One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 4/regulon4.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 4/regulon4.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m3_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_m3_shift0 (oligos_5-7nt_m3)
; oligos_5-7nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=13; kwCGATGAwv--- ; Alignment reference a 8 14 0 0 51 0 0 51 19 13 0 0 0 c 7 12 51 0 0 0 0 0 6 15 0 0 0 g 18 6 0 51 0 0 51 0 12 15 0 0 0 t 18 19 0 0 0 51 0 0 14 8 0 0 0

Opaque-2_M00374_TRANSFAC_shift3 (Opaque-2_M00374_TRANSFAC) 0.911 0.490 9.625 0.507 0.913 0.749 0.946 1 15 1 10 1 4 2 4.857 1
; oligos_5-7nt_m3 versus Opaque-2_M00374_TRANSFAC; m=1/1; ncol2=10; w=7; offset=3; strand=D; shift=3; score= 4.8571; ---GATGAyRTGR ; cor=0.911; Ncor=0.490; logoDP=9.625; NIcor=0.507; NsEucl=0.913; SSD=0.749; NSW=0.946; rcor=1; rNcor=15; rlogoDP=1; rNIcor=10; rNsEucl=1; rSSD=4; rNSW=2; rank_mean=4.857; match_rank=1 a 0 0 0 0 5 0 0 5 0 3 0 0 1 c 0 0 0 0 0 0 0 0 2 0 0 0 0 g 0 0 0 5 0 0 5 0 0 1 0 5 3 t 0 0 0 0 0 5 0 0 2 0 5 0 0

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-7nt_m3_shift0 (oligos_5-7nt_m3)																		; oligos_5-7nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=13; kwCGATGAwv--- ; Alignment reference a 8 14 0 0 51 0 0 51 19 13 0 0 0 c 7 12 51 0 0 0 0 0 6 15 0 0 0 g 18 6 0 51 0 0 51 0 12 15 0 0 0 t 18 19 0 0 0 51 0 0 14 8 0 0 0
Opaque-2_M00374_TRANSFAC_shift3 (Opaque-2_M00374_TRANSFAC)		0.911	0.490	9.625	0.507	0.913	0.749	0.946	1	15	1	10	1	4	2	4.857	1	; oligos_5-7nt_m3 versus Opaque-2_M00374_TRANSFAC; m=1/1; ncol2=10; w=7; offset=3; strand=D; shift=3; score= 4.8571; ---GATGAyRTGR ; cor=0.911; Ncor=0.490; logoDP=9.625; NIcor=0.507; NsEucl=0.913; SSD=0.749; NSW=0.946; rcor=1; rNcor=15; rlogoDP=1; rNIcor=10; rNsEucl=1; rSSD=4; rNSW=2; rank_mean=4.857; match_rank=1 a 0 0 0 0 5 0 0 5 0 3 0 0 1 c 0 0 0 0 0 0 0 0 2 0 0 0 0 g 0 0 0 5 0 0 5 0 0 1 0 5 3 t 0 0 0 0 0 5 0 0 2 0 5 0 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m2_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_m2_shift3 (oligos_5-7nt_m2)
; oligos_5-7nt_m2; m=0 (reference); ncol1=9; shift=3; ncol=12; ---hsATTCGdt ; Alignment reference a 0 0 0 26 23 100 0 0 0 0 28 23 c 0 0 0 27 29 0 0 0 100 0 21 23 g 0 0 0 16 27 0 0 0 0 100 26 23 t 0 0 0 31 21 0 100 100 0 0 25 31

AT3G04030_M1325_1.02_CISBP_shift3 (AT3G04030_M1325_1.02_CISBP) 0.804 0.804 3.925 0.784 0.908 1.358 0.925 10 1 9 1 4 10 8 6.143 2
; oligos_5-7nt_m2 versus AT3G04030_M1325_1.02_CISBP; m=1/14; ncol2=9; w=9; offset=0; strand=D; shift=3; score= 6.1429; ---wkATtCbsy ; cor=0.804; Ncor=0.804; logoDP=3.925; NIcor=0.784; NsEucl=0.908; SSD=1.358; NSW=0.925; rcor=10; rNcor=1; rlogoDP=9; rNIcor=1; rNsEucl=4; rSSD=10; rNSW=8; rank_mean=6.143; match_rank=2 a 0 0 0 38 10 79 0 17 3 8 21 22 c 0 0 0 19 8 2 0 12 88 36 31 27 g 0 0 0 18 55 15 0 22 4 28 25 23 t 0 0 0 25 27 4 100 49 5 28 23 28

AT3G24120_M1328_1.02_CISBP_shift2 (AT3G24120_M1328_1.02_CISBP) 0.814 0.733 3.524 0.714 0.909 1.334 0.926 9 2 12 2 3 9 7 6.286 3
; oligos_5-7nt_m2 versus AT3G24120_M1328_1.02_CISBP; m=2/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score= 6.2857; --wwkATtCbby ; cor=0.814; Ncor=0.733; logoDP=3.524; NIcor=0.714; NsEucl=0.909; SSD=1.334; NSW=0.926; rcor=9; rNcor=2; rlogoDP=12; rNIcor=2; rNsEucl=3; rSSD=9; rNSW=7; rank_mean=6.286; match_rank=3 a 0 0 28 37 10 78 0 18 7 10 22 24 c 0 0 21 18 10 1 0 12 79 34 28 27 g 0 0 20 17 46 16 0 20 6 28 25 22 t 0 0 31 28 34 5 100 50 8 28 25 27

KAN1_MA1027.1_JASPAR_shift1 (KAN1_MA1027.1_JASPAR) 0.878 0.479 3.573 0.479 0.902 0.691 0.942 6 16 11 12 7 2 4 8.286 4
; oligos_5-7nt_m2 versus KAN1_MA1027.1_JASPAR; m=3/14; ncol2=8; w=6; offset=-2; strand=D; shift=1; score= 8.2857; -arwtATtC--- ; cor=0.878; Ncor=0.479; logoDP=3.573; NIcor=0.479; NsEucl=0.902; SSD=0.691; NSW=0.942; rcor=6; rNcor=16; rlogoDP=11; rNIcor=12; rNsEucl=7; rSSD=2; rNSW=4; rank_mean=8.286; match_rank=4 a 0 433 259 618 128 898 54 36 63 0 0 0 c 0 129 213 16 192 14 87 147 876 0 0 0 g 0 237 285 43 58 68 19 169 18 0 0 0 t 0 200 242 323 623 20 840 648 44 0 0 0

LOC_Os02g22020_M1363_1.02_CISBP_shift2 (LOC_Os02g22020_M1363_1.02_CISBP) 0.757 0.681 3.368 0.672 0.900 1.614 0.910 17 5 13 3 9 14 12 10.429 7
; oligos_5-7nt_m2 versus LOC_Os02g22020_M1363_1.02_CISBP; m=4/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score=10.4286; --wagATtCysy ; cor=0.757; Ncor=0.681; logoDP=3.368; NIcor=0.672; NsEucl=0.900; SSD=1.614; NSW=0.910; rcor=17; rNcor=5; rlogoDP=13; rNIcor=3; rNsEucl=9; rSSD=14; rNSW=12; rank_mean=10.429; match_rank=7 a 0 0 26 46 5 86 7 20 3 15 22 22 c 0 0 23 13 6 2 3 21 89 38 29 29 g 0 0 24 19 66 7 2 11 2 21 27 23 t 0 0 27 22 23 5 88 48 6 26 22 26

KAN1_KAN1_ArabidopsisPBM_shift0 (KAN1_KAN1_ArabidopsisPBM) 0.846 0.493 3.756 0.485 0.895 1.087 0.922 7 14 10 11 17 7 10 10.857 8
; oligos_5-7nt_m2 versus KAN1_KAN1_ArabidopsisPBM; m=5/14; ncol2=10; w=7; offset=-3; strand=D; shift=0; score=10.8571; barwtATtCk-- ; cor=0.846; Ncor=0.493; logoDP=3.756; NIcor=0.485; NsEucl=0.895; SSD=1.087; NSW=0.922; rcor=7; rNcor=14; rlogoDP=10; rNIcor=11; rNsEucl=17; rSSD=7; rNSW=10; rank_mean=10.857; match_rank=8 a 15 43 26 62 13 90 5 3 6 5 0 0 c 27 13 21 2 19 1 9 15 88 20 0 0 g 33 24 29 4 6 7 2 17 2 47 0 0 t 25 20 24 32 62 2 84 65 4 28 0 0

AT1G25550_M1320_1.02_CISBP_shift2 (AT1G25550_M1320_1.02_CISBP) 0.756 0.681 5.282 0.669 0.899 1.665 0.908 18 6 4 4 13 19 16 11.429 10
; oligos_5-7nt_m2 versus AT1G25550_M1320_1.02_CISBP; m=6/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score=11.4286; --waGATtCysy ; cor=0.756; Ncor=0.681; logoDP=5.282; NIcor=0.669; NsEucl=0.899; SSD=1.665; NSW=0.908; rcor=18; rNcor=6; rlogoDP=4; rNIcor=4; rNsEucl=13; rSSD=19; rNSW=16; rank_mean=11.429; match_rank=10 a 0 0 30 64 3 95 3 18 0 12 24 21 c 0 0 20 7 2 1 0 14 98 40 28 28 g 0 0 24 14 75 4 0 6 0 20 26 20 t 0 0 26 15 20 0 97 62 2 28 22 31

AtPHR1_M1334_1.02_CISBP_shift2 (AtPHR1_M1334_1.02_CISBP) 0.754 0.679 4.575 0.666 0.900 1.630 0.909 21 8 6 6 10 16 13 11.429 11
; oligos_5-7nt_m2 versus AtPHR1_M1334_1.02_CISBP; m=7/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score=11.4286; --wakATkCbsy ; cor=0.754; Ncor=0.679; logoDP=4.575; NIcor=0.666; NsEucl=0.900; SSD=1.630; NSW=0.909; rcor=21; rNcor=8; rlogoDP=6; rNIcor=6; rNsEucl=10; rSSD=16; rNSW=13; rank_mean=11.429; match_rank=11 a 0 0 33 53 8 83 3 18 0 5 23 22 c 0 0 18 10 3 1 0 20 99 38 28 27 g 0 0 23 13 53 15 0 26 0 29 25 21 t 0 0 26 24 36 1 97 36 1 28 24 30

ATMYR1_M1341_1.02_CISBP_rc_shift3 (ATMYR1_M1341_1.02_CISBP_rc) 0.804 0.724 0.118 -0.162 0.908 1.361 0.924 11 3 21 21 5 11 9 11.571 12
; oligos_5-7nt_m2 versus ATMYR1_M1341_1.02_CISBP_rc; m=8/14; ncol2=10; w=9; offset=0; strand=R; shift=3; score=11.5714; ---akATtCsss ; cor=0.804; Ncor=0.724; logoDP=0.118; NIcor=-0.162; NsEucl=0.908; SSD=1.361; NSW=0.924; rcor=11; rNcor=3; rlogoDP=21; rNIcor=21; rNsEucl=5; rSSD=11; rNSW=9; rank_mean=11.571; match_rank=12 a 0 0 0 40 8 79 8 15 0 4 18 21 c 0 0 0 16 8 5 4 14 95 41 35 31 g 0 0 0 21 57 14 0 21 2 32 27 25 t 0 0 0 23 27 2 88 50 3 23 20 23

LOC_Os03g21240_M1364_1.02_CISBP_shift2 (LOC_Os03g21240_M1364_1.02_CISBP) 0.753 0.678 4.600 0.667 0.899 1.637 0.909 22 9 5 5 11 17 14 11.857 13
; oligos_5-7nt_m2 versus LOC_Os03g21240_M1364_1.02_CISBP; m=9/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score=11.8571; --wakATkCbyy ; cor=0.753; Ncor=0.678; logoDP=4.600; NIcor=0.667; NsEucl=0.899; SSD=1.637; NSW=0.909; rcor=22; rNcor=9; rlogoDP=5; rNIcor=5; rNsEucl=11; rSSD=17; rNSW=14; rank_mean=11.857; match_rank=13 a 0 0 37 56 9 87 4 19 0 5 24 23 c 0 0 16 9 3 0 0 17 98 39 26 26 g 0 0 21 11 53 11 0 25 0 26 24 19 t 0 0 26 24 35 2 96 39 2 30 26 32

PK14402.1_M1308_1.02_CISBP_shift1 (PK14402.1_M1308_1.02_CISBP) 0.769 0.629 7.297 0.618 0.896 1.762 0.902 15 10 2 8 16 20 17 12.571 15
; oligos_5-7nt_m2 versus PK14402.1_M1308_1.02_CISBP; m=10/14; ncol2=11; w=9; offset=-2; strand=D; shift=1; score=12.5714; -rtaGATTCsgy ; cor=0.769; Ncor=0.629; logoDP=7.297; NIcor=0.618; NsEucl=0.896; SSD=1.762; NSW=0.902; rcor=15; rNcor=10; rlogoDP=2; rNIcor=8; rNsEucl=16; rSSD=20; rNSW=17; rank_mean=12.571; match_rank=15 a 0 30 24 58 0 100 0 0 0 5 13 20 c 0 19 12 4 0 0 0 9 100 65 22 30 g 0 31 22 14 89 0 0 0 0 25 44 20 t 0 20 42 24 11 0 100 91 0 5 21 30

KAN4_MA1028.1_JASPAR_shift1 (KAN4_MA1028.1_JASPAR) 0.817 0.445 5.628 0.427 0.869 1.230 0.897 8 19 3 13 22 8 19 13.143 16
; oligos_5-7nt_m2 versus KAN4_MA1028.1_JASPAR; m=11/14; ncol2=8; w=6; offset=-2; strand=D; shift=1; score=13.1429; -GAATATTC--- ; cor=0.817; Ncor=0.445; logoDP=5.628; NIcor=0.427; NsEucl=0.869; SSD=1.230; NSW=0.897; rcor=8; rNcor=19; rlogoDP=3; rNIcor=13; rNsEucl=22; rSSD=8; rNSW=19; rank_mean=13.143; match_rank=16 a 0 11 941 905 2 893 92 21 14 0 0 0 c 0 10 12 2 102 3 2 26 965 0 0 0 g 0 965 26 2 3 102 2 12 10 0 0 0 t 0 14 21 92 893 2 905 941 11 0 0 0

PK19779.1_M1310_1.02_CISBP_shift2 (PK19779.1_M1310_1.02_CISBP) 0.756 0.681 3.020 0.656 0.899 1.663 0.908 19 7 15 7 12 18 15 13.286 17
; oligos_5-7nt_m2 versus PK19779.1_M1310_1.02_CISBP; m=12/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score=13.2857; --wwkATwCyvy ; cor=0.756; Ncor=0.681; logoDP=3.020; NIcor=0.656; NsEucl=0.899; SSD=1.663; NSW=0.908; rcor=19; rNcor=7; rlogoDP=15; rNIcor=7; rNsEucl=12; rSSD=18; rNSW=15; rank_mean=13.286; match_rank=17 a 0 0 26 37 11 72 0 25 11 20 25 24 c 0 0 24 18 9 4 0 21 74 30 27 28 g 0 0 24 20 54 14 0 15 7 23 26 22 t 0 0 26 25 26 10 100 39 8 27 22 26

AT1G68670_M1321_1.02_CISBP_rc_shift2 (AT1G68670_M1321_1.02_CISBP_rc) 0.768 0.691 0.251 -0.175 0.902 1.565 0.913 16 4 20 22 8 12 11 13.286 18
; oligos_5-7nt_m2 versus AT1G68670_M1321_1.02_CISBP_rc; m=13/14; ncol2=10; w=9; offset=-1; strand=R; shift=2; score=13.2857; --wagATtCymy ; cor=0.768; Ncor=0.691; logoDP=0.251; NIcor=-0.175; NsEucl=0.902; SSD=1.565; NSW=0.913; rcor=16; rNcor=4; rlogoDP=20; rNIcor=22; rNsEucl=8; rSSD=12; rNSW=11; rank_mean=13.286; match_rank=18 a 0 0 31 49 9 86 2 24 9 16 26 23 c 0 0 21 12 9 0 3 15 76 31 26 27 g 0 0 22 17 59 6 0 12 8 21 24 21 t 0 0 26 22 23 8 95 49 7 32 24 29

AT3G13040_M1326_1.02_CISBP_shift1 (AT3G13040_M1326_1.02_CISBP) 0.754 0.549 4.500 0.536 0.887 1.627 0.898 20 11 7 9 18 15 18 14.000 19
; oligos_5-7nt_m2 versus AT3G13040_M1326_1.02_CISBP; m=14/14; ncol2=10; w=8; offset=-2; strand=D; shift=1; score= 14; -dwakATtCbc- ; cor=0.754; Ncor=0.549; logoDP=4.500; NIcor=0.536; NsEucl=0.887; SSD=1.627; NSW=0.898; rcor=20; rNcor=11; rlogoDP=7; rNIcor=9; rNsEucl=18; rSSD=15; rNSW=18; rank_mean=14.000; match_rank=19 a 0 26 34 53 7 90 1 18 1 7 24 0 c 0 22 18 11 3 0 0 19 92 38 29 0 g 0 27 20 13 58 9 0 23 3 25 24 0 t 0 25 28 23 32 1 99 40 4 30 23 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=9; shift=3; ncol=12; ---hsATTCGdt ; Alignment reference a 0 0 0 26 23 100 0 0 0 0 28 23 c 0 0 0 27 29 0 0 0 100 0 21 23 g 0 0 0 16 27 0 0 0 0 100 26 23 t 0 0 0 31 21 0 100 100 0 0 25 31
AT3G04030_M1325_1.02_CISBP_shift3 (AT3G04030_M1325_1.02_CISBP)	0.804	0.804	3.925	0.784	0.908	1.358	0.925	10	1	9	1	4	10	8	6.143	2	; oligos_5-7nt_m2 versus AT3G04030_M1325_1.02_CISBP; m=1/14; ncol2=9; w=9; offset=0; strand=D; shift=3; score= 6.1429; ---wkATtCbsy ; cor=0.804; Ncor=0.804; logoDP=3.925; NIcor=0.784; NsEucl=0.908; SSD=1.358; NSW=0.925; rcor=10; rNcor=1; rlogoDP=9; rNIcor=1; rNsEucl=4; rSSD=10; rNSW=8; rank_mean=6.143; match_rank=2 a 0 0 0 38 10 79 0 17 3 8 21 22 c 0 0 0 19 8 2 0 12 88 36 31 27 g 0 0 0 18 55 15 0 22 4 28 25 23 t 0 0 0 25 27 4 100 49 5 28 23 28
AT3G24120_M1328_1.02_CISBP_shift2 (AT3G24120_M1328_1.02_CISBP)	0.814	0.733	3.524	0.714	0.909	1.334	0.926	9	2	12	2	3	9	7	6.286	3	; oligos_5-7nt_m2 versus AT3G24120_M1328_1.02_CISBP; m=2/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score= 6.2857; --wwkATtCbby ; cor=0.814; Ncor=0.733; logoDP=3.524; NIcor=0.714; NsEucl=0.909; SSD=1.334; NSW=0.926; rcor=9; rNcor=2; rlogoDP=12; rNIcor=2; rNsEucl=3; rSSD=9; rNSW=7; rank_mean=6.286; match_rank=3 a 0 0 28 37 10 78 0 18 7 10 22 24 c 0 0 21 18 10 1 0 12 79 34 28 27 g 0 0 20 17 46 16 0 20 6 28 25 22 t 0 0 31 28 34 5 100 50 8 28 25 27
KAN1_MA1027.1_JASPAR_shift1 (KAN1_MA1027.1_JASPAR)	0.878	0.479	3.573	0.479	0.902	0.691	0.942	6	16	11	12	7	2	4	8.286	4	; oligos_5-7nt_m2 versus KAN1_MA1027.1_JASPAR; m=3/14; ncol2=8; w=6; offset=-2; strand=D; shift=1; score= 8.2857; -arwtATtC--- ; cor=0.878; Ncor=0.479; logoDP=3.573; NIcor=0.479; NsEucl=0.902; SSD=0.691; NSW=0.942; rcor=6; rNcor=16; rlogoDP=11; rNIcor=12; rNsEucl=7; rSSD=2; rNSW=4; rank_mean=8.286; match_rank=4 a 0 433 259 618 128 898 54 36 63 0 0 0 c 0 129 213 16 192 14 87 147 876 0 0 0 g 0 237 285 43 58 68 19 169 18 0 0 0 t 0 200 242 323 623 20 840 648 44 0 0 0
LOC_Os02g22020_M1363_1.02_CISBP_shift2 (LOC_Os02g22020_M1363_1.02_CISBP)	0.757	0.681	3.368	0.672	0.900	1.614	0.910	17	5	13	3	9	14	12	10.429	7	; oligos_5-7nt_m2 versus LOC_Os02g22020_M1363_1.02_CISBP; m=4/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score=10.4286; --wagATtCysy ; cor=0.757; Ncor=0.681; logoDP=3.368; NIcor=0.672; NsEucl=0.900; SSD=1.614; NSW=0.910; rcor=17; rNcor=5; rlogoDP=13; rNIcor=3; rNsEucl=9; rSSD=14; rNSW=12; rank_mean=10.429; match_rank=7 a 0 0 26 46 5 86 7 20 3 15 22 22 c 0 0 23 13 6 2 3 21 89 38 29 29 g 0 0 24 19 66 7 2 11 2 21 27 23 t 0 0 27 22 23 5 88 48 6 26 22 26
KAN1_KAN1_ArabidopsisPBM_shift0 (KAN1_KAN1_ArabidopsisPBM)	0.846	0.493	3.756	0.485	0.895	1.087	0.922	7	14	10	11	17	7	10	10.857	8	; oligos_5-7nt_m2 versus KAN1_KAN1_ArabidopsisPBM; m=5/14; ncol2=10; w=7; offset=-3; strand=D; shift=0; score=10.8571; barwtATtCk-- ; cor=0.846; Ncor=0.493; logoDP=3.756; NIcor=0.485; NsEucl=0.895; SSD=1.087; NSW=0.922; rcor=7; rNcor=14; rlogoDP=10; rNIcor=11; rNsEucl=17; rSSD=7; rNSW=10; rank_mean=10.857; match_rank=8 a 15 43 26 62 13 90 5 3 6 5 0 0 c 27 13 21 2 19 1 9 15 88 20 0 0 g 33 24 29 4 6 7 2 17 2 47 0 0 t 25 20 24 32 62 2 84 65 4 28 0 0
AT1G25550_M1320_1.02_CISBP_shift2 (AT1G25550_M1320_1.02_CISBP)	0.756	0.681	5.282	0.669	0.899	1.665	0.908	18	6	4	4	13	19	16	11.429	10	; oligos_5-7nt_m2 versus AT1G25550_M1320_1.02_CISBP; m=6/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score=11.4286; --waGATtCysy ; cor=0.756; Ncor=0.681; logoDP=5.282; NIcor=0.669; NsEucl=0.899; SSD=1.665; NSW=0.908; rcor=18; rNcor=6; rlogoDP=4; rNIcor=4; rNsEucl=13; rSSD=19; rNSW=16; rank_mean=11.429; match_rank=10 a 0 0 30 64 3 95 3 18 0 12 24 21 c 0 0 20 7 2 1 0 14 98 40 28 28 g 0 0 24 14 75 4 0 6 0 20 26 20 t 0 0 26 15 20 0 97 62 2 28 22 31
AtPHR1_M1334_1.02_CISBP_shift2 (AtPHR1_M1334_1.02_CISBP)	0.754	0.679	4.575	0.666	0.900	1.630	0.909	21	8	6	6	10	16	13	11.429	11	; oligos_5-7nt_m2 versus AtPHR1_M1334_1.02_CISBP; m=7/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score=11.4286; --wakATkCbsy ; cor=0.754; Ncor=0.679; logoDP=4.575; NIcor=0.666; NsEucl=0.900; SSD=1.630; NSW=0.909; rcor=21; rNcor=8; rlogoDP=6; rNIcor=6; rNsEucl=10; rSSD=16; rNSW=13; rank_mean=11.429; match_rank=11 a 0 0 33 53 8 83 3 18 0 5 23 22 c 0 0 18 10 3 1 0 20 99 38 28 27 g 0 0 23 13 53 15 0 26 0 29 25 21 t 0 0 26 24 36 1 97 36 1 28 24 30
ATMYR1_M1341_1.02_CISBP_rc_shift3 (ATMYR1_M1341_1.02_CISBP_rc)	0.804	0.724	0.118	-0.162	0.908	1.361	0.924	11	3	21	21	5	11	9	11.571	12	; oligos_5-7nt_m2 versus ATMYR1_M1341_1.02_CISBP_rc; m=8/14; ncol2=10; w=9; offset=0; strand=R; shift=3; score=11.5714; ---akATtCsss ; cor=0.804; Ncor=0.724; logoDP=0.118; NIcor=-0.162; NsEucl=0.908; SSD=1.361; NSW=0.924; rcor=11; rNcor=3; rlogoDP=21; rNIcor=21; rNsEucl=5; rSSD=11; rNSW=9; rank_mean=11.571; match_rank=12 a 0 0 0 40 8 79 8 15 0 4 18 21 c 0 0 0 16 8 5 4 14 95 41 35 31 g 0 0 0 21 57 14 0 21 2 32 27 25 t 0 0 0 23 27 2 88 50 3 23 20 23
LOC_Os03g21240_M1364_1.02_CISBP_shift2 (LOC_Os03g21240_M1364_1.02_CISBP)	0.753	0.678	4.600	0.667	0.899	1.637	0.909	22	9	5	5	11	17	14	11.857	13	; oligos_5-7nt_m2 versus LOC_Os03g21240_M1364_1.02_CISBP; m=9/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score=11.8571; --wakATkCbyy ; cor=0.753; Ncor=0.678; logoDP=4.600; NIcor=0.667; NsEucl=0.899; SSD=1.637; NSW=0.909; rcor=22; rNcor=9; rlogoDP=5; rNIcor=5; rNsEucl=11; rSSD=17; rNSW=14; rank_mean=11.857; match_rank=13 a 0 0 37 56 9 87 4 19 0 5 24 23 c 0 0 16 9 3 0 0 17 98 39 26 26 g 0 0 21 11 53 11 0 25 0 26 24 19 t 0 0 26 24 35 2 96 39 2 30 26 32
PK14402.1_M1308_1.02_CISBP_shift1 (PK14402.1_M1308_1.02_CISBP)	0.769	0.629	7.297	0.618	0.896	1.762	0.902	15	10	2	8	16	20	17	12.571	15	; oligos_5-7nt_m2 versus PK14402.1_M1308_1.02_CISBP; m=10/14; ncol2=11; w=9; offset=-2; strand=D; shift=1; score=12.5714; -rtaGATTCsgy ; cor=0.769; Ncor=0.629; logoDP=7.297; NIcor=0.618; NsEucl=0.896; SSD=1.762; NSW=0.902; rcor=15; rNcor=10; rlogoDP=2; rNIcor=8; rNsEucl=16; rSSD=20; rNSW=17; rank_mean=12.571; match_rank=15 a 0 30 24 58 0 100 0 0 0 5 13 20 c 0 19 12 4 0 0 0 9 100 65 22 30 g 0 31 22 14 89 0 0 0 0 25 44 20 t 0 20 42 24 11 0 100 91 0 5 21 30
KAN4_MA1028.1_JASPAR_shift1 (KAN4_MA1028.1_JASPAR)	0.817	0.445	5.628	0.427	0.869	1.230	0.897	8	19	3	13	22	8	19	13.143	16	; oligos_5-7nt_m2 versus KAN4_MA1028.1_JASPAR; m=11/14; ncol2=8; w=6; offset=-2; strand=D; shift=1; score=13.1429; -GAATATTC--- ; cor=0.817; Ncor=0.445; logoDP=5.628; NIcor=0.427; NsEucl=0.869; SSD=1.230; NSW=0.897; rcor=8; rNcor=19; rlogoDP=3; rNIcor=13; rNsEucl=22; rSSD=8; rNSW=19; rank_mean=13.143; match_rank=16 a 0 11 941 905 2 893 92 21 14 0 0 0 c 0 10 12 2 102 3 2 26 965 0 0 0 g 0 965 26 2 3 102 2 12 10 0 0 0 t 0 14 21 92 893 2 905 941 11 0 0 0
PK19779.1_M1310_1.02_CISBP_shift2 (PK19779.1_M1310_1.02_CISBP)	0.756	0.681	3.020	0.656	0.899	1.663	0.908	19	7	15	7	12	18	15	13.286	17	; oligos_5-7nt_m2 versus PK19779.1_M1310_1.02_CISBP; m=12/14; ncol2=10; w=9; offset=-1; strand=D; shift=2; score=13.2857; --wwkATwCyvy ; cor=0.756; Ncor=0.681; logoDP=3.020; NIcor=0.656; NsEucl=0.899; SSD=1.663; NSW=0.908; rcor=19; rNcor=7; rlogoDP=15; rNIcor=7; rNsEucl=12; rSSD=18; rNSW=15; rank_mean=13.286; match_rank=17 a 0 0 26 37 11 72 0 25 11 20 25 24 c 0 0 24 18 9 4 0 21 74 30 27 28 g 0 0 24 20 54 14 0 15 7 23 26 22 t 0 0 26 25 26 10 100 39 8 27 22 26
AT1G68670_M1321_1.02_CISBP_rc_shift2 (AT1G68670_M1321_1.02_CISBP_rc)	0.768	0.691	0.251	-0.175	0.902	1.565	0.913	16	4	20	22	8	12	11	13.286	18	; oligos_5-7nt_m2 versus AT1G68670_M1321_1.02_CISBP_rc; m=13/14; ncol2=10; w=9; offset=-1; strand=R; shift=2; score=13.2857; --wagATtCymy ; cor=0.768; Ncor=0.691; logoDP=0.251; NIcor=-0.175; NsEucl=0.902; SSD=1.565; NSW=0.913; rcor=16; rNcor=4; rlogoDP=20; rNIcor=22; rNsEucl=8; rSSD=12; rNSW=11; rank_mean=13.286; match_rank=18 a 0 0 31 49 9 86 2 24 9 16 26 23 c 0 0 21 12 9 0 3 15 76 31 26 27 g 0 0 22 17 59 6 0 12 8 21 24 21 t 0 0 26 22 23 8 95 49 7 32 24 29
AT3G13040_M1326_1.02_CISBP_shift1 (AT3G13040_M1326_1.02_CISBP)	0.754	0.549	4.500	0.536	0.887	1.627	0.898	20	11	7	9	18	15	18	14.000	19	; oligos_5-7nt_m2 versus AT3G13040_M1326_1.02_CISBP; m=14/14; ncol2=10; w=8; offset=-2; strand=D; shift=1; score= 14; -dwakATtCbc- ; cor=0.754; Ncor=0.549; logoDP=4.500; NIcor=0.536; NsEucl=0.887; SSD=1.627; NSW=0.898; rcor=20; rNcor=11; rlogoDP=7; rNIcor=9; rNsEucl=18; rSSD=15; rNSW=18; rank_mean=14.000; match_rank=19 a 0 26 34 53 7 90 1 18 1 7 24 0 c 0 22 18 11 3 0 0 19 92 38 29 0 g 0 27 20 13 58 9 0 23 3 25 24 0 t 0 25 28 23 32 1 99 40 4 30 23 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m4_shift3 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_5-7nt_m4_shift3 (oligos_5-7nt_m4)
; oligos_5-7nt_m4; m=0 (reference); ncol1=9; shift=3; ncol=12; ---mdGCACAwk ; Alignment reference a 0 0 0 54 44 0 0 159 0 159 46 36 c 0 0 0 44 31 0 159 0 159 0 38 39 g 0 0 0 25 43 159 0 0 0 0 22 42 t 0 0 0 36 41 0 0 0 0 0 53 42

CONS_ARATH_CONS2_EEADannot_rc_shift0 (CONS_ARATH_CONS2_EEADannot_rc) 0.892 0.520 1.930 0.036 0.911 0.772 0.945 3 12 18 18 2 6 3 8.857 5
; oligos_5-7nt_m4 versus CONS_ARATH_CONS2_EEADannot_rc; m=1/3; ncol2=10; w=7; offset=-3; strand=R; shift=0; score= 8.8571; CATnnnCACA-- ; cor=0.892; Ncor=0.520; logoDP=1.930; NIcor=0.036; NsEucl=0.911; SSD=0.772; NSW=0.945; rcor=3; rNcor=12; rlogoDP=18; rNIcor=18; rNsEucl=2; rSSD=6; rNSW=3; rank_mean=8.857; match_rank=5 a 0.00 1.00 0.00 25 25 25 0.00 1.00 0.00 1.00 0 0 c 1.00 0.00 0.00 25 25 25 1.00 0.00 1.00 0.00 0 0 g 0.00 0.00 0.00 25 25 25 0.00 0.00 0.00 0.00 0 0 t 0.00 0.00 1.00 25 25 25 0.00 0.00 0.00 0.00 0 0

NAC_domain-containing_protein_19_3swm_B_3D-footprint_rc_shift2 (NAC_domain-containing_protein_19_3swm_B_3D-footprint_rc) 0.898 0.449 0.080 -0.107 0.903 0.468 0.953 2 17 22 20 6 1 1 9.857 6
; oligos_5-7nt_m4 versus NAC_domain-containing_protein_19_3swm_B_3D-footprint_rc; m=2/3; ncol2=6; w=5; offset=-1; strand=R; shift=2; score= 9.8571; --CAnGCA---- ; cor=0.898; Ncor=0.449; logoDP=0.080; NIcor=-0.107; NsEucl=0.903; SSD=0.468; NSW=0.953; rcor=2; rNcor=17; rlogoDP=22; rNIcor=20; rNsEucl=6; rSSD=1; rNSW=1; rank_mean=9.857; match_rank=6 a 0 0 0 73 24 7 7 73 0 0 0 0 c 0 0 96 7 24 7 73 7 0 0 0 0 g 0 0 0 9 24 75 9 7 0 0 0 0 t 0 0 0 7 24 7 7 9 0 0 0 0

CONS_ARATH_CONS1_EEADannot_rc_shift1 (CONS_ARATH_CONS1_EEADannot_rc) 0.791 0.504 1.937 0.016 0.873 1.569 0.888 14 13 17 19 21 13 20 16.714 20
; oligos_5-7nt_m4 versus CONS_ARATH_CONS1_EEADannot_rc; m=3/3; ncol2=9; w=7; offset=-2; strand=R; shift=1; score=16.7143; -CATnnCACA-- ; cor=0.791; Ncor=0.504; logoDP=1.937; NIcor=0.016; NsEucl=0.873; SSD=1.569; NSW=0.888; rcor=14; rNcor=13; rlogoDP=17; rNIcor=19; rNsEucl=21; rSSD=13; rNSW=20; rank_mean=16.714; match_rank=20 a 0 0.00 1.00 0.00 25 25 0.00 1.00 0.00 1.00 0 0 c 0 1.00 0.00 0.00 25 25 1.00 0.00 1.00 0.00 0 0 g 0 0.00 0.00 0.00 25 25 0.00 0.00 0.00 0.00 0 0 t 0 0.00 0.00 1.00 25 25 0.00 0.00 0.00 0.00 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_shift3 (oligos_5-7nt_m4)																	; oligos_5-7nt_m4; m=0 (reference); ncol1=9; shift=3; ncol=12; ---mdGCACAwk ; Alignment reference a 0 0 0 54 44 0 0 159 0 159 46 36 c 0 0 0 44 31 0 159 0 159 0 38 39 g 0 0 0 25 43 159 0 0 0 0 22 42 t 0 0 0 36 41 0 0 0 0 0 53 42
CONS_ARATH_CONS2_EEADannot_rc_shift0 (CONS_ARATH_CONS2_EEADannot_rc)	0.892	0.520	1.930	0.036	0.911	0.772	0.945	3	12	18	18	2	6	3	8.857	5	; oligos_5-7nt_m4 versus CONS_ARATH_CONS2_EEADannot_rc; m=1/3; ncol2=10; w=7; offset=-3; strand=R; shift=0; score= 8.8571; CATnnnCACA-- ; cor=0.892; Ncor=0.520; logoDP=1.930; NIcor=0.036; NsEucl=0.911; SSD=0.772; NSW=0.945; rcor=3; rNcor=12; rlogoDP=18; rNIcor=18; rNsEucl=2; rSSD=6; rNSW=3; rank_mean=8.857; match_rank=5 a 0.00 1.00 0.00 25 25 25 0.00 1.00 0.00 1.00 0 0 c 1.00 0.00 0.00 25 25 25 1.00 0.00 1.00 0.00 0 0 g 0.00 0.00 0.00 25 25 25 0.00 0.00 0.00 0.00 0 0 t 0.00 0.00 1.00 25 25 25 0.00 0.00 0.00 0.00 0 0
NAC_domain-containing_protein_19_3swm_B_3D-footprint_rc_shift2 (NAC_domain-containing_protein_19_3swm_B_3D-footprint_rc)	0.898	0.449	0.080	-0.107	0.903	0.468	0.953	2	17	22	20	6	1	1	9.857	6	; oligos_5-7nt_m4 versus NAC_domain-containing_protein_19_3swm_B_3D-footprint_rc; m=2/3; ncol2=6; w=5; offset=-1; strand=R; shift=2; score= 9.8571; --CAnGCA---- ; cor=0.898; Ncor=0.449; logoDP=0.080; NIcor=-0.107; NsEucl=0.903; SSD=0.468; NSW=0.953; rcor=2; rNcor=17; rlogoDP=22; rNIcor=20; rNsEucl=6; rSSD=1; rNSW=1; rank_mean=9.857; match_rank=6 a 0 0 0 73 24 7 7 73 0 0 0 0 c 0 0 96 7 24 7 73 7 0 0 0 0 g 0 0 0 9 24 75 9 7 0 0 0 0 t 0 0 0 7 24 7 7 9 0 0 0 0
CONS_ARATH_CONS1_EEADannot_rc_shift1 (CONS_ARATH_CONS1_EEADannot_rc)	0.791	0.504	1.937	0.016	0.873	1.569	0.888	14	13	17	19	21	13	20	16.714	20	; oligos_5-7nt_m4 versus CONS_ARATH_CONS1_EEADannot_rc; m=3/3; ncol2=9; w=7; offset=-2; strand=R; shift=1; score=16.7143; -CATnnCACA-- ; cor=0.791; Ncor=0.504; logoDP=1.937; NIcor=0.016; NsEucl=0.873; SSD=1.569; NSW=0.888; rcor=14; rNcor=13; rlogoDP=17; rNIcor=19; rNsEucl=21; rSSD=13; rNSW=20; rank_mean=16.714; match_rank=20 a 0 0.00 1.00 0.00 25 25 0.00 1.00 0.00 1.00 0 0 c 0 1.00 0.00 0.00 25 25 1.00 0.00 1.00 0.00 0 0 g 0 0.00 0.00 0.00 25 25 0.00 0.00 0.00 0.00 0 0 t 0 0.00 0.00 1.00 25 25 0.00 0.00 0.00 0.00 0 0

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift6 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_test_vs_ctrl_m1_shift6 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=10; shift=6; ncol=16; ------wyGTTTTAwr ; Alignment reference a 0 0 0 0 0 0 22 10 0 0 0 0 0 65 17 20 c 0 0 0 0 0 0 10 17 0 0 0 0 0 0 12 16 g 0 0 0 0 0 0 10 16 65 0 0 0 0 0 15 21 t 0 0 0 0 0 0 23 22 0 65 65 65 65 0 21 8

TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc_shift10 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc) 0.887 0.443 2.596 0.139 0.899 0.742 0.938 4 20 16 14 14 3 5 10.857 9
; dyads_test_vs_ctrl_m1 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc; m=1/2; ncol2=8; w=6; offset=4; strand=R; shift=10; score=10.8571; ----------TTTAAA ; cor=0.887; Ncor=0.443; logoDP=2.596; NIcor=0.139; NsEucl=0.899; SSD=0.742; NSW=0.938; rcor=4; rNcor=20; rlogoDP=16; rNIcor=14; rNsEucl=14; rSSD=3; rNSW=5; rank_mean=10.857; match_rank=9 a 0 0 0 0 0 0 0 0 0 0 0 0 9 96 78 72 c 0 0 0 0 0 0 0 0 0 0 8 0 0 0 8 8 g 0 0 0 0 0 0 0 0 0 0 1 0 0 0 8 8 t 0 0 0 0 0 0 0 0 0 0 87 96 87 0 2 8

SR1_SR1_Athamap_rc_shift0 (SR1_SR1_Athamap_rc) 0.801 0.400 3.965 0.053 0.874 2.044 0.872 12 22 8 17 20 21 21 17.286 21
; dyads_test_vs_ctrl_m1 versus SR1_SR1_Athamap_rc; m=2/2; ncol2=14; w=8; offset=-6; strand=R; shift=0; score=17.2857; TGTTsCGCGkTTTA-- ; cor=0.801; Ncor=0.400; logoDP=3.965; NIcor=0.053; NsEucl=0.874; SSD=2.044; NSW=0.872; rcor=12; rNcor=22; rlogoDP=8; rNIcor=17; rNsEucl=20; rSSD=21; rNSW=21; rank_mean=17.286; match_rank=21 a 0 0 0 0 1 0 0 0 0 0 0 0 0 5 0 0 c 0 0 0 0 2 5 0 5 0 0 0 0 0 0 0 0 g 0 5 0 0 2 0 5 0 5 2 0 0 0 0 0 0 t 5 0 5 5 0 0 0 0 0 3 5 5 5 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_shift6 (dyads_test_vs_ctrl_m1)																	; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=10; shift=6; ncol=16; ------wyGTTTTAwr ; Alignment reference a 0 0 0 0 0 0 22 10 0 0 0 0 0 65 17 20 c 0 0 0 0 0 0 10 17 0 0 0 0 0 0 12 16 g 0 0 0 0 0 0 10 16 65 0 0 0 0 0 15 21 t 0 0 0 0 0 0 23 22 0 65 65 65 65 0 21 8
TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc_shift10 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc)	0.887	0.443	2.596	0.139	0.899	0.742	0.938	4	20	16	14	14	3	5	10.857	9	; dyads_test_vs_ctrl_m1 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc; m=1/2; ncol2=8; w=6; offset=4; strand=R; shift=10; score=10.8571; ----------TTTAAA ; cor=0.887; Ncor=0.443; logoDP=2.596; NIcor=0.139; NsEucl=0.899; SSD=0.742; NSW=0.938; rcor=4; rNcor=20; rlogoDP=16; rNIcor=14; rNsEucl=14; rSSD=3; rNSW=5; rank_mean=10.857; match_rank=9 a 0 0 0 0 0 0 0 0 0 0 0 0 9 96 78 72 c 0 0 0 0 0 0 0 0 0 0 8 0 0 0 8 8 g 0 0 0 0 0 0 0 0 0 0 1 0 0 0 8 8 t 0 0 0 0 0 0 0 0 0 0 87 96 87 0 2 8
SR1_SR1_Athamap_rc_shift0 (SR1_SR1_Athamap_rc)	0.801	0.400	3.965	0.053	0.874	2.044	0.872	12	22	8	17	20	21	21	17.286	21	; dyads_test_vs_ctrl_m1 versus SR1_SR1_Athamap_rc; m=2/2; ncol2=14; w=8; offset=-6; strand=R; shift=0; score=17.2857; TGTTsCGCGkTTTA-- ; cor=0.801; Ncor=0.400; logoDP=3.965; NIcor=0.053; NsEucl=0.874; SSD=2.044; NSW=0.872; rcor=12; rNcor=22; rlogoDP=8; rNIcor=17; rNsEucl=20; rSSD=21; rNSW=21; rank_mean=17.286; match_rank=21 a 0 0 0 0 1 0 0 0 0 0 0 0 0 5 0 0 c 0 0 0 0 2 5 0 5 0 0 0 0 0 0 0 0 g 0 5 0 0 2 0 5 0 5 2 0 0 0 0 0 0 t 5 0 5 5 0 0 0 0 0 3 5 5 5 0 0 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m1_shift5 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_5-7nt_m1_shift5 (oligos_5-7nt_m1)
; oligos_5-7nt_m1; m=0 (reference); ncol1=11; shift=5; ncol=16; -----wwcGTTTTAtr ; Alignment reference a 0 0 0 0 0 39 42 10 2 5 2 1 2 123 32 40 c 0 0 0 0 0 21 24 85 5 2 9 7 4 7 28 32 g 0 0 0 0 0 27 26 16 121 4 2 5 3 2 29 34 t 0 0 0 0 0 46 41 22 5 122 120 120 124 1 44 27

TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc_shift10 (TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc) 0.883 0.408 1.732 0.135 0.897 0.759 0.937 5 21 19 15 15 5 6 12.286 14
; oligos_5-7nt_m1 versus TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint_rc; m=1/2; ncol2=8; w=6; offset=5; strand=R; shift=10; score=12.2857; ----------TTTAAA ; cor=0.883; Ncor=0.408; logoDP=1.732; NIcor=0.135; NsEucl=0.897; SSD=0.759; NSW=0.937; rcor=5; rNcor=21; rlogoDP=19; rNIcor=15; rNsEucl=15; rSSD=5; rNSW=6; rank_mean=12.286; match_rank=14 a 0 0 0 0 0 0 0 0 0 0 0 0 9 96 78 72 c 0 0 0 0 0 0 0 0 0 0 8 0 0 0 8 8 g 0 0 0 0 0 0 0 0 0 0 1 0 0 0 8 8 t 0 0 0 0 0 0 0 0 0 0 87 96 87 0 2 8

SR1_SR1_Athamap_rc_shift0 (SR1_SR1_Athamap_rc) 0.796 0.448 3.081 0.097 0.881 2.302 0.872 13 18 14 16 19 22 22 17.714 22
; oligos_5-7nt_m1 versus SR1_SR1_Athamap_rc; m=2/2; ncol2=14; w=9; offset=-5; strand=R; shift=0; score=17.7143; TGTTsCGCGkTTTA-- ; cor=0.796; Ncor=0.448; logoDP=3.081; NIcor=0.097; NsEucl=0.881; SSD=2.302; NSW=0.872; rcor=13; rNcor=18; rlogoDP=14; rNIcor=16; rNsEucl=19; rSSD=22; rNSW=22; rank_mean=17.714; match_rank=22 a 0 0 0 0 1 0 0 0 0 0 0 0 0 5 0 0 c 0 0 0 0 2 5 0 5 0 0 0 0 0 0 0 0 g 0 5 0 0 2 0 5 0 5 2 0 0 0 0 0 0 t 5 0 5 5 0 0 0 0 0 3 5 5 5 0 0 0