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_m2/peak-motifs_oligos_6nt_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_6nt_mkv1_m2/peak-motifs_oligos_6nt_mkv1_m2_vs_db_ArabidopsisPBM

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

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