One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 3/regulon3.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 3/regulon3.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_shift0 ; 8 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_5-7nt_m1_shift0 (oligos_5-7nt_m1)
; oligos_5-7nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=14; rwACGAAAGCdw-- ; Alignment reference a 18 18 40 2 1 46 50 52 1 8 13 15 0 0 c 10 10 5 44 0 2 1 0 1 38 10 11 0 0 g 17 11 5 3 50 0 1 0 49 3 14 10 0 0 t 7 13 2 3 1 4 0 0 1 3 15 16 0 0

Dof2_MA0020.1_JASPAR_shift5 (Dof2_MA0020.1_JASPAR) 0.990 0.495 6.238 0.495 0.969 0.069 0.994 1 5 2 4 1 1 1 2.143 1
; oligos_5-7nt_m1 versus Dof2_MA0020.1_JASPAR; m=1/7; ncol2=6; w=6; offset=5; strand=D; shift=5; score= 2.1429; -----AAAGcm--- ; cor=0.990; Ncor=0.495; logoDP=6.238; NIcor=0.495; NsEucl=0.969; SSD=0.069; NSW=0.994; rcor=1; rNcor=5; rlogoDP=2; rNIcor=4; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.143; match_rank=1 a 0 0 0 0 0 21 21 21 0 3 7 0 0 0 c 0 0 0 0 0 0 0 0 0 14 6 0 0 0 g 0 0 0 0 0 0 0 0 21 2 3 0 0 0 t 0 0 0 0 0 0 0 0 0 2 5 0 0 0

MNB1A_MA0053.1_JASPAR_shift5 (MNB1A_MA0053.1_JASPAR) 0.989 0.412 6.241 0.411 0.963 0.070 0.993 2 12 1 7 2 2 2 4.000 2
; oligos_5-7nt_m1 versus MNB1A_MA0053.1_JASPAR; m=2/7; ncol2=5; w=5; offset=5; strand=D; shift=5; score= 4; -----AAAGc---- ; cor=0.989; Ncor=0.412; logoDP=6.241; NIcor=0.411; NsEucl=0.963; SSD=0.070; NSW=0.993; rcor=2; rNcor=12; rlogoDP=1; rNIcor=7; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=4.000; match_rank=2 a 0 0 0 0 0 15 15 15 0 3 0 0 0 0 c 0 0 0 0 0 0 0 0 0 9 0 0 0 0 g 0 0 0 0 0 0 0 0 15 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 3 0 0 0 0

Dof3_MA0021.1_JASPAR_shift5 (Dof3_MA0021.1_JASPAR) 0.945 0.473 6.208 0.483 0.931 0.346 0.971 4 6 5 5 4 4 4 4.571 3
; oligos_5-7nt_m1 versus Dof3_MA0021.1_JASPAR; m=3/7; ncol2=6; w=6; offset=5; strand=D; shift=5; score= 4.5714; -----AAAGyv--- ; cor=0.945; Ncor=0.473; logoDP=6.208; NIcor=0.483; NsEucl=0.931; SSD=0.346; NSW=0.971; rcor=4; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.571; match_rank=3 a 0 0 0 0 0 21 21 21 0 0 6 0 0 0 c 0 0 0 0 0 0 0 0 0 10 6 0 0 0 g 0 0 0 0 0 0 0 0 21 3 9 0 0 0 t 0 0 0 0 0 0 0 0 0 8 0 0 0 0

PBF_MA0064.1_JASPAR_shift5 (PBF_MA0064.1_JASPAR) 0.980 0.408 6.213 0.409 0.949 0.129 0.987 3 14 4 8 3 3 3 5.429 5
; oligos_5-7nt_m1 versus PBF_MA0064.1_JASPAR; m=4/7; ncol2=5; w=5; offset=5; strand=D; shift=5; score= 5.4286; -----AAAGy---- ; cor=0.980; Ncor=0.408; logoDP=6.213; NIcor=0.409; NsEucl=0.949; SSD=0.129; NSW=0.987; rcor=3; rNcor=14; rlogoDP=4; rNIcor=8; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=5.429; match_rank=5 a 0 0 0 0 0 16 16 16 0 1 0 0 0 0 c 0 0 0 0 0 0 0 0 0 9 0 0 0 0 g 0 0 0 0 0 0 0 0 16 1 0 0 0 0 t 0 0 0 0 0 0 0 0 0 5 0 0 0 0

Dof3_M00354_TRANSFAC_shift1 (Dof3_M00354_TRANSFAC) 0.779 0.714 6.222 0.710 0.914 1.791 0.919 12 2 3 2 6 13 8 6.571 7
; oligos_5-7nt_m1 versus Dof3_M00354_TRANSFAC; m=5/7; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 6.5714; -gmswAAAGcvm-- ; cor=0.779; Ncor=0.714; logoDP=6.222; NIcor=0.710; NsEucl=0.914; SSD=1.791; NSW=0.919; rcor=12; rNcor=2; rlogoDP=3; rNIcor=2; rNsEucl=6; rSSD=13; rNSW=8; rank_mean=6.571; match_rank=7 a 0 5 10 5 8 21 21 21 0 3 6 8 0 0 c 0 3 6 6 3 0 0 0 0 10 6 6 0 0 g 0 10 3 6 3 0 0 0 21 3 7 4 0 0 t 0 3 2 4 7 0 0 0 0 5 2 3 0 0

CBNAC_M01188_TRANSFAC_rc_shift6 (CBNAC_M01188_TRANSFAC_rc) 0.939 0.469 2.087 0.153 0.924 0.421 0.965 5 7 10 10 5 5 5 6.714 8
; oligos_5-7nt_m1 versus CBNAC_M01188_TRANSFAC_rc; m=6/7; ncol2=6; w=6; offset=6; strand=R; shift=6; score= 6.7143; ------AAGCaa-- ; cor=0.939; Ncor=0.469; logoDP=2.087; NIcor=0.153; NsEucl=0.924; SSD=0.421; NSW=0.965; rcor=5; rNcor=7; rlogoDP=10; rNIcor=10; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=6.714; match_rank=8 a 0 0 0 0 0 0 44 44 0 0 22 23 0 0 c 0 0 0 0 0 0 0 0 0 44 5 9 0 0 g 0 0 0 0 0 0 0 0 44 0 4 5 0 0 t 0 0 0 0 0 0 0 0 0 0 9 1 0 0

SED_M01128_TRANSFAC_rc_shift4 (SED_M01128_TRANSFAC_rc) 0.807 0.461 0.884 0.037 0.898 1.339 0.916 7 10 11 11 9 9 9 9.429 9
; oligos_5-7nt_m1 versus SED_M01128_TRANSFAC_rc; m=7/7; ncol2=10; w=8; offset=4; strand=R; shift=4; score= 9.4286; ----dAAAGbddrb ; cor=0.807; Ncor=0.461; logoDP=0.884; NIcor=0.037; NsEucl=0.898; SSD=1.339; NSW=0.916; rcor=7; rNcor=10; rlogoDP=11; rNIcor=11; rNsEucl=9; rSSD=9; rNSW=9; rank_mean=9.429; match_rank=9 a 0 0 0 0 4 8 8 8 0 0 2 2 5 0 c 0 0 0 0 0 0 0 0 0 2 1 1 0 3 g 0 0 0 0 2 0 0 0 8 4 3 2 3 2 t 0 0 0 0 2 0 0 0 0 2 2 3 0 3

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-7nt_m1_shift0 (oligos_5-7nt_m1)																	; oligos_5-7nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=14; rwACGAAAGCdw-- ; Alignment reference a 18 18 40 2 1 46 50 52 1 8 13 15 0 0 c 10 10 5 44 0 2 1 0 1 38 10 11 0 0 g 17 11 5 3 50 0 1 0 49 3 14 10 0 0 t 7 13 2 3 1 4 0 0 1 3 15 16 0 0
Dof2_MA0020.1_JASPAR_shift5 (Dof2_MA0020.1_JASPAR)	0.990	0.495	6.238	0.495	0.969	0.069	0.994	1	5	2	4	1	1	1	2.143	1	; oligos_5-7nt_m1 versus Dof2_MA0020.1_JASPAR; m=1/7; ncol2=6; w=6; offset=5; strand=D; shift=5; score= 2.1429; -----AAAGcm--- ; cor=0.990; Ncor=0.495; logoDP=6.238; NIcor=0.495; NsEucl=0.969; SSD=0.069; NSW=0.994; rcor=1; rNcor=5; rlogoDP=2; rNIcor=4; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.143; match_rank=1 a 0 0 0 0 0 21 21 21 0 3 7 0 0 0 c 0 0 0 0 0 0 0 0 0 14 6 0 0 0 g 0 0 0 0 0 0 0 0 21 2 3 0 0 0 t 0 0 0 0 0 0 0 0 0 2 5 0 0 0
MNB1A_MA0053.1_JASPAR_shift5 (MNB1A_MA0053.1_JASPAR)	0.989	0.412	6.241	0.411	0.963	0.070	0.993	2	12	1	7	2	2	2	4.000	2	; oligos_5-7nt_m1 versus MNB1A_MA0053.1_JASPAR; m=2/7; ncol2=5; w=5; offset=5; strand=D; shift=5; score= 4; -----AAAGc---- ; cor=0.989; Ncor=0.412; logoDP=6.241; NIcor=0.411; NsEucl=0.963; SSD=0.070; NSW=0.993; rcor=2; rNcor=12; rlogoDP=1; rNIcor=7; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=4.000; match_rank=2 a 0 0 0 0 0 15 15 15 0 3 0 0 0 0 c 0 0 0 0 0 0 0 0 0 9 0 0 0 0 g 0 0 0 0 0 0 0 0 15 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 3 0 0 0 0
Dof3_MA0021.1_JASPAR_shift5 (Dof3_MA0021.1_JASPAR)	0.945	0.473	6.208	0.483	0.931	0.346	0.971	4	6	5	5	4	4	4	4.571	3	; oligos_5-7nt_m1 versus Dof3_MA0021.1_JASPAR; m=3/7; ncol2=6; w=6; offset=5; strand=D; shift=5; score= 4.5714; -----AAAGyv--- ; cor=0.945; Ncor=0.473; logoDP=6.208; NIcor=0.483; NsEucl=0.931; SSD=0.346; NSW=0.971; rcor=4; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.571; match_rank=3 a 0 0 0 0 0 21 21 21 0 0 6 0 0 0 c 0 0 0 0 0 0 0 0 0 10 6 0 0 0 g 0 0 0 0 0 0 0 0 21 3 9 0 0 0 t 0 0 0 0 0 0 0 0 0 8 0 0 0 0
PBF_MA0064.1_JASPAR_shift5 (PBF_MA0064.1_JASPAR)	0.980	0.408	6.213	0.409	0.949	0.129	0.987	3	14	4	8	3	3	3	5.429	5	; oligos_5-7nt_m1 versus PBF_MA0064.1_JASPAR; m=4/7; ncol2=5; w=5; offset=5; strand=D; shift=5; score= 5.4286; -----AAAGy---- ; cor=0.980; Ncor=0.408; logoDP=6.213; NIcor=0.409; NsEucl=0.949; SSD=0.129; NSW=0.987; rcor=3; rNcor=14; rlogoDP=4; rNIcor=8; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=5.429; match_rank=5 a 0 0 0 0 0 16 16 16 0 1 0 0 0 0 c 0 0 0 0 0 0 0 0 0 9 0 0 0 0 g 0 0 0 0 0 0 0 0 16 1 0 0 0 0 t 0 0 0 0 0 0 0 0 0 5 0 0 0 0
Dof3_M00354_TRANSFAC_shift1 (Dof3_M00354_TRANSFAC)	0.779	0.714	6.222	0.710	0.914	1.791	0.919	12	2	3	2	6	13	8	6.571	7	; oligos_5-7nt_m1 versus Dof3_M00354_TRANSFAC; m=5/7; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 6.5714; -gmswAAAGcvm-- ; cor=0.779; Ncor=0.714; logoDP=6.222; NIcor=0.710; NsEucl=0.914; SSD=1.791; NSW=0.919; rcor=12; rNcor=2; rlogoDP=3; rNIcor=2; rNsEucl=6; rSSD=13; rNSW=8; rank_mean=6.571; match_rank=7 a 0 5 10 5 8 21 21 21 0 3 6 8 0 0 c 0 3 6 6 3 0 0 0 0 10 6 6 0 0 g 0 10 3 6 3 0 0 0 21 3 7 4 0 0 t 0 3 2 4 7 0 0 0 0 5 2 3 0 0
CBNAC_M01188_TRANSFAC_rc_shift6 (CBNAC_M01188_TRANSFAC_rc)	0.939	0.469	2.087	0.153	0.924	0.421	0.965	5	7	10	10	5	5	5	6.714	8	; oligos_5-7nt_m1 versus CBNAC_M01188_TRANSFAC_rc; m=6/7; ncol2=6; w=6; offset=6; strand=R; shift=6; score= 6.7143; ------AAGCaa-- ; cor=0.939; Ncor=0.469; logoDP=2.087; NIcor=0.153; NsEucl=0.924; SSD=0.421; NSW=0.965; rcor=5; rNcor=7; rlogoDP=10; rNIcor=10; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=6.714; match_rank=8 a 0 0 0 0 0 0 44 44 0 0 22 23 0 0 c 0 0 0 0 0 0 0 0 0 44 5 9 0 0 g 0 0 0 0 0 0 0 0 44 0 4 5 0 0 t 0 0 0 0 0 0 0 0 0 0 9 1 0 0
SED_M01128_TRANSFAC_rc_shift4 (SED_M01128_TRANSFAC_rc)	0.807	0.461	0.884	0.037	0.898	1.339	0.916	7	10	11	11	9	9	9	9.429	9	; oligos_5-7nt_m1 versus SED_M01128_TRANSFAC_rc; m=7/7; ncol2=10; w=8; offset=4; strand=R; shift=4; score= 9.4286; ----dAAAGbddrb ; cor=0.807; Ncor=0.461; logoDP=0.884; NIcor=0.037; NsEucl=0.898; SSD=1.339; NSW=0.916; rcor=7; rNcor=10; rlogoDP=11; rNIcor=11; rNsEucl=9; rSSD=9; rNSW=9; rank_mean=9.429; match_rank=9 a 0 0 0 0 4 8 8 8 0 0 2 2 5 0 c 0 0 0 0 0 0 0 0 0 2 1 1 0 3 g 0 0 0 0 2 0 0 0 8 4 3 2 3 2 t 0 0 0 0 2 0 0 0 0 2 2 3 0 3

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m2_shift1 ; 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
oligos_5-7nt_m2_shift1 (oligos_5-7nt_m2)
; oligos_5-7nt_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -ywAGCTAGGhd ; Alignment reference a 0 39 46 161 5 5 9 152 7 12 50 52 c 0 53 36 2 2 164 8 9 3 27 46 29 g 0 36 33 11 168 6 9 6 162 130 35 46 t 0 50 63 4 3 3 152 11 6 9 47 51

STY1_STY1_2_ArabidopsisPBM_rc_shift0 (STY1_STY1_2_ArabidopsisPBM_rc) 0.854 0.640 5.111 0.614 0.910 1.309 0.927 6 3 6 3 7 7 6 5.429 4
; oligos_5-7nt_m2 versus STY1_STY1_2_ArabidopsisPBM_rc; m=1/5; ncol2=10; w=9; offset=-1; strand=R; shift=0; score= 5.4286; rCTAGCTAGt-- ; cor=0.854; Ncor=0.640; logoDP=5.111; NIcor=0.614; NsEucl=0.910; SSD=1.309; NSW=0.927; rcor=6; rNcor=3; rlogoDP=6; rNIcor=3; rNsEucl=7; rSSD=7; rNSW=6; rank_mean=5.429; match_rank=4 a 31 3 5 92 2 2 6 92 3 16 0 0 c 8 89 1 0 1 95 3 2 5 20 0 0 g 50 5 2 3 95 1 0 1 89 23 0 0 t 11 3 92 5 2 2 91 5 3 41 0 0

ATTRB2_M1346_1.02_CISBP_rc_shift5 (ATTRB2_M1346_1.02_CISBP_rc) 0.799 0.466 0.423 -0.128 0.885 1.303 0.907 9 8 13 12 10 6 10 9.714 10
; oligos_5-7nt_m2 versus ATTRB2_M1346_1.02_CISBP_rc; m=2/5; ncol2=8; w=7; offset=4; strand=R; shift=5; score= 9.7143; -----yTAGGky ; cor=0.799; Ncor=0.466; logoDP=0.423; NIcor=-0.128; NsEucl=0.885; SSD=1.303; NSW=0.907; rcor=9; rNcor=8; rlogoDP=13; rNIcor=12; rNsEucl=10; rSSD=6; rNSW=10; rank_mean=9.714; match_rank=10 a 0 0 0 0 0 8 1 99 0 0 0 4 c 0 0 0 0 0 40 1 0 0 0 0 61 g 0 0 0 0 0 7 0 1 100 100 63 0 t 0 0 0 0 0 45 98 0 0 0 37 35

TRB2_MA1073.1_JASPAR_rc_shift5 (TRB2_MA1073.1_JASPAR_rc) 0.799 0.466 0.424 -0.128 0.884 1.309 0.906 10 9 12 13 11 8 11 10.571 11
; oligos_5-7nt_m2 versus TRB2_MA1073.1_JASPAR_rc; m=3/5; ncol2=8; w=7; offset=4; strand=R; shift=5; score=10.5714; -----yTAGGky ; cor=0.799; Ncor=0.466; logoDP=0.424; NIcor=-0.128; NsEucl=0.884; SSD=1.309; NSW=0.906; rcor=10; rNcor=9; rlogoDP=12; rNIcor=13; rNsEucl=11; rSSD=8; rNSW=11; rank_mean=10.571; match_rank=11 a 0 0 0 0 0 74 13 994 0 0 0 40 c 0 0 0 0 0 398 7 0 0 0 0 611 g 0 0 0 0 0 74 0 6 1000 1000 628 0 t 0 0 0 0 0 454 980 0 0 0 372 349

PK06103.1_M1304_1.02_CISBP_shift5 (PK06103.1_M1304_1.02_CISBP) 0.771 0.450 4.399 0.439 0.857 2.017 0.856 13 11 7 6 13 14 14 11.143 12
; oligos_5-7nt_m2 versus PK06103.1_M1304_1.02_CISBP; m=4/5; ncol2=8; w=7; offset=4; strand=D; shift=5; score=11.1429; -----CTAGGGC ; cor=0.771; Ncor=0.450; logoDP=4.399; NIcor=0.439; NsEucl=0.857; SSD=2.017; NSW=0.856; rcor=13; rNcor=11; rlogoDP=7; rNIcor=6; rNsEucl=13; rSSD=14; rNSW=14; rank_mean=11.143; match_rank=12 a 0 0 0 0 0 0 0 100 0 0 0 0 c 0 0 0 0 0 80 0 0 0 0 0 100 g 0 0 0 0 0 0 0 0 100 100 100 0 t 0 0 0 0 0 20 100 0 0 0 0 0

CBNAC_M01188_TRANSFAC_rc_shift2 (CBNAC_M01188_TRANSFAC_rc) 0.752 0.410 3.851 0.315 0.854 1.538 0.872 14 13 8 9 14 11 13 11.714 14
; oligos_5-7nt_m2 versus CBNAC_M01188_TRANSFAC_rc; m=5/5; ncol2=6; w=6; offset=1; strand=R; shift=2; score=11.7143; --AAGCaa---- ; cor=0.752; Ncor=0.410; logoDP=3.851; NIcor=0.315; NsEucl=0.854; SSD=1.538; NSW=0.872; rcor=14; rNcor=13; rlogoDP=8; rNIcor=9; rNsEucl=14; rSSD=11; rNSW=13; rank_mean=11.714; match_rank=14 a 0 0 44 44 0 0 22 23 0 0 0 0 c 0 0 0 0 0 44 5 9 0 0 0 0 g 0 0 0 0 44 0 4 5 0 0 0 0 t 0 0 0 0 0 0 9 1 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_shift1 (oligos_5-7nt_m2)																	; oligos_5-7nt_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -ywAGCTAGGhd ; Alignment reference a 0 39 46 161 5 5 9 152 7 12 50 52 c 0 53 36 2 2 164 8 9 3 27 46 29 g 0 36 33 11 168 6 9 6 162 130 35 46 t 0 50 63 4 3 3 152 11 6 9 47 51
STY1_STY1_2_ArabidopsisPBM_rc_shift0 (STY1_STY1_2_ArabidopsisPBM_rc)	0.854	0.640	5.111	0.614	0.910	1.309	0.927	6	3	6	3	7	7	6	5.429	4	; oligos_5-7nt_m2 versus STY1_STY1_2_ArabidopsisPBM_rc; m=1/5; ncol2=10; w=9; offset=-1; strand=R; shift=0; score= 5.4286; rCTAGCTAGt-- ; cor=0.854; Ncor=0.640; logoDP=5.111; NIcor=0.614; NsEucl=0.910; SSD=1.309; NSW=0.927; rcor=6; rNcor=3; rlogoDP=6; rNIcor=3; rNsEucl=7; rSSD=7; rNSW=6; rank_mean=5.429; match_rank=4 a 31 3 5 92 2 2 6 92 3 16 0 0 c 8 89 1 0 1 95 3 2 5 20 0 0 g 50 5 2 3 95 1 0 1 89 23 0 0 t 11 3 92 5 2 2 91 5 3 41 0 0
ATTRB2_M1346_1.02_CISBP_rc_shift5 (ATTRB2_M1346_1.02_CISBP_rc)	0.799	0.466	0.423	-0.128	0.885	1.303	0.907	9	8	13	12	10	6	10	9.714	10	; oligos_5-7nt_m2 versus ATTRB2_M1346_1.02_CISBP_rc; m=2/5; ncol2=8; w=7; offset=4; strand=R; shift=5; score= 9.7143; -----yTAGGky ; cor=0.799; Ncor=0.466; logoDP=0.423; NIcor=-0.128; NsEucl=0.885; SSD=1.303; NSW=0.907; rcor=9; rNcor=8; rlogoDP=13; rNIcor=12; rNsEucl=10; rSSD=6; rNSW=10; rank_mean=9.714; match_rank=10 a 0 0 0 0 0 8 1 99 0 0 0 4 c 0 0 0 0 0 40 1 0 0 0 0 61 g 0 0 0 0 0 7 0 1 100 100 63 0 t 0 0 0 0 0 45 98 0 0 0 37 35
TRB2_MA1073.1_JASPAR_rc_shift5 (TRB2_MA1073.1_JASPAR_rc)	0.799	0.466	0.424	-0.128	0.884	1.309	0.906	10	9	12	13	11	8	11	10.571	11	; oligos_5-7nt_m2 versus TRB2_MA1073.1_JASPAR_rc; m=3/5; ncol2=8; w=7; offset=4; strand=R; shift=5; score=10.5714; -----yTAGGky ; cor=0.799; Ncor=0.466; logoDP=0.424; NIcor=-0.128; NsEucl=0.884; SSD=1.309; NSW=0.906; rcor=10; rNcor=9; rlogoDP=12; rNIcor=13; rNsEucl=11; rSSD=8; rNSW=11; rank_mean=10.571; match_rank=11 a 0 0 0 0 0 74 13 994 0 0 0 40 c 0 0 0 0 0 398 7 0 0 0 0 611 g 0 0 0 0 0 74 0 6 1000 1000 628 0 t 0 0 0 0 0 454 980 0 0 0 372 349
PK06103.1_M1304_1.02_CISBP_shift5 (PK06103.1_M1304_1.02_CISBP)	0.771	0.450	4.399	0.439	0.857	2.017	0.856	13	11	7	6	13	14	14	11.143	12	; oligos_5-7nt_m2 versus PK06103.1_M1304_1.02_CISBP; m=4/5; ncol2=8; w=7; offset=4; strand=D; shift=5; score=11.1429; -----CTAGGGC ; cor=0.771; Ncor=0.450; logoDP=4.399; NIcor=0.439; NsEucl=0.857; SSD=2.017; NSW=0.856; rcor=13; rNcor=11; rlogoDP=7; rNIcor=6; rNsEucl=13; rSSD=14; rNSW=14; rank_mean=11.143; match_rank=12 a 0 0 0 0 0 0 0 100 0 0 0 0 c 0 0 0 0 0 80 0 0 0 0 0 100 g 0 0 0 0 0 0 0 0 100 100 100 0 t 0 0 0 0 0 20 100 0 0 0 0 0
CBNAC_M01188_TRANSFAC_rc_shift2 (CBNAC_M01188_TRANSFAC_rc)	0.752	0.410	3.851	0.315	0.854	1.538	0.872	14	13	8	9	14	11	13	11.714	14	; oligos_5-7nt_m2 versus CBNAC_M01188_TRANSFAC_rc; m=5/5; ncol2=6; w=6; offset=1; strand=R; shift=2; score=11.7143; --AAGCaa---- ; cor=0.752; Ncor=0.410; logoDP=3.851; NIcor=0.315; NsEucl=0.854; SSD=1.538; NSW=0.872; rcor=14; rNcor=13; rlogoDP=8; rNIcor=9; rNsEucl=14; rSSD=11; rNSW=13; rank_mean=11.714; match_rank=14 a 0 0 44 44 0 0 22 23 0 0 0 0 c 0 0 0 0 0 44 5 9 0 0 0 0 g 0 0 0 0 44 0 4 5 0 0 0 0 t 0 0 0 0 0 0 9 1 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_5-7nt_m5_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_m5_shift0 (oligos_5-7nt_m5)
; oligos_5-7nt_m5; m=0 (reference); ncol1=9; shift=0; ncol=10; rmACAGCdm- ; Alignment reference a 28 32 106 0 106 0 0 27 33 0 c 26 34 0 106 0 0 106 20 31 0 g 28 24 0 0 0 106 0 29 21 0 t 24 16 0 0 0 0 0 30 21 0

AT2G40620_M0262_1.02_CISBP_shift0 (AT2G40620_M0262_1.02_CISBP) 0.802 0.721 3.083 0.729 0.907 1.398 0.922 8 1 9 1 8 10 7 6.286 6
; oligos_5-7nt_m5 versus AT2G40620_M0262_1.02_CISBP; m=1/1; ncol2=10; w=9; offset=0; strand=D; shift=0; score= 6.2857; tkmCAgctgk ; cor=0.802; Ncor=0.721; logoDP=3.083; NIcor=0.729; NsEucl=0.907; SSD=1.398; NSW=0.922; rcor=8; rNcor=1; rlogoDP=9; rNIcor=1; rNsEucl=8; rSSD=10; rNSW=7; rank_mean=6.286; match_rank=6 a 21 16 56 6 94 24 14 17 23 22 c 22 2 40 79 0 7 52 21 16 13 g 18 54 1 1 0 58 13 11 38 33 t 39 28 3 14 6 11 21 51 23 32

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=9; shift=0; ncol=10; rmACAGCdm- ; Alignment reference a 28 32 106 0 106 0 0 27 33 0 c 26 34 0 106 0 0 106 20 31 0 g 28 24 0 0 0 106 0 29 21 0 t 24 16 0 0 0 0 0 30 21 0
AT2G40620_M0262_1.02_CISBP_shift0 (AT2G40620_M0262_1.02_CISBP)		0.802	0.721	3.083	0.729	0.907	1.398	0.922	8	1	9	1	8	10	7	6.286	6	; oligos_5-7nt_m5 versus AT2G40620_M0262_1.02_CISBP; m=1/1; ncol2=10; w=9; offset=0; strand=D; shift=0; score= 6.2857; tkmCAgctgk ; cor=0.802; Ncor=0.721; logoDP=3.083; NIcor=0.729; NsEucl=0.907; SSD=1.398; NSW=0.922; rcor=8; rNcor=1; rlogoDP=9; rNIcor=1; rNsEucl=8; rSSD=10; rNSW=7; rank_mean=6.286; match_rank=6 a 21 16 56 6 94 24 14 17 23 22 c 22 2 40 79 0 7 52 21 16 13 g 18 54 1 1 0 58 13 11 38 33 t 39 28 3 14 6 11 21 51 23 32

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=11; shift=0; ncol=11; ywCCTACTCmy ; Alignment reference a 25 37 12 7 5 104 4 5 5 42 34 c 51 27 122 130 8 21 136 3 131 51 40 g 29 29 6 7 2 8 3 3 3 26 22 t 40 52 5 1 130 12 2 134 6 26 49

AtMYB68_II_AthaMYB_rc_shift0 (AtMYB68_II_AthaMYB_rc) 0.783 0.570 0.200 -0.209 0.883 1.751 0.891 11 4 14 14 12 12 12 11.286 13
; oligos_5-7nt_m4 versus AtMYB68_II_AthaMYB_rc; m=1/1; ncol2=8; w=8; offset=0; strand=R; shift=0; score=11.2857; yAmCTACy--- ; cor=0.783; Ncor=0.570; logoDP=0.200; NIcor=-0.209; NsEucl=0.883; SSD=1.751; NSW=0.891; rcor=11; rNcor=4; rlogoDP=14; rNIcor=14; rNsEucl=12; rSSD=12; rNSW=12; rank_mean=11.286; match_rank=13 a 0 2 1 0 0 2 0 0 0 0 0 c 1 0 1 2 0 0 2 1 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 t 1 0 0 0 2 0 0 1 0 0 0