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_7nt_mkv1_m2/peak-motifs_oligos_7nt_mkv1_m2.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_7nt_mkv1_m2/peak-motifs_oligos_7nt_mkv1_m2_vs_db_ArabidopsisPBM

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

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