_M01800_TRANSFAC_rc) 0.840 0.504 2.388 0.072 0.873 1.162 0.903 16 16 27 34 26 12 21 21.714 23
; oligos_5-7nt_m1 versus HMGIY_M01800_TRANSFAC_rc; m=9/14; ncol2=6; w=6; offset=2; strand=R; shift=5; score=21.7143; -----AAAWww------ ; cor=0.840; Ncor=0.504; logoDP=2.388; NIcor=0.072; NsEucl=0.873; SSD=1.162; NSW=0.903; rcor=16; rNcor=16; rlogoDP=27; rNIcor=34; rNsEucl=26; rSSD=12; rNSW=21; rank_mean=21.714; match_rank=23 a 0 0 0 0 0 9 13 11 10 7 9 0 0 0 0 0 0 c 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 t 0 0 0 0 0 1 1 3 4 6 5 0 0 0 0 0 0

AHL25_AHL25_2_ArabidopsisPBM_shift6 (AHL25_AHL25_2_ArabidopsisPBM) 0.790 0.425 3.008 0.422 0.879 1.429 0.898 27 36 25 15 22 23 23 24.429 26
; oligos_5-7nt_m1 versus AHL25_AHL25_2_ArabidopsisPBM; m=10/14; ncol2=10; w=7; offset=3; strand=D; shift=6; score=24.4286; ------aAwwWWwwTw- ; cor=0.790; Ncor=0.425; logoDP=3.008; NIcor=0.422; NsEucl=0.879; SSD=1.429; NSW=0.898; rcor=27; rNcor=36; rlogoDP=25; rNIcor=15; rNsEucl=22; rSSD=23; rNSW=23; rank_mean=24.429; match_rank=26 a 0 0 0 0 0 0 49 86 64 35 70 29 64 34 4 36 0 c 0 0 0 0 0 0 14 4 0 0 1 0 1 2 6 16 0 g 0 0 0 0 0 0 13 6 2 1 0 1 0 0 4 12 0 t 0 0 0 0 0 0 24 4 34 64 29 70 35 64 86 36 0

KAN_M1340_1.02_CISBP_shift5 (KAN_M1340_1.02_CISBP) 0.760 0.507 1.468 0.491 0.881 1.822 0.886 36 15 37 11 21 35 28 26.143 29
; oligos_5-7nt_m1 versus KAN_M1340_1.02_CISBP; m=11/14; ncol2=10; w=8; offset=2; strand=D; shift=5; score=26.1429; -----rrwaTAtwyy-- ; cor=0.760; Ncor=0.507; logoDP=1.468; NIcor=0.491; NsEucl=0.881; SSD=1.822; NSW=0.886; rcor=36; rNcor=15; rlogoDP=37; rNIcor=11; rNsEucl=21; rSSD=35; rNSW=28; rank_mean=26.143; match_rank=29 a 0 0 0 0 0 41 26 44 55 13 73 23 26 20 16 0 0 c 0 0 0 0 0 16 11 15 8 13 1 14 15 43 27 0 0 g 0 0 0 0 0 27 43 15 14 1 13 8 15 11 16 0 0 t 0 0 0 0 0 16 20 26 23 73 13 55 44 26 41 0 0

gw1.20.00.89.1_M0601_1.02_CISBP_shift0 (gw1.20.00.89.1_M0601_1.02_CISBP) 0.773 0.416 0.697 0.405 0.877 1.484 0.894 33 37 38 19 23 25 24 28.429 32
; oligos_5-7nt_m1 versus gw1.20.00.89.1_M0601_1.02_CISBP; m=12/14; ncol2=10; w=7; offset=-3; strand=D; shift=0; score=28.4286; awttyraawt------- ; cor=0.773; Ncor=0.416; logoDP=0.697; NIcor=0.405; NsEucl=0.877; SSD=1.484; NSW=0.894; rcor=33; rNcor=37; rlogoDP=38; rNIcor=19; rNsEucl=23; rSSD=25; rNSW=24; rank_mean=28.429; match_rank=32 a 54 28 10 20 8 43 59 61 38 23 0 0 0 0 0 0 0 c 12 14 18 12 28 21 9 12 20 11 0 0 0 0 0 0 0 g 11 20 12 9 21 28 12 18 14 12 0 0 0 0 0 0 0 t 23 38 60 59 43 8 20 9 28 54 0 0 0 0 0 0 0

AHL25_AHL25_3_ArabidopsisPBM_rc_shift6 (AHL25_AHL25_3_ArabidopsisPBM_rc) 0.755 0.407 1.867 0.224 0.871 1.623 0.884 38 39 34 26 27 29 30 31.857 35
; oligos_5-7nt_m1 versus AHL25_AHL25_3_ArabidopsisPBM_rc; m=13/14; ncol2=10; w=7; offset=3; strand=R; shift=6; score=31.8571; ------wAwTwWwWtw- ; cor=0.755; Ncor=0.407; logoDP=1.867; NIcor=0.224; NsEucl=0.871; SSD=1.623; NSW=0.884; rcor=38; rNcor=39; rlogoDP=34; rNIcor=26; rNsEucl=27; rSSD=29; rNSW=30; rank_mean=31.857; match_rank=35 a 0 0 0 0 0 0 56 83 62 16 51 71 60 25 22 29 0 c 0 0 0 0 0 0 6 6 0 1 0 0 0 1 15 16 0 g 0 0 0 0 0 0 10 3 1 0 0 0 1 0 9 18 0 t 0 0 0 0 0 0 28 8 37 83 49 29 39 74 54 37 0

PK02532.1_M1303_1.02_CISBP_rc_shift6 (PK02532.1_M1303_1.02_CISBP_rc) 0.785 0.458 1.941 -0.011 0.862 1.876 0.866 29 23 32 37 36 36 37 32.857 37
; oligos_5-7nt_m1 versus PK02532.1_M1303_1.02_CISBP_rc; m=14/14; ncol2=9; w=7; offset=3; strand=R; shift=6; score=32.8571; ------wAATATCTn-- ; cor=0.785; Ncor=0.458; logoDP=1.941; NIcor=-0.011; NsEucl=0.862; SSD=1.876; NSW=0.866; rcor=29; rNcor=23; rlogoDP=32; rNIcor=37; rNsEucl=36; rSSD=36; rNSW=37; rank_mean=32.857; match_rank=37 a 0 0 0 0 0 0 50 100 100 0 100 0 0 0 25 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 100 0 25 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 t 0 0 0 0 0 0 50 0 0 100 0 100 0 100 25 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_shift3 (oligos_5-7nt_m1)																	; oligos_5-7nt_m1; m=0 (reference); ncol1=10; shift=3; ncol=17; ---waaAAATAtw---- ; Alignment reference a 0 0 0 52 55 79 163 163 163 0 163 38 54 0 0 0 0 c 0 0 0 36 36 30 0 0 0 0 0 33 35 0 0 0 0 g 0 0 0 21 35 25 0 0 0 0 0 33 31 0 0 0 0 t 0 0 0 54 37 29 0 0 0 163 0 59 43 0 0 0 0
CCA1_CCA1_ArabidopsisPBM_shift5 (CCA1_CCA1_ArabidopsisPBM)	0.851	0.567	8.375	0.540	0.895	1.404	0.912	12	10	2	7	12	21	16	11.429	5	; oligos_5-7nt_m1 versus CCA1_CCA1_ArabidopsisPBM; m=1/14; ncol2=10; w=8; offset=2; strand=D; shift=5; score=11.4286; -----aAAATATCTt-- ; cor=0.851; Ncor=0.567; logoDP=8.375; NIcor=0.540; NsEucl=0.895; SSD=1.404; NSW=0.912; rcor=12; rNcor=10; rlogoDP=2; rNIcor=7; rNsEucl=12; rSSD=21; rNSW=16; rank_mean=11.429; match_rank=5 a 0 0 0 0 0 60 93 96 98 4 100 0 0 3 17 0 0 c 0 0 0 0 0 8 0 0 0 0 0 1 100 9 21 0 0 g 0 0 0 0 0 10 1 4 2 0 0 0 0 1 11 0 0 t 0 0 0 0 0 22 6 0 0 96 0 99 0 87 51 0 0
Medtr8g106590.1_M0145_1.02_CISBP_shift5 (Medtr8g106590.1_M0145_1.02_CISBP)	0.825	0.660	5.248	0.635	0.900	1.289	0.919	18	6	16	4	11	16	12	11.857	6	; oligos_5-7nt_m1 versus Medtr8g106590.1_M0145_1.02_CISBP; m=2/14; ncol2=8; w=8; offset=2; strand=D; shift=5; score=11.8571; -----AAAWTAAT---- ; cor=0.825; Ncor=0.660; logoDP=5.248; NIcor=0.635; NsEucl=0.900; SSD=1.289; NSW=0.919; rcor=18; rNcor=6; rlogoDP=16; rNIcor=4; rNsEucl=11; rSSD=16; rNSW=12; rank_mean=11.857; match_rank=6 a 0 0 0 0 0 84 88 83 69 17 83 76 19 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 3 4 0 0 0 0 g 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 4 12 17 31 83 17 21 77 0 0 0 0
RVE1_RVE1_ArabidopsisPBM_shift5 (RVE1_RVE1_ArabidopsisPBM)	0.843	0.562	7.524	0.532	0.895	1.419	0.911	15	11	7	8	13	22	17	13.286	7	; oligos_5-7nt_m1 versus RVE1_RVE1_ArabidopsisPBM; m=3/14; ncol2=10; w=8; offset=2; strand=D; shift=5; score=13.2857; -----wAAATATCTk-- ; cor=0.843; Ncor=0.562; logoDP=7.524; NIcor=0.532; NsEucl=0.895; SSD=1.419; NSW=0.911; rcor=15; rNcor=11; rlogoDP=7; rNIcor=8; rNsEucl=13; rSSD=22; rNSW=17; rank_mean=13.286; match_rank=7 a 0 0 0 0 0 65 92 92 98 7 99 0 1 2 9 0 0 c 0 0 0 0 0 4 0 0 0 0 1 1 98 10 20 0 0 g 0 0 0 0 0 6 2 7 1 4 0 0 0 4 28 0 0 t 0 0 0 0 0 25 6 1 1 89 0 99 1 84 43 0 0
CCA1_MA0972.1_JASPAR_shift6 (CCA1_MA0972.1_JASPAR)	0.851	0.542	8.273	0.514	0.883	1.346	0.904	11	13	4	10	20	19	20	13.857	9	; oligos_5-7nt_m1 versus CCA1_MA0972.1_JASPAR; m=4/14; ncol2=8; w=7; offset=3; strand=D; shift=6; score=13.8571; ------AAATATCT--- ; cor=0.851; Ncor=0.542; logoDP=8.273; NIcor=0.514; NsEucl=0.883; SSD=1.346; NSW=0.904; rcor=11; rNcor=13; rlogoDP=4; rNIcor=10; rNsEucl=20; rSSD=19; rNSW=20; rank_mean=13.857; match_rank=9 a 0 0 0 0 0 0 934 960 985 35 992 1 5 21 0 0 0 c 0 0 0 0 0 0 1 1 4 0 5 12 991 91 0 0 0 g 0 0 0 0 0 0 10 37 10 5 1 1 0 14 0 0 0 t 0 0 0 0 0 0 54 2 1 960 2 986 4 874 0 0 0
TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qnc_B_3D-footprint_rc_shift7 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qnc_B_3D-footprint_rc)	0.923	0.462	0.203	-0.034	0.915	0.517	0.957	4	21	40	38	8	2	4	16.714	14	; oligos_5-7nt_m1 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qnc_B_3D-footprint_rc; m=5/14; ncol2=8; w=6; offset=4; strand=R; shift=7; score=16.7143; -------AATAAaAG-- ; cor=0.923; Ncor=0.462; logoDP=0.203; NIcor=-0.034; NsEucl=0.915; SSD=0.517; NSW=0.957; rcor=4; rNcor=21; rlogoDP=40; rNIcor=38; rNsEucl=8; rSSD=2; rNSW=4; rank_mean=16.714; match_rank=14 a 0 0 0 0 0 0 0 96 96 0 96 74 53 96 10 0 0 c 0 0 0 0 0 0 0 0 0 0 0 10 10 0 12 0 0 g 0 0 0 0 0 0 0 0 0 0 0 12 21 0 74 0 0 t 0 0 0 0 0 0 0 0 0 96 0 0 12 0 0 0 0
HMGA_M0118_1.02_CISBP_shift1 (HMGA_M0118_1.02_CISBP)	0.810	0.472	2.283	0.476	0.891	1.160	0.917	22	19	28	12	15	11	13	17.143	15	; oligos_5-7nt_m1 versus HMGA_M0118_1.02_CISBP; m=6/14; ncol2=9; w=7; offset=-2; strand=D; shift=1; score=17.1429; -ssrrwAAwt------- ; cor=0.810; Ncor=0.472; logoDP=2.283; NIcor=0.476; NsEucl=0.891; SSD=1.160; NSW=0.917; rcor=22; rNcor=19; rlogoDP=28; rNIcor=12; rNsEucl=15; rSSD=11; rNSW=13; rank_mean=17.143; match_rank=15 a 0 24 21 35 33 41 71 89 45 21 0 0 0 0 0 0 0 c 0 27 31 18 18 4 5 0 1 18 0 0 0 0 0 0 0 g 0 26 25 30 25 21 0 4 4 10 0 0 0 0 0 0 0 t 0 23 23 17 24 34 24 7 50 51 0 0 0 0 0 0 0
AHL20_AHL20_ArabidopsisPBM_shift6 (AHL20_AHL20_ArabidopsisPBM)	0.820	0.441	5.335	0.405	0.884	1.312	0.906	20	30	14	20	19	18	18	19.857	18	; oligos_5-7nt_m1 versus AHL20_AHL20_ArabidopsisPBM; m=7/14; ncol2=10; w=7; offset=3; strand=D; shift=6; score=19.8571; ------wAATATATTw- ; cor=0.820; Ncor=0.441; logoDP=5.335; NIcor=0.405; NsEucl=0.884; SSD=1.312; NSW=0.906; rcor=20; rNcor=30; rlogoDP=14; rNIcor=20; rNsEucl=19; rSSD=18; rNSW=18; rank_mean=19.857; match_rank=18 a 0 0 0 0 0 0 44 95 88 8 87 13 91 11 3 44 0 c 0 0 0 0 0 0 16 1 0 1 0 0 1 1 1 10 0 g 0 0 0 0 0 0 11 1 1 0 0 0 1 0 1 21 0 t 0 0 0 0 0 0 29 3 11 91 13 87 7 88 95 25 0
CCA1_M01819_TRANSFAC_shift0 (CCA1_M01819_TRANSFAC)	0.780	0.459	8.358	0.427	0.894	2.255	0.887	31	22	3	14	14	41	27	21.714	22	; oligos_5-7nt_m1 versus CCA1_M01819_TRANSFAC; m=8/14; ncol2=17; w=10; offset=-3; strand=D; shift=0; score=21.7143; smharAAAAwATCTAar ; cor=0.780; Ncor=0.459; logoDP=8.358; NIcor=0.427; NsEucl=0.894; SSD=2.255; NSW=0.887; rcor=31; rNcor=22; rlogoDP=3; rNIcor=14; rNsEucl=14; rSSD=41; rNSW=27; rank_mean=21.714; match_rank=22 a 0 3 2 3 3 6 7 7 7 3 7 0 0 1 5 3 2 c 4 3 2 1 0 0 0 0 0 0 0 0 7 0 0 1 1 g 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 1 2 t 0 0 2 1 1 0 0 0 0 4 0 7 0 6 1 1 1
HMGIY_M01800_TRANSFAC_rc_shift5 (HMGIY_M01800_TRANSFAC_rc)	0.840	0.504	2.388	0.072	0.873	1.162	0.903	16	16	27	34	26	12	21	21.714	23	; oligos_5-7nt_m1 versus HMGIY_M01800_TRANSFAC_rc; m=9/14; ncol2=6; w=6; offset=2; strand=R; shift=5; score=21.7143; -----AAAWww------ ; cor=0.840; Ncor=0.504; logoDP=2.388; NIcor=0.072; NsEucl=0.873; SSD=1.162; NSW=0.903; rcor=16; rNcor=16; rlogoDP=27; rNIcor=34; rNsEucl=26; rSSD=12; rNSW=21; rank_mean=21.714; match_rank=23 a 0 0 0 0 0 9 13 11 10 7 9 0 0 0 0 0 0 c 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 t 0 0 0 0 0 1 1 3 4 6 5 0 0 0 0 0 0
AHL25_AHL25_2_ArabidopsisPBM_shift6 (AHL25_AHL25_2_ArabidopsisPBM)	0.790	0.425	3.008	0.422	0.879	1.429	0.898	27	36	25	15	22	23	23	24.429	26	; oligos_5-7nt_m1 versus AHL25_AHL25_2_ArabidopsisPBM; m=10/14; ncol2=10; w=7; offset=3; strand=D; shift=6; score=24.4286; ------aAwwWWwwTw- ; cor=0.790; Ncor=0.425; logoDP=3.008; NIcor=0.422; NsEucl=0.879; SSD=1.429; NSW=0.898; rcor=27; rNcor=36; rlogoDP=25; rNIcor=15; rNsEucl=22; rSSD=23; rNSW=23; rank_mean=24.429; match_rank=26 a 0 0 0 0 0 0 49 86 64 35 70 29 64 34 4 36 0 c 0 0 0 0 0 0 14 4 0 0 1 0 1 2 6 16 0 g 0 0 0 0 0 0 13 6 2 1 0 1 0 0 4 12 0 t 0 0 0 0 0 0 24 4 34 64 29 70 35 64 86 36 0
KAN_M1340_1.02_CISBP_shift5 (KAN_M1340_1.02_CISBP)	0.760	0.507	1.468	0.491	0.881	1.822	0.886	36	15	37	11	21	35	28	26.143	29	; oligos_5-7nt_m1 versus KAN_M1340_1.02_CISBP; m=11/14; ncol2=10; w=8; offset=2; strand=D; shift=5; score=26.1429; -----rrwaTAtwyy-- ; cor=0.760; Ncor=0.507; logoDP=1.468; NIcor=0.491; NsEucl=0.881; SSD=1.822; NSW=0.886; rcor=36; rNcor=15; rlogoDP=37; rNIcor=11; rNsEucl=21; rSSD=35; rNSW=28; rank_mean=26.143; match_rank=29 a 0 0 0 0 0 41 26 44 55 13 73 23 26 20 16 0 0 c 0 0 0 0 0 16 11 15 8 13 1 14 15 43 27 0 0 g 0 0 0 0 0 27 43 15 14 1 13 8 15 11 16 0 0 t 0 0 0 0 0 16 20 26 23 73 13 55 44 26 41 0 0
gw1.20.00.89.1_M0601_1.02_CISBP_shift0 (gw1.20.00.89.1_M0601_1.02_CISBP)	0.773	0.416	0.697	0.405	0.877	1.484	0.894	33	37	38	19	23	25	24	28.429	32	; oligos_5-7nt_m1 versus gw1.20.00.89.1_M0601_1.02_CISBP; m=12/14; ncol2=10; w=7; offset=-3; strand=D; shift=0; score=28.4286; awttyraawt------- ; cor=0.773; Ncor=0.416; logoDP=0.697; NIcor=0.405; NsEucl=0.877; SSD=1.484; NSW=0.894; rcor=33; rNcor=37; rlogoDP=38; rNIcor=19; rNsEucl=23; rSSD=25; rNSW=24; rank_mean=28.429; match_rank=32 a 54 28 10 20 8 43 59 61 38 23 0 0 0 0 0 0 0 c 12 14 18 12 28 21 9 12 20 11 0 0 0 0 0 0 0 g 11 20 12 9 21 28 12 18 14 12 0 0 0 0 0 0 0 t 23 38 60 59 43 8 20 9 28 54 0 0 0 0 0 0 0
AHL25_AHL25_3_ArabidopsisPBM_rc_shift6 (AHL25_AHL25_3_ArabidopsisPBM_rc)	0.755	0.407	1.867	0.224	0.871	1.623	0.884	38	39	34	26	27	29	30	31.857	35	; oligos_5-7nt_m1 versus AHL25_AHL25_3_ArabidopsisPBM_rc; m=13/14; ncol2=10; w=7; offset=3; strand=R; shift=6; score=31.8571; ------wAwTwWwWtw- ; cor=0.755; Ncor=0.407; logoDP=1.867; NIcor=0.224; NsEucl=0.871; SSD=1.623; NSW=0.884; rcor=38; rNcor=39; rlogoDP=34; rNIcor=26; rNsEucl=27; rSSD=29; rNSW=30; rank_mean=31.857; match_rank=35 a 0 0 0 0 0 0 56 83 62 16 51 71 60 25 22 29 0 c 0 0 0 0 0 0 6 6 0 1 0 0 0 1 15 16 0 g 0 0 0 0 0 0 10 3 1 0 0 0 1 0 9 18 0 t 0 0 0 0 0 0 28 8 37 83 49 29 39 74 54 37 0
PK02532.1_M1303_1.02_CISBP_rc_shift6 (PK02532.1_M1303_1.02_CISBP_rc)	0.785	0.458	1.941	-0.011	0.862	1.876	0.866	29	23	32	37	36	36	37	32.857	37	; oligos_5-7nt_m1 versus PK02532.1_M1303_1.02_CISBP_rc; m=14/14; ncol2=9; w=7; offset=3; strand=R; shift=6; score=32.8571; ------wAATATCTn-- ; cor=0.785; Ncor=0.458; logoDP=1.941; NIcor=-0.011; NsEucl=0.862; SSD=1.876; NSW=0.866; rcor=29; rNcor=23; rlogoDP=32; rNIcor=37; rNsEucl=36; rSSD=36; rNSW=37; rank_mean=32.857; match_rank=37 a 0 0 0 0 0 0 50 100 100 0 100 0 0 0 25 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 100 0 25 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 t 0 0 0 0 0 0 50 0 0 100 0 100 0 100 25 0 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m4_shift1 ; 15 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_shift1 (oligos_5-7nt_m4)
; oligos_5-7nt_m4; m=0 (reference); ncol1=9; shift=1; ncol=12; -ggCGGGCss-- ; Alignment reference a 0 16 15 0 0 0 0 0 13 18 0 0 c 0 19 20 83 0 0 0 83 26 28 0 0 g 0 32 30 0 83 83 83 0 28 22 0 0 t 0 16 18 0 0 0 0 0 16 15 0 0

E2L_M01839_TRANSFAC_shift0 (E2L_M01839_TRANSFAC) 0.848 0.509 6.206 0.467 0.875 1.131 0.906 13 14 9 13 25 10 19 14.714 11
; oligos_5-7nt_m4 versus E2L_M01839_TRANSFAC; m=1/14; ncol2=7; w=6; offset=-1; strand=D; shift=0; score=14.7143; WGGCGGG----- ; cor=0.848; Ncor=0.509; logoDP=6.206; NIcor=0.467; NsEucl=0.875; SSD=1.131; NSW=0.906; rcor=13; rNcor=14; rlogoDP=9; rNIcor=13; rNsEucl=25; rSSD=10; rNSW=19; rank_mean=14.714; match_rank=11 a 2 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 7 0 1 1 0 0 0 0 0 g 0 7 7 0 7 6 6 0 0 0 0 0 t 5 0 0 0 0 0 0 0 0 0 0 0

TCP23_MA1066.1_JASPAR_shift4 (TCP23_MA1066.1_JASPAR) 0.835 0.455 5.923 0.422 0.870 1.212 0.899 17 25 11 16 28 14 22 19.000 17
; oligos_5-7nt_m4 versus TCP23_MA1066.1_JASPAR; m=2/14; ncol2=8; w=6; offset=3; strand=D; shift=4; score= 19; ----GGGCCCAC ; cor=0.835; Ncor=0.455; logoDP=5.923; NIcor=0.422; NsEucl=0.870; SSD=1.212; NSW=0.899; rcor=17; rNcor=25; rlogoDP=11; rNIcor=16; rNsEucl=28; rSSD=14; rNSW=22; rank_mean=19.000; match_rank=17 a 0 0 0 0 5 10 37 7 4 12 954 10 c 0 0 0 0 3 5 88 971 984 980 10 959 g 0 0 0 0 966 980 835 8 8 3 31 11 t 0 0 0 0 26 5 41 13 4 6 5 21

DREB1B_M01700_TRANSFAC_rc_shift1 (DREB1B_M01700_TRANSFAC_rc) 0.859 0.477 0.147 -0.147 0.890 0.602 0.940 10 18 41 41 16 4 9 19.857 20
; oligos_5-7nt_m4 versus DREB1B_M01700_TRANSFAC_rc; m=3/14; ncol2=5; w=5; offset=0; strand=R; shift=1; score=19.8571; -GtcGG------ ; cor=0.859; Ncor=0.477; logoDP=0.147; NIcor=-0.147; NsEucl=0.890; SSD=0.602; NSW=0.940; rcor=10; rNcor=18; rlogoDP=41; rNIcor=41; rNsEucl=16; rSSD=4; rNSW=9; rank_mean=19.857; match_rank=20 a 0 123 124 52 1 23 0 0 0 0 0 0 c 0 49 34 519 7 38 0 0 0 0 0 0 g 0 572 192 84 763 563 0 0 0 0 0 0 t 0 28 422 117 1 150 0 0 0 0 0 0

TCP15_MA1062.1_JASPAR_shift4 (TCP15_MA1062.1_JASPAR) 0.823 0.449 5.750 0.412 0.867 1.275 0.894 19 27 12 18 30 15 26 21.000 21
; oligos_5-7nt_m4 versus TCP15_MA1062.1_JASPAR; m=4/14; ncol2=8; w=6; offset=3; strand=D; shift=4; score= 21; ----GGGCCCAC ; cor=0.823; Ncor=0.449; logoDP=5.750; NIcor=0.412; NsEucl=0.867; SSD=1.275; NSW=0.894; rcor=19; rNcor=27; rlogoDP=12; rNIcor=18; rNsEucl=30; rSSD=15; rNSW=26; rank_mean=21.000; match_rank=21 a 0 0 0 0 6 5 60 8 2 3 949 6 c 0 0 0 0 2 3 138 950 990 986 12 962 g 0 0 0 0 978 989 771 6 1 2 36 20 t 0 0 0 0 14 2 30 36 7 9 3 12

ERF13_M03170_TRANSFAC_rc_shift3 (ERF13_M03170_TRANSFAC_rc) 0.820 0.478 4.286 0.228 0.877 1.487 0.894 21 17 18 25 24 27 25 22.429 24
; oligos_5-7nt_m4 versus ERF13_M03170_TRANSFAC_rc; m=5/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=22.4286; ---CGGGCGGCm ; cor=0.820; Ncor=0.478; logoDP=4.286; NIcor=0.228; NsEucl=0.877; SSD=1.487; NSW=0.894; rcor=21; rNcor=17; rlogoDP=18; rNIcor=25; rNsEucl=24; rSSD=27; rNSW=25; rank_mean=22.429; match_rank=24 a 0 0 0 1 0 11 0 0 0 0 0 27 c 0 0 0 72 4 0 6 100 0 0 100 61 g 0 0 0 12 95 89 92 0 100 100 0 12 t 0 0 0 15 1 0 2 0 0 0 0 0

ESR1_M03213_TRANSFAC_rc_shift3 (ESR1_M03213_TRANSFAC_rc) 0.795 0.464 5.633 0.278 0.869 1.671 0.881 25 20 13 24 29 30 31 24.571 27
; oligos_5-7nt_m4 versus ESR1_M03213_TRANSFAC_rc; m=6/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=24.5714; ---cGGGCGGCC ; cor=0.795; Ncor=0.464; logoDP=5.633; NIcor=0.278; NsEucl=0.869; SSD=1.671; NSW=0.881; rcor=25; rNcor=20; rlogoDP=13; rNIcor=24; rNsEucl=29; rSSD=30; rNSW=31; rank_mean=24.571; match_rank=27 a 0 0 0 7 0 1 1 0 0 0 0 0 c 0 0 0 52 6 0 6 100 0 0 100 98 g 0 0 0 22 93 99 92 0 100 100 0 2 t 0 0 0 19 1 0 1 0 0 0 0 0

OsI_08196_M1658_1.02_CISBP_shift4 (OsI_08196_M1658_1.02_CISBP) 0.797 0.435 4.736 0.387 0.862 1.374 0.886 24 34 17 23 35 20 29 26.000 28
; oligos_5-7nt_m4 versus OsI_08196_M1658_1.02_CISBP; m=7/14; ncol2=8; w=6; offset=3; strand=D; shift=4; score= 26; ----GGGCCCAC ; cor=0.797; Ncor=0.435; logoDP=4.736; NIcor=0.387; NsEucl=0.862; SSD=1.374; NSW=0.886; rcor=24; rNcor=34; rlogoDP=17; rNIcor=23; rNsEucl=35; rSSD=20; rNSW=29; rank_mean=26.000; match_rank=28 a 0 0 0 0 0 5 9 0 0 0 90 0 c 0 0 0 0 0 0 9 86 100 100 5 86 g 0 0 0 0 95 95 73 5 0 0 5 7 t 0 0 0 0 5 0 9 9 0 0 0 7

LjSGA_053525.1_M1662_1.02_CISBP_shift4 (LjSGA_053525.1_M1662_1.02_CISBP) 0.794 0.433 5.996 0.388 0.857 1.471 0.877 26 35 10 22 41 24 32 27.143 30
; oligos_5-7nt_m4 versus LjSGA_053525.1_M1662_1.02_CISBP; m=8/14; ncol2=8; w=6; offset=3; strand=D; shift=4; score=27.1429; ----GGgCCCAC ; cor=0.794; Ncor=0.433; logoDP=5.996; NIcor=0.388; NsEucl=0.857; SSD=1.471; NSW=0.877; rcor=26; rNcor=35; rlogoDP=10; rNIcor=22; rNsEucl=41; rSSD=24; rNSW=32; rank_mean=27.143; match_rank=30 a 0 0 0 0 0 0 14 0 0 0 100 0 c 0 0 0 0 0 0 14 100 100 100 0 100 g 0 0 0 0 100 100 58 0 0 0 0 0 t 0 0 0 0 0 0 14 0 0 0 0 0

CRF1_M03193_TRANSFAC_rc_shift3 (CRF1_M03193_TRANSFAC_rc) 0.781 0.455 4.176 0.213 0.866 1.754 0.875 30 24 19 27 32 32 34 28.286 31
; oligos_5-7nt_m4 versus CRF1_M03193_TRANSFAC_rc; m=9/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=28.2857; ---sGGGCGGCm ; cor=0.781; Ncor=0.455; logoDP=4.176; NIcor=0.213; NsEucl=0.866; SSD=1.754; NSW=0.875; rcor=30; rNcor=24; rlogoDP=19; rNIcor=27; rNsEucl=32; rSSD=32; rNSW=34; rank_mean=28.286; match_rank=31 a 0 0 0 2 1 4 0 0 0 0 0 28 c 0 0 0 55 8 0 0 100 0 0 100 54 g 0 0 0 36 77 96 97 0 100 100 0 18 t 0 0 0 7 14 0 3 0 0 0 0 0

AT5G07580_M03194_TRANSFAC_rc_shift3 (AT5G07580_M03194_TRANSFAC_rc) 0.778 0.454 4.005 0.183 0.866 1.748 0.875 32 26 24 32 31 31 33 29.857 33
; oligos_5-7nt_m4 versus AT5G07580_M03194_TRANSFAC_rc; m=10/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=29.8571; ---CGGkCGGCg ; cor=0.778; Ncor=0.454; logoDP=4.005; NIcor=0.183; NsEucl=0.866; SSD=1.748; NSW=0.875; rcor=32; rNcor=26; rlogoDP=24; rNIcor=32; rNsEucl=31; rSSD=31; rNSW=33; rank_mean=29.857; match_rank=33 a 0 0 0 5 1 5 1 0 0 0 0 15 c 0 0 0 68 2 0 8 100 0 0 100 21 g 0 0 0 4 96 95 61 0 100 100 0 63 t 0 0 0 23 1 0 30 0 0 0 0 1

ERF6_M03208_TRANSFAC_rc_shift3 (ERF6_M03208_TRANSFAC_rc) 0.763 0.445 4.031 0.190 0.864 1.806 0.871 34 28 22 29 34 34 36 31.000 34
; oligos_5-7nt_m4 versus ERF6_M03208_TRANSFAC_rc; m=11/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score= 31; ---sGGGCGGCs ; cor=0.763; Ncor=0.445; logoDP=4.031; NIcor=0.190; NsEucl=0.864; SSD=1.806; NSW=0.871; rcor=34; rNcor=28; rlogoDP=22; rNIcor=29; rNsEucl=34; rSSD=34; rNSW=36; rank_mean=31.000; match_rank=34 a 0 0 0 2 1 10 1 0 0 0 0 17 c 0 0 0 58 4 0 10 100 0 0 100 27 g 0 0 0 35 87 90 71 0 100 100 0 56 t 0 0 0 5 8 0 18 0 0 0 0 0

RAP2.11_M03202_TRANSFAC_rc_shift3 (RAP2.11_M03202_TRANSFAC_rc) 0.762 0.444 4.156 0.200 0.860 1.930 0.862 35 29 20 28 38 38 39 32.429 36
; oligos_5-7nt_m4 versus RAP2.11_M03202_TRANSFAC_rc; m=12/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=32.4286; ---sGGGCGGCm ; cor=0.762; Ncor=0.444; logoDP=4.156; NIcor=0.200; NsEucl=0.860; SSD=1.930; NSW=0.862; rcor=35; rNcor=29; rlogoDP=20; rNIcor=28; rNsEucl=38; rSSD=38; rNSW=39; rank_mean=32.429; match_rank=36 a 0 0 0 21 0 0 1 0 0 0 0 47 c 0 0 0 38 11 0 0 100 0 0 100 45 g 0 0 0 37 89 100 94 0 100 100 0 7 t 0 0 0 4 0 0 5 0 0 0 0 1

CRF3_M03190_TRANSFAC_rc_shift3 (CRF3_M03190_TRANSFAC_rc) 0.755 0.440 4.031 0.190 0.861 1.898 0.864 39 31 23 31 37 37 38 33.714 39
; oligos_5-7nt_m4 versus CRF3_M03190_TRANSFAC_rc; m=13/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=33.7143; ---ckGGCGGCm ; cor=0.755; Ncor=0.440; logoDP=4.031; NIcor=0.190; NsEucl=0.861; SSD=1.898; NSW=0.864; rcor=39; rNcor=31; rlogoDP=23; rNIcor=31; rNsEucl=37; rSSD=37; rNSW=38; rank_mean=33.714; match_rank=39 a 0 0 0 4 1 3 1 0 0 0 0 44 c 0 0 0 54 2 0 0 100 0 0 100 36 g 0 0 0 23 63 97 93 0 100 100 0 19 t 0 0 0 19 34 0 6 0 0 0 0 1

ERF-1_M03189_TRANSFAC_rc_shift3 (ERF-1_M03189_TRANSFAC_rc) 0.752 0.439 4.040 0.190 0.859 1.951 0.861 41 33 21 30 40 40 41 35.143 40
; oligos_5-7nt_m4 versus ERF-1_M03189_TRANSFAC_rc; m=14/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=35.1429; ---CGGkCGGCs ; cor=0.752; Ncor=0.439; logoDP=4.040; NIcor=0.190; NsEucl=0.859; SSD=1.951; NSW=0.861; rcor=41; rNcor=33; rlogoDP=21; rNIcor=30; rNsEucl=40; rSSD=40; rNSW=41; rank_mean=35.143; match_rank=40 a 0 0 0 1 0 20 1 0 0 0 0 14 c 0 0 0 86 2 0 7 100 0 0 100 26 g 0 0 0 4 98 80 46 0 100 100 0 60 t 0 0 0 9 0 0 46 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_shift1 (oligos_5-7nt_m4)																	; oligos_5-7nt_m4; m=0 (reference); ncol1=9; shift=1; ncol=12; -ggCGGGCss-- ; Alignment reference a 0 16 15 0 0 0 0 0 13 18 0 0 c 0 19 20 83 0 0 0 83 26 28 0 0 g 0 32 30 0 83 83 83 0 28 22 0 0 t 0 16 18 0 0 0 0 0 16 15 0 0
E2L_M01839_TRANSFAC_shift0 (E2L_M01839_TRANSFAC)	0.848	0.509	6.206	0.467	0.875	1.131	0.906	13	14	9	13	25	10	19	14.714	11	; oligos_5-7nt_m4 versus E2L_M01839_TRANSFAC; m=1/14; ncol2=7; w=6; offset=-1; strand=D; shift=0; score=14.7143; WGGCGGG----- ; cor=0.848; Ncor=0.509; logoDP=6.206; NIcor=0.467; NsEucl=0.875; SSD=1.131; NSW=0.906; rcor=13; rNcor=14; rlogoDP=9; rNIcor=13; rNsEucl=25; rSSD=10; rNSW=19; rank_mean=14.714; match_rank=11 a 2 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 7 0 1 1 0 0 0 0 0 g 0 7 7 0 7 6 6 0 0 0 0 0 t 5 0 0 0 0 0 0 0 0 0 0 0
TCP23_MA1066.1_JASPAR_shift4 (TCP23_MA1066.1_JASPAR)	0.835	0.455	5.923	0.422	0.870	1.212	0.899	17	25	11	16	28	14	22	19.000	17	; oligos_5-7nt_m4 versus TCP23_MA1066.1_JASPAR; m=2/14; ncol2=8; w=6; offset=3; strand=D; shift=4; score= 19; ----GGGCCCAC ; cor=0.835; Ncor=0.455; logoDP=5.923; NIcor=0.422; NsEucl=0.870; SSD=1.212; NSW=0.899; rcor=17; rNcor=25; rlogoDP=11; rNIcor=16; rNsEucl=28; rSSD=14; rNSW=22; rank_mean=19.000; match_rank=17 a 0 0 0 0 5 10 37 7 4 12 954 10 c 0 0 0 0 3 5 88 971 984 980 10 959 g 0 0 0 0 966 980 835 8 8 3 31 11 t 0 0 0 0 26 5 41 13 4 6 5 21
DREB1B_M01700_TRANSFAC_rc_shift1 (DREB1B_M01700_TRANSFAC_rc)	0.859	0.477	0.147	-0.147	0.890	0.602	0.940	10	18	41	41	16	4	9	19.857	20	; oligos_5-7nt_m4 versus DREB1B_M01700_TRANSFAC_rc; m=3/14; ncol2=5; w=5; offset=0; strand=R; shift=1; score=19.8571; -GtcGG------ ; cor=0.859; Ncor=0.477; logoDP=0.147; NIcor=-0.147; NsEucl=0.890; SSD=0.602; NSW=0.940; rcor=10; rNcor=18; rlogoDP=41; rNIcor=41; rNsEucl=16; rSSD=4; rNSW=9; rank_mean=19.857; match_rank=20 a 0 123 124 52 1 23 0 0 0 0 0 0 c 0 49 34 519 7 38 0 0 0 0 0 0 g 0 572 192 84 763 563 0 0 0 0 0 0 t 0 28 422 117 1 150 0 0 0 0 0 0
TCP15_MA1062.1_JASPAR_shift4 (TCP15_MA1062.1_JASPAR)	0.823	0.449	5.750	0.412	0.867	1.275	0.894	19	27	12	18	30	15	26	21.000	21	; oligos_5-7nt_m4 versus TCP15_MA1062.1_JASPAR; m=4/14; ncol2=8; w=6; offset=3; strand=D; shift=4; score= 21; ----GGGCCCAC ; cor=0.823; Ncor=0.449; logoDP=5.750; NIcor=0.412; NsEucl=0.867; SSD=1.275; NSW=0.894; rcor=19; rNcor=27; rlogoDP=12; rNIcor=18; rNsEucl=30; rSSD=15; rNSW=26; rank_mean=21.000; match_rank=21 a 0 0 0 0 6 5 60 8 2 3 949 6 c 0 0 0 0 2 3 138 950 990 986 12 962 g 0 0 0 0 978 989 771 6 1 2 36 20 t 0 0 0 0 14 2 30 36 7 9 3 12
ERF13_M03170_TRANSFAC_rc_shift3 (ERF13_M03170_TRANSFAC_rc)	0.820	0.478	4.286	0.228	0.877	1.487	0.894	21	17	18	25	24	27	25	22.429	24	; oligos_5-7nt_m4 versus ERF13_M03170_TRANSFAC_rc; m=5/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=22.4286; ---CGGGCGGCm ; cor=0.820; Ncor=0.478; logoDP=4.286; NIcor=0.228; NsEucl=0.877; SSD=1.487; NSW=0.894; rcor=21; rNcor=17; rlogoDP=18; rNIcor=25; rNsEucl=24; rSSD=27; rNSW=25; rank_mean=22.429; match_rank=24 a 0 0 0 1 0 11 0 0 0 0 0 27 c 0 0 0 72 4 0 6 100 0 0 100 61 g 0 0 0 12 95 89 92 0 100 100 0 12 t 0 0 0 15 1 0 2 0 0 0 0 0
ESR1_M03213_TRANSFAC_rc_shift3 (ESR1_M03213_TRANSFAC_rc)	0.795	0.464	5.633	0.278	0.869	1.671	0.881	25	20	13	24	29	30	31	24.571	27	; oligos_5-7nt_m4 versus ESR1_M03213_TRANSFAC_rc; m=6/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=24.5714; ---cGGGCGGCC ; cor=0.795; Ncor=0.464; logoDP=5.633; NIcor=0.278; NsEucl=0.869; SSD=1.671; NSW=0.881; rcor=25; rNcor=20; rlogoDP=13; rNIcor=24; rNsEucl=29; rSSD=30; rNSW=31; rank_mean=24.571; match_rank=27 a 0 0 0 7 0 1 1 0 0 0 0 0 c 0 0 0 52 6 0 6 100 0 0 100 98 g 0 0 0 22 93 99 92 0 100 100 0 2 t 0 0 0 19 1 0 1 0 0 0 0 0
OsI_08196_M1658_1.02_CISBP_shift4 (OsI_08196_M1658_1.02_CISBP)	0.797	0.435	4.736	0.387	0.862	1.374	0.886	24	34	17	23	35	20	29	26.000	28	; oligos_5-7nt_m4 versus OsI_08196_M1658_1.02_CISBP; m=7/14; ncol2=8; w=6; offset=3; strand=D; shift=4; score= 26; ----GGGCCCAC ; cor=0.797; Ncor=0.435; logoDP=4.736; NIcor=0.387; NsEucl=0.862; SSD=1.374; NSW=0.886; rcor=24; rNcor=34; rlogoDP=17; rNIcor=23; rNsEucl=35; rSSD=20; rNSW=29; rank_mean=26.000; match_rank=28 a 0 0 0 0 0 5 9 0 0 0 90 0 c 0 0 0 0 0 0 9 86 100 100 5 86 g 0 0 0 0 95 95 73 5 0 0 5 7 t 0 0 0 0 5 0 9 9 0 0 0 7
LjSGA_053525.1_M1662_1.02_CISBP_shift4 (LjSGA_053525.1_M1662_1.02_CISBP)	0.794	0.433	5.996	0.388	0.857	1.471	0.877	26	35	10	22	41	24	32	27.143	30	; oligos_5-7nt_m4 versus LjSGA_053525.1_M1662_1.02_CISBP; m=8/14; ncol2=8; w=6; offset=3; strand=D; shift=4; score=27.1429; ----GGgCCCAC ; cor=0.794; Ncor=0.433; logoDP=5.996; NIcor=0.388; NsEucl=0.857; SSD=1.471; NSW=0.877; rcor=26; rNcor=35; rlogoDP=10; rNIcor=22; rNsEucl=41; rSSD=24; rNSW=32; rank_mean=27.143; match_rank=30 a 0 0 0 0 0 0 14 0 0 0 100 0 c 0 0 0 0 0 0 14 100 100 100 0 100 g 0 0 0 0 100 100 58 0 0 0 0 0 t 0 0 0 0 0 0 14 0 0 0 0 0
CRF1_M03193_TRANSFAC_rc_shift3 (CRF1_M03193_TRANSFAC_rc)	0.781	0.455	4.176	0.213	0.866	1.754	0.875	30	24	19	27	32	32	34	28.286	31	; oligos_5-7nt_m4 versus CRF1_M03193_TRANSFAC_rc; m=9/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=28.2857; ---sGGGCGGCm ; cor=0.781; Ncor=0.455; logoDP=4.176; NIcor=0.213; NsEucl=0.866; SSD=1.754; NSW=0.875; rcor=30; rNcor=24; rlogoDP=19; rNIcor=27; rNsEucl=32; rSSD=32; rNSW=34; rank_mean=28.286; match_rank=31 a 0 0 0 2 1 4 0 0 0 0 0 28 c 0 0 0 55 8 0 0 100 0 0 100 54 g 0 0 0 36 77 96 97 0 100 100 0 18 t 0 0 0 7 14 0 3 0 0 0 0 0
AT5G07580_M03194_TRANSFAC_rc_shift3 (AT5G07580_M03194_TRANSFAC_rc)	0.778	0.454	4.005	0.183	0.866	1.748	0.875	32	26	24	32	31	31	33	29.857	33	; oligos_5-7nt_m4 versus AT5G07580_M03194_TRANSFAC_rc; m=10/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=29.8571; ---CGGkCGGCg ; cor=0.778; Ncor=0.454; logoDP=4.005; NIcor=0.183; NsEucl=0.866; SSD=1.748; NSW=0.875; rcor=32; rNcor=26; rlogoDP=24; rNIcor=32; rNsEucl=31; rSSD=31; rNSW=33; rank_mean=29.857; match_rank=33 a 0 0 0 5 1 5 1 0 0 0 0 15 c 0 0 0 68 2 0 8 100 0 0 100 21 g 0 0 0 4 96 95 61 0 100 100 0 63 t 0 0 0 23 1 0 30 0 0 0 0 1
ERF6_M03208_TRANSFAC_rc_shift3 (ERF6_M03208_TRANSFAC_rc)	0.763	0.445	4.031	0.190	0.864	1.806	0.871	34	28	22	29	34	34	36	31.000	34	; oligos_5-7nt_m4 versus ERF6_M03208_TRANSFAC_rc; m=11/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score= 31; ---sGGGCGGCs ; cor=0.763; Ncor=0.445; logoDP=4.031; NIcor=0.190; NsEucl=0.864; SSD=1.806; NSW=0.871; rcor=34; rNcor=28; rlogoDP=22; rNIcor=29; rNsEucl=34; rSSD=34; rNSW=36; rank_mean=31.000; match_rank=34 a 0 0 0 2 1 10 1 0 0 0 0 17 c 0 0 0 58 4 0 10 100 0 0 100 27 g 0 0 0 35 87 90 71 0 100 100 0 56 t 0 0 0 5 8 0 18 0 0 0 0 0
RAP2.11_M03202_TRANSFAC_rc_shift3 (RAP2.11_M03202_TRANSFAC_rc)	0.762	0.444	4.156	0.200	0.860	1.930	0.862	35	29	20	28	38	38	39	32.429	36	; oligos_5-7nt_m4 versus RAP2.11_M03202_TRANSFAC_rc; m=12/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=32.4286; ---sGGGCGGCm ; cor=0.762; Ncor=0.444; logoDP=4.156; NIcor=0.200; NsEucl=0.860; SSD=1.930; NSW=0.862; rcor=35; rNcor=29; rlogoDP=20; rNIcor=28; rNsEucl=38; rSSD=38; rNSW=39; rank_mean=32.429; match_rank=36 a 0 0 0 21 0 0 1 0 0 0 0 47 c 0 0 0 38 11 0 0 100 0 0 100 45 g 0 0 0 37 89 100 94 0 100 100 0 7 t 0 0 0 4 0 0 5 0 0 0 0 1
CRF3_M03190_TRANSFAC_rc_shift3 (CRF3_M03190_TRANSFAC_rc)	0.755	0.440	4.031	0.190	0.861	1.898	0.864	39	31	23	31	37	37	38	33.714	39	; oligos_5-7nt_m4 versus CRF3_M03190_TRANSFAC_rc; m=13/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=33.7143; ---ckGGCGGCm ; cor=0.755; Ncor=0.440; logoDP=4.031; NIcor=0.190; NsEucl=0.861; SSD=1.898; NSW=0.864; rcor=39; rNcor=31; rlogoDP=23; rNIcor=31; rNsEucl=37; rSSD=37; rNSW=38; rank_mean=33.714; match_rank=39 a 0 0 0 4 1 3 1 0 0 0 0 44 c 0 0 0 54 2 0 0 100 0 0 100 36 g 0 0 0 23 63 97 93 0 100 100 0 19 t 0 0 0 19 34 0 6 0 0 0 0 1
ERF-1_M03189_TRANSFAC_rc_shift3 (ERF-1_M03189_TRANSFAC_rc)	0.752	0.439	4.040	0.190	0.859	1.951	0.861	41	33	21	30	40	40	41	35.143	40	; oligos_5-7nt_m4 versus ERF-1_M03189_TRANSFAC_rc; m=14/14; ncol2=10; w=7; offset=2; strand=R; shift=3; score=35.1429; ---CGGkCGGCs ; cor=0.752; Ncor=0.439; logoDP=4.040; NIcor=0.190; NsEucl=0.859; SSD=1.951; NSW=0.861; rcor=41; rNcor=33; rlogoDP=21; rNIcor=30; rNsEucl=40; rSSD=40; rNSW=41; rank_mean=35.143; match_rank=40 a 0 0 0 1 0 20 1 0 0 0 0 14 c 0 0 0 86 2 0 7 100 0 0 100 26 g 0 0 0 4 98 80 46 0 100 100 0 60 t 0 0 0 9 0 0 46 0 0 0 0 0