One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_vs_db/peak-motifs_motifs_vs_db_ArabidopsisPBM.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m5_shift1 ; 15 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m5_shift1 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -scCGCCGCsg ; Alignment reference a 0 2 2 0 0 0 0 0 0 5 3 c 0 8 10 21 0 21 21 0 21 6 5 g 0 9 5 0 21 0 0 21 0 6 11 t 0 2 4 0 0 0 0 0 0 4 2

7251_RAP2.6_ArabidopsisPBM_20140210__shift1 (7251_RAP2.6_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7251_RAP2.6_ArabidopsisPBM_20140210_; m=1/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.904468; -gSCGCCGCCr ; cor=; Ncor= a 0 12 4 2 1 0 1 0 2 7 30 c 0 19 27 96 0 90 99 0 95 92 3 g 0 48 68 1 99 10 0 100 1 0 61 t 0 21 1 1 0 0 0 0 2 1 6

7248_RAP2.3_ArabidopsisPBM_20140210__shift1 (7248_RAP2.3_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7248_RAP2.3_ArabidopsisPBM_20140210_; m=2/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.883529; -rgCGCCGCmw ; cor=; Ncor= a 0 26 12 15 1 1 2 1 11 26 49 c 0 13 23 76 1 75 98 0 78 66 9 g 0 46 54 3 98 24 0 98 2 1 17 t 0 15 11 6 0 0 0 1 9 7 25

7256_RRTF1_ArabidopsisPBM_20140210__shift1 (7256_RRTF1_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7256_RRTF1_ArabidopsisPBM_20140210_; m=3/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.873121; -gsCGCCGCCA ; cor=; Ncor= a 0 24 4 5 0 0 1 0 4 21 69 c 0 15 29 93 0 83 99 2 86 77 2 g 0 46 66 1 100 17 0 98 1 0 21 t 0 15 1 1 0 0 0 0 9 2 8

7221_ERF1_ArabidopsisPBM_20140210__shift1 (7221_ERF1_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7221_ERF1_ArabidopsisPBM_20140210_; m=4/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.865762; -rsCGCCGCCr ; cor=; Ncor= a 0 38 6 15 1 0 4 2 5 1 58 c 0 12 33 82 1 96 95 0 90 97 5 g 0 27 46 1 97 3 0 97 2 1 25 t 0 23 15 2 1 1 1 1 3 1 12

7216_DEAR4_2_ArabidopsisPBM_20140210__shift1 (7216_DEAR4_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7216_DEAR4_2_ArabidopsisPBM_20140210_; m=5/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.846702; -rGCGCCGCCt ; cor=; Ncor= a 0 29 3 2 12 1 0 1 0 3 4 c 0 22 13 94 0 91 98 1 84 86 21 g 0 37 76 1 87 8 1 95 9 2 14 t 0 12 8 3 1 0 1 3 7 9 61

7246_ORA47_2_ArabidopsisPBM_20140210__shift1 (7246_ORA47_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7246_ORA47_2_ArabidopsisPBM_20140210_; m=6/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.821471; -kGCGCCGmCy ; cor=; Ncor= a 0 17 9 2 7 0 1 1 25 4 21 c 0 5 13 93 0 97 98 0 65 93 25 g 0 31 73 1 92 3 1 97 5 1 13 t 0 47 5 4 1 0 0 2 5 2 41

7202_ATERF1_ArabidopsisPBM_20140210__shift1 (7202_ATERF1_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7202_ATERF1_ArabidopsisPBM_20140210_; m=7/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.733679; -GGcGsCGsCb ; cor=; Ncor= a 0 5 4 19 3 4 6 6 8 7 9 c 0 3 15 60 2 48 85 9 52 80 37 g 0 84 71 15 93 38 5 73 35 9 29 t 0 8 10 6 2 10 4 12 5 4 25

7257_RRTF1_2_ArabidopsisPBM_20140210__shift2 (7257_RRTF1_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7257_RRTF1_2_ArabidopsisPBM_20140210_; m=8/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.717291; --sCGCCGCmA ; cor=; Ncor= a 0 0 7 10 0 0 1 0 3 45 90 c 0 0 46 87 1 98 99 1 91 54 2 g 0 0 43 2 99 2 0 98 2 0 3 t 0 0 4 1 0 0 0 1 4 1 5

7258_RRTF1_3_ArabidopsisPBM_20140210__shift2 (7258_RRTF1_3_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7258_RRTF1_3_ArabidopsisPBM_20140210_; m=9/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.709518; --sCGCCGCCA ; cor=; Ncor= a 0 0 6 5 0 0 2 1 6 17 81 c 0 0 30 92 0 97 97 1 81 77 4 g 0 0 60 2 100 3 0 98 2 0 8 t 0 0 4 1 0 0 1 0 11 6 7

7249_RAP2.3_2_ArabidopsisPBM_20140210__shift2 (7249_RAP2.3_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7249_RAP2.3_2_ArabidopsisPBM_20140210_; m=10/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.709169; --smGCCGCma ; cor=; Ncor= a 0 0 9 34 0 0 1 1 2 28 62 c 0 0 29 56 0 96 98 1 87 67 7 g 0 0 57 4 100 3 1 97 3 1 11 t 0 0 5 6 0 1 0 1 8 4 20

7213_DEAR3_ArabidopsisPBM_20140210__shift2 (7213_DEAR3_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7213_DEAR3_ArabidopsisPBM_20140210_; m=11/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.700976; --kCrCCGmCs ; cor=; Ncor= a 0 0 20 15 33 3 4 7 32 7 10 c 0 0 23 79 2 89 93 4 52 83 42 g 0 0 32 2 63 5 2 86 6 7 33 t 0 0 25 4 2 3 1 3 10 3 15

7250_RAP2.3_3_ArabidopsisPBM_20140210__shift2 (7250_RAP2.3_3_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7250_RAP2.3_3_ArabidopsisPBM_20140210_; m=12/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.651314; --gCGCCGCCA ; cor=; Ncor= a 0 0 14 21 0 0 9 1 16 8 73 c 0 0 16 70 0 98 91 23 70 90 4 g 0 0 65 3 100 1 0 75 4 0 6 t 0 0 5 6 0 1 0 1 10 2 17

7252_RAP2.6_2_ArabidopsisPBM_20140210__shift2 (7252_RAP2.6_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7252_RAP2.6_2_ArabidopsisPBM_20140210_; m=13/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.601406; --mrGCCGCmA ; cor=; Ncor= a 0 0 38 56 5 2 1 3 5 49 68 c 0 0 36 6 0 95 94 0 77 46 15 g 0 0 7 29 94 1 4 96 7 1 1 t 0 0 19 9 1 2 1 1 11 4 16

7219_DREB2C_ArabidopsisPBM_20140210__shift0 (7219_DREB2C_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m5 versus 7219_DREB2C_ArabidopsisPBM_20140210_; m=14/14; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.600674; GGCGGCCGCc- ; cor=; Ncor= a 14 2 0 1 2 0 0 4 3 13 0 c 4 2 96 5 0 97 94 0 93 67 0 g 68 93 0 94 98 0 5 96 2 7 0 t 14 3 4 0 0 3 1 0 2 13 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; rtATATATat ; Alignment reference a 14 7 30 0 32 0 33 0 18 5 c 8 8 3 1 1 2 1 2 3 8 g 9 3 2 0 2 1 1 3 8 8 t 4 17 0 34 0 32 0 30 6 14

7186_AHL20_ArabidopsisPBM_20140210__shift0 (7186_AHL20_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m3 versus 7186_AHL20_ArabidopsisPBM_20140210_; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.76704; wAATATATTw ; cor=; Ncor= a 44 95 88 8 87 13 90 11 3 44 c 16 1 0 1 0 0 1 1 1 10 g 11 1 1 0 0 0 1 0 1 21 t 29 3 11 91 13 87 8 88 95 25

7185_AHL12_3_ArabidopsisPBM_20140210__shift1 (7185_AHL12_3_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m3 versus 7185_AHL12_3_ArabidopsisPBM_20140210_; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.578425; -wAwwwwwwT ; cor=; Ncor= a 0 42 83 44 55 36 64 43 54 11 c 0 11 2 1 1 0 0 1 1 4 g 0 11 5 1 1 0 0 1 0 2 t 0 36 10 54 43 64 36 55 45 83

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=1; ncol=11; -vcCCCGCCsc ; Alignment reference a 0 6 3 0 0 0 0 0 0 4 3 c 0 8 9 22 22 22 0 22 22 6 10 g 0 7 5 0 0 0 22 0 0 11 4 t 0 1 5 0 0 0 0 0 0 1 5

7213_DEAR3_ArabidopsisPBM_20140210__shift1 (7213_DEAR3_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m2 versus 7213_DEAR3_ArabidopsisPBM_20140210_; m=1/8; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.716251; -kCrCCGmCsw ; cor=; Ncor= a 0 20 15 33 3 4 7 32 7 10 32 c 0 23 79 2 89 93 4 52 83 42 23 g 0 32 2 63 5 2 86 6 7 33 15 t 0 25 4 2 3 1 3 10 3 15 30

7251_RAP2.6_ArabidopsisPBM_20140210__shift0 (7251_RAP2.6_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m2 versus 7251_RAP2.6_ArabidopsisPBM_20140210_; m=2/8; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.595675; gSCGCCGCCr- ; cor=; Ncor= a 12 4 2 1 0 1 0 2 7 30 0 c 19 27 96 0 90 99 0 95 92 3 0 g 48 68 1 99 10 0 100 1 0 61 0 t 21 1 1 0 0 0 0 2 1 6 0

7221_ERF1_ArabidopsisPBM_20140210__shift0 (7221_ERF1_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m2 versus 7221_ERF1_ArabidopsisPBM_20140210_; m=3/8; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.595149; rsCGCCGCCr- ; cor=; Ncor= a 38 6 15 1 0 4 2 5 1 58 0 c 12 33 82 1 96 95 0 90 97 5 0 g 27 46 1 97 3 0 97 2 1 25 0 t 23 15 2 1 1 1 1 3 1 12 0

7256_RRTF1_ArabidopsisPBM_20140210__shift3 (7256_RRTF1_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m2 versus 7256_RRTF1_ArabidopsisPBM_20140210_; m=4/8; ncol2=10; w=0; offset=2; strand=D; shift=3; score=0.472299; ---gsCGCCGC ; cor=; Ncor= a 0 0 0 24 4 5 0 0 1 0 4 c 0 0 0 15 29 93 0 83 99 2 86 g 0 0 0 46 66 1 100 17 0 98 1 t 0 0 0 15 1 1 0 0 0 0 9

7257_RRTF1_2_ArabidopsisPBM_20140210__shift4 (7257_RRTF1_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m2 versus 7257_RRTF1_2_ArabidopsisPBM_20140210_; m=5/8; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.463375; ----sCGCCGC ; cor=; Ncor= a 0 0 0 0 7 10 0 0 1 0 3 c 0 0 0 0 46 87 1 98 99 1 91 g 0 0 0 0 43 2 99 2 0 98 2 t 0 0 0 0 4 1 0 0 0 1 4

7258_RRTF1_3_ArabidopsisPBM_20140210__shift4 (7258_RRTF1_3_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m2 versus 7258_RRTF1_3_ArabidopsisPBM_20140210_; m=6/8; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.446152; ----sCGCCGC ; cor=; Ncor= a 0 0 0 0 6 5 0 0 2 1 6 c 0 0 0 0 30 92 0 97 97 1 81 g 0 0 0 0 60 2 100 3 0 98 2 t 0 0 0 0 4 1 0 0 1 0 11

7250_RAP2.3_3_ArabidopsisPBM_20140210__shift4 (7250_RAP2.3_3_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m2 versus 7250_RAP2.3_3_ArabidopsisPBM_20140210_; m=7/8; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.42735; ----gCGCCGC ; cor=; Ncor= a 0 0 0 0 14 21 0 0 9 1 16 c 0 0 0 0 16 70 0 98 91 23 70 g 0 0 0 0 65 3 100 1 0 75 4 t 0 0 0 0 5 6 0 1 0 1 10

7249_RAP2.3_2_ArabidopsisPBM_20140210__shift4 (7249_RAP2.3_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m2 versus 7249_RAP2.3_2_ArabidopsisPBM_20140210_; m=8/8; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.417776; ----smGCCGC ; cor=; Ncor= a 0 0 0 0 9 34 0 0 1 1 2 c 0 0 0 0 29 56 0 96 98 1 87 g 0 0 0 0 57 4 100 3 1 97 3 t 0 0 0 0 5 6 0 1 0 1 8

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---sgAGGTAGwm ; Alignment reference a 0 0 0 3 3 16 0 0 0 18 0 6 5 c 0 0 0 7 4 0 0 2 0 0 1 3 5 g 0 0 0 5 7 0 17 16 0 0 16 4 4 t 0 0 0 3 4 2 1 0 18 0 1 5 4

7265_STY1_2_ArabidopsisPBM_20140210__rc_shift2 (7265_STY1_2_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv1_m4 versus 7265_STY1_2_ArabidopsisPBM_20140210__rc; m=1/5; ncol2=10; w=-1; offset=-1; strand=R; shift=2; score=0.578813; --rCTAGCTAGt- ; cor=; Ncor= a 0 0 31 3 5 91 2 2 5 91 3 16 0 c 0 0 8 89 1 0 1 95 4 3 5 20 0 g 0 0 50 5 3 4 95 1 0 1 89 23 0 t 0 0 11 3 91 5 2 2 91 5 3 41 0

7237_MYB111_2_ArabidopsisPBM_20140210__shift5 (7237_MYB111_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m4 versus 7237_MYB111_2_ArabidopsisPBM_20140210_; m=2/5; ncol2=10; w=0; offset=2; strand=D; shift=5; score=0.526712; -----aGGTwGKT ; cor=; Ncor= a 0 0 0 0 0 57 6 1 0 59 2 0 2 c 0 0 0 0 0 10 0 0 0 1 0 1 1 g 0 0 0 0 0 11 93 85 1 3 98 73 0 t 0 0 0 0 0 22 1 14 99 37 0 26 97

7236_MYB111_ArabidopsisPBM_20140210__shift1 (7236_MYB111_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m4 versus 7236_MYB111_ArabidopsisPBM_20140210_; m=3/5; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.506784; -dGkTAGGTrs-- ; cor=; Ncor= a 0 28 23 0 0 87 2 1 1 53 7 0 0 c 0 10 0 0 2 1 0 1 0 3 32 0 0 g 0 28 76 64 0 1 98 85 0 39 46 0 0 t 0 34 1 36 98 11 0 13 99 5 15 0 0

7238_MYB46_ArabidopsisPBM_20140210__shift1 (7238_MYB46_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m4 versus 7238_MYB46_ArabidopsisPBM_20140210_; m=4/5; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.499562; -aGkTAGGTrr-- ; cor=; Ncor= a 0 42 8 0 1 84 0 0 0 58 26 0 0 c 0 16 0 0 1 3 0 0 4 2 22 0 0 g 0 22 91 39 0 1 100 91 0 36 37 0 0 t 0 20 1 61 98 12 0 9 96 4 15 0 0

7242_MYB55_ArabidopsisPBM_20140210__rc_shift0 (7242_MYB55_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv1_m4 versus 7242_MYB55_ArabidopsisPBM_20140210__rc; m=5/5; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.407551; bCGKTAGGTr--- ; cor=; Ncor= a 17 7 4 0 0 70 1 0 0 48 0 0 0 c 30 76 0 0 2 2 0 0 2 5 0 0 0 g 28 5 96 73 0 5 99 95 0 36 0 0 0 t 25 12 0 27 98 23 0 5 98 11 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 15 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; shCCCGCCGhs ; Alignment reference a 4 6 0 2 0 0 2 0 0 6 1 c 8 6 21 18 21 0 20 23 0 8 10 g 10 5 2 2 2 23 0 0 23 3 7 t 1 6 0 1 0 0 1 0 0 6 5

7256_RRTF1_ArabidopsisPBM_20140210__shift2 (7256_RRTF1_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7256_RRTF1_ArabidopsisPBM_20140210_; m=1/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.577692; --gsCGCCGCC ; cor=; Ncor= a 0 0 24 4 5 0 0 1 0 4 21 c 0 0 15 29 93 0 83 99 2 86 77 g 0 0 46 66 1 100 17 0 98 1 0 t 0 0 15 1 1 0 0 0 0 9 2

7251_RAP2.6_ArabidopsisPBM_20140210__shift2 (7251_RAP2.6_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7251_RAP2.6_ArabidopsisPBM_20140210_; m=2/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.573859; --gSCGCCGCC ; cor=; Ncor= a 0 0 12 4 2 1 0 1 0 2 7 c 0 0 19 27 96 0 90 99 0 95 92 g 0 0 48 68 1 99 10 0 100 1 0 t 0 0 21 1 1 0 0 0 0 2 1

7221_ERF1_ArabidopsisPBM_20140210__shift2 (7221_ERF1_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7221_ERF1_ArabidopsisPBM_20140210_; m=3/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.573693; --rsCGCCGCC ; cor=; Ncor= a 0 0 38 6 15 1 0 4 2 5 1 c 0 0 12 33 82 1 96 95 0 90 97 g 0 0 27 46 1 97 3 0 97 2 1 t 0 0 23 15 2 1 1 1 1 3 1

7248_RAP2.3_ArabidopsisPBM_20140210__shift2 (7248_RAP2.3_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7248_RAP2.3_ArabidopsisPBM_20140210_; m=4/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.572248; --rgCGCCGCm ; cor=; Ncor= a 0 0 26 12 15 1 1 2 1 11 26 c 0 0 13 23 76 1 75 98 0 78 66 g 0 0 46 54 3 98 24 0 98 2 1 t 0 0 15 11 6 0 0 0 1 9 7

7216_DEAR4_2_ArabidopsisPBM_20140210__shift2 (7216_DEAR4_2_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7216_DEAR4_2_ArabidopsisPBM_20140210_; m=5/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.562038; --rGCGCCGCC ; cor=; Ncor= a 0 0 29 3 2 12 1 0 1 0 3 c 0 0 22 13 94 0 91 98 1 84 86 g 0 0 37 76 1 87 8 1 95 9 2 t 0 0 12 8 3 1 0 1 3 7 9

7246_ORA47_2_ArabidopsisPBM_20140210__shift2 (7246_ORA47_2_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7246_ORA47_2_ArabidopsisPBM_20140210_; m=6/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.547047; --kGCGCCGmC ; cor=; Ncor= a 0 0 17 9 2 7 0 1 1 25 4 c 0 0 5 13 93 0 97 98 0 65 93 g 0 0 31 73 1 92 3 1 97 5 1 t 0 0 47 5 4 1 0 0 2 5 2

7257_RRTF1_2_ArabidopsisPBM_20140210__shift3 (7257_RRTF1_2_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7257_RRTF1_2_ArabidopsisPBM_20140210_; m=7/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.541374; ---sCGCCGCm ; cor=; Ncor= a 0 0 0 7 10 0 0 1 0 3 45 c 0 0 0 46 87 1 98 99 1 91 54 g 0 0 0 43 2 99 2 0 98 2 0 t 0 0 0 4 1 0 0 0 1 4 1

7258_RRTF1_3_ArabidopsisPBM_20140210__shift3 (7258_RRTF1_3_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7258_RRTF1_3_ArabidopsisPBM_20140210_; m=8/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.538023; ---sCGCCGCC ; cor=; Ncor= a 0 0 0 6 5 0 0 2 1 6 17 c 0 0 0 30 92 0 97 97 1 81 77 g 0 0 0 60 2 100 3 0 98 2 0 t 0 0 0 4 1 0 0 1 0 11 6

7213_DEAR3_ArabidopsisPBM_20140210__shift3 (7213_DEAR3_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7213_DEAR3_ArabidopsisPBM_20140210_; m=9/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.524073; ---kCrCCGmC ; cor=; Ncor= a 0 0 0 20 15 33 3 4 7 32 7 c 0 0 0 23 79 2 89 93 4 52 83 g 0 0 0 32 2 63 5 2 86 6 7 t 0 0 0 25 4 2 3 1 3 10 3

7249_RAP2.3_2_ArabidopsisPBM_20140210__shift3 (7249_RAP2.3_2_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7249_RAP2.3_2_ArabidopsisPBM_20140210_; m=10/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.509559; ---smGCCGCm ; cor=; Ncor= a 0 0 0 9 34 0 0 1 1 2 28 c 0 0 0 29 56 0 96 98 1 87 67 g 0 0 0 57 4 100 3 1 97 3 1 t 0 0 0 5 6 0 1 0 1 8 4

7250_RAP2.3_3_ArabidopsisPBM_20140210__shift3 (7250_RAP2.3_3_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7250_RAP2.3_3_ArabidopsisPBM_20140210_; m=11/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.496139; ---gCGCCGCC ; cor=; Ncor= a 0 0 0 14 21 0 0 9 1 16 8 c 0 0 0 16 70 0 98 91 23 70 90 g 0 0 0 65 3 100 1 0 75 4 0 t 0 0 0 5 6 0 1 0 1 10 2

7252_RAP2.6_2_ArabidopsisPBM_20140210__shift3 (7252_RAP2.6_2_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7252_RAP2.6_2_ArabidopsisPBM_20140210_; m=12/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.448578; ---mrGCCGCm ; cor=; Ncor= a 0 0 0 38 56 5 2 1 3 5 49 c 0 0 0 36 6 0 95 94 0 77 46 g 0 0 0 7 29 94 1 4 96 7 1 t 0 0 0 19 9 1 2 1 1 11 4

7220_DREB2C_2_ArabidopsisPBM_20140210__shift3 (7220_DREB2C_2_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7220_DREB2C_2_ArabidopsisPBM_20140210_; m=13/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.440117; ---sCACCGAC ; cor=; Ncor= a 0 0 0 9 11 81 0 1 2 78 1 c 0 0 0 52 76 0 98 99 0 16 98 g 0 0 0 27 12 19 0 0 98 4 0 t 0 0 0 12 1 0 2 0 0 2 1

7206_At1g77200_ArabidopsisPBM_20140210__shift3 (7206_At1g77200_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m2 versus 7206_At1g77200_ArabidopsisPBM_20140210_; m=14/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.436242; ---cCRCCGAC ; cor=; Ncor= a 0 0 0 6 8 75 0 0 0 99 0 c 0 0 0 56 76 0 100 100 0 0 100 g 0 0 0 15 4 25 0 0 100 0 0 t 0 0 0 23 12 0 0 0 0 1 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; raAAAAAAAww ; Alignment reference a 32 29 69 70 73 71 70 71 74 33 33 c 15 16 3 4 5 3 3 1 0 9 8 g 22 19 7 5 2 5 4 4 4 18 19 t 12 17 2 2 1 2 4 5 3 21 21

7217_DOF5.7_ArabidopsisPBM_20140210__shift2 (7217_DOF5.7_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv1_m1 versus 7217_DOF5.7_ArabidopsisPBM_20140210_; m=1/1; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.54141; --raAAArrkg ; cor=; Ncor= a 0 0 39 45 68 97 90 36 48 10 18 c 0 0 21 9 1 0 0 4 6 19 21 g 0 0 27 22 7 1 8 59 44 46 41 t 0 0 13 24 24 2 2 1 2 25 20

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; ysCTCCTCkk ; Alignment reference a 2 3 0 0 0 0 0 0 1 4 c 8 9 18 0 18 18 0 18 4 3 g 3 5 0 0 0 0 0 0 6 5 t 5 1 0 18 0 0 18 0 7 6

7274_TOE2_ArabidopsisPBM_20140210__shift3 (7274_TOE2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m1 versus 7274_TOE2_ArabidopsisPBM_20140210_; m=1/1; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.405123; ---wCCTCGT ; cor=; Ncor= a 0 0 0 61 0 13 0 6 1 0 c 0 0 0 2 92 85 0 92 0 0 g 0 0 0 4 0 1 2 1 98 11 t 0 0 0 33 8 1 98 1 1 89

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m5_shift1 (oligos_6nt_mkv1_m5)				; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -scCGCCGCsg ; Alignment reference a 0 2 2 0 0 0 0 0 0 5 3 c 0 8 10 21 0 21 21 0 21 6 5 g 0 9 5 0 21 0 0 21 0 6 11 t 0 2 4 0 0 0 0 0 0 4 2
7251_RAP2.6_ArabidopsisPBM_20140210__shift1 (7251_RAP2.6_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7251_RAP2.6_ArabidopsisPBM_20140210_; m=1/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.904468; -gSCGCCGCCr ; cor=; Ncor= a 0 12 4 2 1 0 1 0 2 7 30 c 0 19 27 96 0 90 99 0 95 92 3 g 0 48 68 1 99 10 0 100 1 0 61 t 0 21 1 1 0 0 0 0 2 1 6
7248_RAP2.3_ArabidopsisPBM_20140210__shift1 (7248_RAP2.3_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7248_RAP2.3_ArabidopsisPBM_20140210_; m=2/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.883529; -rgCGCCGCmw ; cor=; Ncor= a 0 26 12 15 1 1 2 1 11 26 49 c 0 13 23 76 1 75 98 0 78 66 9 g 0 46 54 3 98 24 0 98 2 1 17 t 0 15 11 6 0 0 0 1 9 7 25
7256_RRTF1_ArabidopsisPBM_20140210__shift1 (7256_RRTF1_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7256_RRTF1_ArabidopsisPBM_20140210_; m=3/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.873121; -gsCGCCGCCA ; cor=; Ncor= a 0 24 4 5 0 0 1 0 4 21 69 c 0 15 29 93 0 83 99 2 86 77 2 g 0 46 66 1 100 17 0 98 1 0 21 t 0 15 1 1 0 0 0 0 9 2 8
7221_ERF1_ArabidopsisPBM_20140210__shift1 (7221_ERF1_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7221_ERF1_ArabidopsisPBM_20140210_; m=4/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.865762; -rsCGCCGCCr ; cor=; Ncor= a 0 38 6 15 1 0 4 2 5 1 58 c 0 12 33 82 1 96 95 0 90 97 5 g 0 27 46 1 97 3 0 97 2 1 25 t 0 23 15 2 1 1 1 1 3 1 12
7216_DEAR4_2_ArabidopsisPBM_20140210__shift1 (7216_DEAR4_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7216_DEAR4_2_ArabidopsisPBM_20140210_; m=5/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.846702; -rGCGCCGCCt ; cor=; Ncor= a 0 29 3 2 12 1 0 1 0 3 4 c 0 22 13 94 0 91 98 1 84 86 21 g 0 37 76 1 87 8 1 95 9 2 14 t 0 12 8 3 1 0 1 3 7 9 61
7246_ORA47_2_ArabidopsisPBM_20140210__shift1 (7246_ORA47_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7246_ORA47_2_ArabidopsisPBM_20140210_; m=6/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.821471; -kGCGCCGmCy ; cor=; Ncor= a 0 17 9 2 7 0 1 1 25 4 21 c 0 5 13 93 0 97 98 0 65 93 25 g 0 31 73 1 92 3 1 97 5 1 13 t 0 47 5 4 1 0 0 2 5 2 41
7202_ATERF1_ArabidopsisPBM_20140210__shift1 (7202_ATERF1_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7202_ATERF1_ArabidopsisPBM_20140210_; m=7/14; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.733679; -GGcGsCGsCb ; cor=; Ncor= a 0 5 4 19 3 4 6 6 8 7 9 c 0 3 15 60 2 48 85 9 52 80 37 g 0 84 71 15 93 38 5 73 35 9 29 t 0 8 10 6 2 10 4 12 5 4 25
7257_RRTF1_2_ArabidopsisPBM_20140210__shift2 (7257_RRTF1_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7257_RRTF1_2_ArabidopsisPBM_20140210_; m=8/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.717291; --sCGCCGCmA ; cor=; Ncor= a 0 0 7 10 0 0 1 0 3 45 90 c 0 0 46 87 1 98 99 1 91 54 2 g 0 0 43 2 99 2 0 98 2 0 3 t 0 0 4 1 0 0 0 1 4 1 5
7258_RRTF1_3_ArabidopsisPBM_20140210__shift2 (7258_RRTF1_3_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7258_RRTF1_3_ArabidopsisPBM_20140210_; m=9/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.709518; --sCGCCGCCA ; cor=; Ncor= a 0 0 6 5 0 0 2 1 6 17 81 c 0 0 30 92 0 97 97 1 81 77 4 g 0 0 60 2 100 3 0 98 2 0 8 t 0 0 4 1 0 0 1 0 11 6 7
7249_RAP2.3_2_ArabidopsisPBM_20140210__shift2 (7249_RAP2.3_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7249_RAP2.3_2_ArabidopsisPBM_20140210_; m=10/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.709169; --smGCCGCma ; cor=; Ncor= a 0 0 9 34 0 0 1 1 2 28 62 c 0 0 29 56 0 96 98 1 87 67 7 g 0 0 57 4 100 3 1 97 3 1 11 t 0 0 5 6 0 1 0 1 8 4 20
7213_DEAR3_ArabidopsisPBM_20140210__shift2 (7213_DEAR3_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7213_DEAR3_ArabidopsisPBM_20140210_; m=11/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.700976; --kCrCCGmCs ; cor=; Ncor= a 0 0 20 15 33 3 4 7 32 7 10 c 0 0 23 79 2 89 93 4 52 83 42 g 0 0 32 2 63 5 2 86 6 7 33 t 0 0 25 4 2 3 1 3 10 3 15
7250_RAP2.3_3_ArabidopsisPBM_20140210__shift2 (7250_RAP2.3_3_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7250_RAP2.3_3_ArabidopsisPBM_20140210_; m=12/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.651314; --gCGCCGCCA ; cor=; Ncor= a 0 0 14 21 0 0 9 1 16 8 73 c 0 0 16 70 0 98 91 23 70 90 4 g 0 0 65 3 100 1 0 75 4 0 6 t 0 0 5 6 0 1 0 1 10 2 17
7252_RAP2.6_2_ArabidopsisPBM_20140210__shift2 (7252_RAP2.6_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7252_RAP2.6_2_ArabidopsisPBM_20140210_; m=13/14; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.601406; --mrGCCGCmA ; cor=; Ncor= a 0 0 38 56 5 2 1 3 5 49 68 c 0 0 36 6 0 95 94 0 77 46 15 g 0 0 7 29 94 1 4 96 7 1 1 t 0 0 19 9 1 2 1 1 11 4 16
7219_DREB2C_ArabidopsisPBM_20140210__shift0 (7219_DREB2C_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m5 versus 7219_DREB2C_ArabidopsisPBM_20140210_; m=14/14; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.600674; GGCGGCCGCc- ; cor=; Ncor= a 14 2 0 1 2 0 0 4 3 13 0 c 4 2 96 5 0 97 94 0 93 67 0 g 68 93 0 94 98 0 5 96 2 7 0 t 14 3 4 0 0 3 1 0 2 13 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=1; ncol=11; -vcCCCGCCsc ; Alignment reference a 0 6 3 0 0 0 0 0 0 4 3 c 0 8 9 22 22 22 0 22 22 6 10 g 0 7 5 0 0 0 22 0 0 11 4 t 0 1 5 0 0 0 0 0 0 1 5
7213_DEAR3_ArabidopsisPBM_20140210__shift1 (7213_DEAR3_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m2 versus 7213_DEAR3_ArabidopsisPBM_20140210_; m=1/8; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.716251; -kCrCCGmCsw ; cor=; Ncor= a 0 20 15 33 3 4 7 32 7 10 32 c 0 23 79 2 89 93 4 52 83 42 23 g 0 32 2 63 5 2 86 6 7 33 15 t 0 25 4 2 3 1 3 10 3 15 30
7251_RAP2.6_ArabidopsisPBM_20140210__shift0 (7251_RAP2.6_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m2 versus 7251_RAP2.6_ArabidopsisPBM_20140210_; m=2/8; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.595675; gSCGCCGCCr- ; cor=; Ncor= a 12 4 2 1 0 1 0 2 7 30 0 c 19 27 96 0 90 99 0 95 92 3 0 g 48 68 1 99 10 0 100 1 0 61 0 t 21 1 1 0 0 0 0 2 1 6 0
7221_ERF1_ArabidopsisPBM_20140210__shift0 (7221_ERF1_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m2 versus 7221_ERF1_ArabidopsisPBM_20140210_; m=3/8; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.595149; rsCGCCGCCr- ; cor=; Ncor= a 38 6 15 1 0 4 2 5 1 58 0 c 12 33 82 1 96 95 0 90 97 5 0 g 27 46 1 97 3 0 97 2 1 25 0 t 23 15 2 1 1 1 1 3 1 12 0
7256_RRTF1_ArabidopsisPBM_20140210__shift3 (7256_RRTF1_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m2 versus 7256_RRTF1_ArabidopsisPBM_20140210_; m=4/8; ncol2=10; w=0; offset=2; strand=D; shift=3; score=0.472299; ---gsCGCCGC ; cor=; Ncor= a 0 0 0 24 4 5 0 0 1 0 4 c 0 0 0 15 29 93 0 83 99 2 86 g 0 0 0 46 66 1 100 17 0 98 1 t 0 0 0 15 1 1 0 0 0 0 9
7257_RRTF1_2_ArabidopsisPBM_20140210__shift4 (7257_RRTF1_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m2 versus 7257_RRTF1_2_ArabidopsisPBM_20140210_; m=5/8; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.463375; ----sCGCCGC ; cor=; Ncor= a 0 0 0 0 7 10 0 0 1 0 3 c 0 0 0 0 46 87 1 98 99 1 91 g 0 0 0 0 43 2 99 2 0 98 2 t 0 0 0 0 4 1 0 0 0 1 4
7258_RRTF1_3_ArabidopsisPBM_20140210__shift4 (7258_RRTF1_3_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m2 versus 7258_RRTF1_3_ArabidopsisPBM_20140210_; m=6/8; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.446152; ----sCGCCGC ; cor=; Ncor= a 0 0 0 0 6 5 0 0 2 1 6 c 0 0 0 0 30 92 0 97 97 1 81 g 0 0 0 0 60 2 100 3 0 98 2 t 0 0 0 0 4 1 0 0 1 0 11
7250_RAP2.3_3_ArabidopsisPBM_20140210__shift4 (7250_RAP2.3_3_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m2 versus 7250_RAP2.3_3_ArabidopsisPBM_20140210_; m=7/8; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.42735; ----gCGCCGC ; cor=; Ncor= a 0 0 0 0 14 21 0 0 9 1 16 c 0 0 0 0 16 70 0 98 91 23 70 g 0 0 0 0 65 3 100 1 0 75 4 t 0 0 0 0 5 6 0 1 0 1 10
7249_RAP2.3_2_ArabidopsisPBM_20140210__shift4 (7249_RAP2.3_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m2 versus 7249_RAP2.3_2_ArabidopsisPBM_20140210_; m=8/8; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.417776; ----smGCCGC ; cor=; Ncor= a 0 0 0 0 9 34 0 0 1 1 2 c 0 0 0 0 29 56 0 96 98 1 87 g 0 0 0 0 57 4 100 3 1 97 3 t 0 0 0 0 5 6 0 1 0 1 8

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)				; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---sgAGGTAGwm ; Alignment reference a 0 0 0 3 3 16 0 0 0 18 0 6 5 c 0 0 0 7 4 0 0 2 0 0 1 3 5 g 0 0 0 5 7 0 17 16 0 0 16 4 4 t 0 0 0 3 4 2 1 0 18 0 1 5 4
7265_STY1_2_ArabidopsisPBM_20140210__rc_shift2 (7265_STY1_2_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv1_m4 versus 7265_STY1_2_ArabidopsisPBM_20140210__rc; m=1/5; ncol2=10; w=-1; offset=-1; strand=R; shift=2; score=0.578813; --rCTAGCTAGt- ; cor=; Ncor= a 0 0 31 3 5 91 2 2 5 91 3 16 0 c 0 0 8 89 1 0 1 95 4 3 5 20 0 g 0 0 50 5 3 4 95 1 0 1 89 23 0 t 0 0 11 3 91 5 2 2 91 5 3 41 0
7237_MYB111_2_ArabidopsisPBM_20140210__shift5 (7237_MYB111_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m4 versus 7237_MYB111_2_ArabidopsisPBM_20140210_; m=2/5; ncol2=10; w=0; offset=2; strand=D; shift=5; score=0.526712; -----aGGTwGKT ; cor=; Ncor= a 0 0 0 0 0 57 6 1 0 59 2 0 2 c 0 0 0 0 0 10 0 0 0 1 0 1 1 g 0 0 0 0 0 11 93 85 1 3 98 73 0 t 0 0 0 0 0 22 1 14 99 37 0 26 97
7236_MYB111_ArabidopsisPBM_20140210__shift1 (7236_MYB111_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m4 versus 7236_MYB111_ArabidopsisPBM_20140210_; m=3/5; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.506784; -dGkTAGGTrs-- ; cor=; Ncor= a 0 28 23 0 0 87 2 1 1 53 7 0 0 c 0 10 0 0 2 1 0 1 0 3 32 0 0 g 0 28 76 64 0 1 98 85 0 39 46 0 0 t 0 34 1 36 98 11 0 13 99 5 15 0 0
7238_MYB46_ArabidopsisPBM_20140210__shift1 (7238_MYB46_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m4 versus 7238_MYB46_ArabidopsisPBM_20140210_; m=4/5; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.499562; -aGkTAGGTrr-- ; cor=; Ncor= a 0 42 8 0 1 84 0 0 0 58 26 0 0 c 0 16 0 0 1 3 0 0 4 2 22 0 0 g 0 22 91 39 0 1 100 91 0 36 37 0 0 t 0 20 1 61 98 12 0 9 96 4 15 0 0
7242_MYB55_ArabidopsisPBM_20140210__rc_shift0 (7242_MYB55_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv1_m4 versus 7242_MYB55_ArabidopsisPBM_20140210__rc; m=5/5; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.407551; bCGKTAGGTr--- ; cor=; Ncor= a 17 7 4 0 0 70 1 0 0 48 0 0 0 c 30 76 0 0 2 2 0 0 2 5 0 0 0 g 28 5 96 73 0 5 99 95 0 36 0 0 0 t 25 12 0 27 98 23 0 5 98 11 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; shCCCGCCGhs ; Alignment reference a 4 6 0 2 0 0 2 0 0 6 1 c 8 6 21 18 21 0 20 23 0 8 10 g 10 5 2 2 2 23 0 0 23 3 7 t 1 6 0 1 0 0 1 0 0 6 5
7256_RRTF1_ArabidopsisPBM_20140210__shift2 (7256_RRTF1_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7256_RRTF1_ArabidopsisPBM_20140210_; m=1/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.577692; --gsCGCCGCC ; cor=; Ncor= a 0 0 24 4 5 0 0 1 0 4 21 c 0 0 15 29 93 0 83 99 2 86 77 g 0 0 46 66 1 100 17 0 98 1 0 t 0 0 15 1 1 0 0 0 0 9 2
7251_RAP2.6_ArabidopsisPBM_20140210__shift2 (7251_RAP2.6_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7251_RAP2.6_ArabidopsisPBM_20140210_; m=2/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.573859; --gSCGCCGCC ; cor=; Ncor= a 0 0 12 4 2 1 0 1 0 2 7 c 0 0 19 27 96 0 90 99 0 95 92 g 0 0 48 68 1 99 10 0 100 1 0 t 0 0 21 1 1 0 0 0 0 2 1
7221_ERF1_ArabidopsisPBM_20140210__shift2 (7221_ERF1_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7221_ERF1_ArabidopsisPBM_20140210_; m=3/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.573693; --rsCGCCGCC ; cor=; Ncor= a 0 0 38 6 15 1 0 4 2 5 1 c 0 0 12 33 82 1 96 95 0 90 97 g 0 0 27 46 1 97 3 0 97 2 1 t 0 0 23 15 2 1 1 1 1 3 1
7248_RAP2.3_ArabidopsisPBM_20140210__shift2 (7248_RAP2.3_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7248_RAP2.3_ArabidopsisPBM_20140210_; m=4/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.572248; --rgCGCCGCm ; cor=; Ncor= a 0 0 26 12 15 1 1 2 1 11 26 c 0 0 13 23 76 1 75 98 0 78 66 g 0 0 46 54 3 98 24 0 98 2 1 t 0 0 15 11 6 0 0 0 1 9 7
7216_DEAR4_2_ArabidopsisPBM_20140210__shift2 (7216_DEAR4_2_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7216_DEAR4_2_ArabidopsisPBM_20140210_; m=5/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.562038; --rGCGCCGCC ; cor=; Ncor= a 0 0 29 3 2 12 1 0 1 0 3 c 0 0 22 13 94 0 91 98 1 84 86 g 0 0 37 76 1 87 8 1 95 9 2 t 0 0 12 8 3 1 0 1 3 7 9
7246_ORA47_2_ArabidopsisPBM_20140210__shift2 (7246_ORA47_2_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7246_ORA47_2_ArabidopsisPBM_20140210_; m=6/14; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.547047; --kGCGCCGmC ; cor=; Ncor= a 0 0 17 9 2 7 0 1 1 25 4 c 0 0 5 13 93 0 97 98 0 65 93 g 0 0 31 73 1 92 3 1 97 5 1 t 0 0 47 5 4 1 0 0 2 5 2
7257_RRTF1_2_ArabidopsisPBM_20140210__shift3 (7257_RRTF1_2_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7257_RRTF1_2_ArabidopsisPBM_20140210_; m=7/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.541374; ---sCGCCGCm ; cor=; Ncor= a 0 0 0 7 10 0 0 1 0 3 45 c 0 0 0 46 87 1 98 99 1 91 54 g 0 0 0 43 2 99 2 0 98 2 0 t 0 0 0 4 1 0 0 0 1 4 1
7258_RRTF1_3_ArabidopsisPBM_20140210__shift3 (7258_RRTF1_3_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7258_RRTF1_3_ArabidopsisPBM_20140210_; m=8/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.538023; ---sCGCCGCC ; cor=; Ncor= a 0 0 0 6 5 0 0 2 1 6 17 c 0 0 0 30 92 0 97 97 1 81 77 g 0 0 0 60 2 100 3 0 98 2 0 t 0 0 0 4 1 0 0 1 0 11 6
7213_DEAR3_ArabidopsisPBM_20140210__shift3 (7213_DEAR3_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7213_DEAR3_ArabidopsisPBM_20140210_; m=9/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.524073; ---kCrCCGmC ; cor=; Ncor= a 0 0 0 20 15 33 3 4 7 32 7 c 0 0 0 23 79 2 89 93 4 52 83 g 0 0 0 32 2 63 5 2 86 6 7 t 0 0 0 25 4 2 3 1 3 10 3
7249_RAP2.3_2_ArabidopsisPBM_20140210__shift3 (7249_RAP2.3_2_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7249_RAP2.3_2_ArabidopsisPBM_20140210_; m=10/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.509559; ---smGCCGCm ; cor=; Ncor= a 0 0 0 9 34 0 0 1 1 2 28 c 0 0 0 29 56 0 96 98 1 87 67 g 0 0 0 57 4 100 3 1 97 3 1 t 0 0 0 5 6 0 1 0 1 8 4
7250_RAP2.3_3_ArabidopsisPBM_20140210__shift3 (7250_RAP2.3_3_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7250_RAP2.3_3_ArabidopsisPBM_20140210_; m=11/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.496139; ---gCGCCGCC ; cor=; Ncor= a 0 0 0 14 21 0 0 9 1 16 8 c 0 0 0 16 70 0 98 91 23 70 90 g 0 0 0 65 3 100 1 0 75 4 0 t 0 0 0 5 6 0 1 0 1 10 2
7252_RAP2.6_2_ArabidopsisPBM_20140210__shift3 (7252_RAP2.6_2_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7252_RAP2.6_2_ArabidopsisPBM_20140210_; m=12/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.448578; ---mrGCCGCm ; cor=; Ncor= a 0 0 0 38 56 5 2 1 3 5 49 c 0 0 0 36 6 0 95 94 0 77 46 g 0 0 0 7 29 94 1 4 96 7 1 t 0 0 0 19 9 1 2 1 1 11 4
7220_DREB2C_2_ArabidopsisPBM_20140210__shift3 (7220_DREB2C_2_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7220_DREB2C_2_ArabidopsisPBM_20140210_; m=13/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.440117; ---sCACCGAC ; cor=; Ncor= a 0 0 0 9 11 81 0 1 2 78 1 c 0 0 0 52 76 0 98 99 0 16 98 g 0 0 0 27 12 19 0 0 98 4 0 t 0 0 0 12 1 0 2 0 0 2 1
7206_At1g77200_ArabidopsisPBM_20140210__shift3 (7206_At1g77200_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv1_m2 versus 7206_At1g77200_ArabidopsisPBM_20140210_; m=14/14; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.436242; ---cCRCCGAC ; cor=; Ncor= a 0 0 0 6 8 75 0 0 0 99 0 c 0 0 0 56 76 0 100 100 0 0 100 g 0 0 0 15 4 25 0 0 100 0 0 t 0 0 0 23 12 0 0 0 0 1 0