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/oligos_6nt_mkv1_m5/peak-motifs_oligos_6nt_mkv1_m5.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_motifs/oligos_6nt_mkv1_m5/peak-motifs_oligos_6nt_mkv1_m5_vs_db_ArabidopsisPBM

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

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