One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3.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/2026/02/26/peak-motifs.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_vs_db_ArabidopsisPBM

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift2 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=2; ncol=12; --wwTAATTAww ; Alignment reference a 0 0 36 29 0 84 84 0 0 84 29 26 c 0 0 11 14 0 0 0 0 0 0 12 11 g 0 0 11 12 0 0 0 0 0 0 14 11 t 0 0 26 29 84 0 0 84 84 0 29 36

7278_WOX13_2_ArabidopsisPBM_20140210__shift2 (7278_WOX13_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv2_m3 versus 7278_WOX13_2_ArabidopsisPBM_20140210_; m=1/9; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.907285; --tttAATTaam ; cor=; Ncor= a 0 0 22 16 20 81 81 8 10 59 57 27 c 0 0 22 15 17 6 2 9 3 4 11 34 g 0 0 19 11 4 3 9 2 6 17 16 20 t 0 0 37 58 59 10 8 81 81 20 16 19

7184_AHL12_2_ArabidopsisPBM_20140210__shift2 (7184_AHL12_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv2_m3 versus 7184_AHL12_2_ArabidopsisPBM_20140210_; m=2/9; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.826396; --rwwAWWTwwT ; cor=; Ncor= a 0 0 34 56 37 79 74 25 20 59 40 5 c 0 0 9 2 2 0 0 1 1 2 2 18 g 0 0 42 2 2 1 1 0 0 2 3 3 t 0 0 15 40 59 20 25 74 79 37 55 74

7231_ICU4_ArabidopsisPBM_20140210__rc_shift1 (7231_ICU4_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv2_m3 versus 7231_ICU4_ArabidopsisPBM_20140210__rc; m=3/9; ncol2=10; w=-1; offset=-1; strand=R; shift=1; score=0.642993; -TAAThATTAc- ; cor=; Ncor= a 0 9 72 93 4 38 93 3 3 68 9 0 c 0 17 19 3 1 28 2 1 6 6 64 0 g 0 6 6 1 2 7 1 3 19 17 7 0 t 0 68 3 3 93 27 4 93 72 9 20 0

7284_YAB5_ArabidopsisPBM_20140210__shift1 (7284_YAB5_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv2_m3 versus 7284_YAB5_ArabidopsisPBM_20140210_; m=4/9; ncol2=10; w=-1; offset=-1; strand=D; shift=1; score=0.634603; -waATgAtTAh- ; cor=; Ncor= a 0 28 53 78 7 18 78 10 15 73 29 0 c 0 23 8 9 16 24 5 18 4 17 26 0 g 0 22 18 5 3 53 2 5 10 6 16 0 t 0 27 21 8 74 5 15 67 71 4 29 0

7189_AHL25_ArabidopsisPBM_20140210__shift0 (7189_AHL25_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv2_m3 versus 7189_AHL25_ArabidopsisPBM_20140210_; m=5/9; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.549813; dAwTTAAwTw-- ; cor=; Ncor= a 30 87 62 21 23 77 79 38 5 39 0 0 c 17 3 0 0 0 0 0 0 5 16 0 0 g 28 5 1 0 0 0 0 0 3 9 0 0 t 25 5 37 79 77 23 21 62 87 36 0 0

7187_AHL20_2_ArabidopsisPBM_20140210__shift4 (7187_AHL20_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv2_m3 versus 7187_AHL20_2_ArabidopsisPBM_20140210_; m=6/9; ncol2=10; w=0; offset=2; strand=D; shift=4; score=0.547395; ----hAATTAAw ; cor=; Ncor= a 0 0 0 0 28 77 75 13 24 77 84 65 c 0 0 0 0 27 7 1 0 1 0 1 1 g 0 0 0 0 9 7 1 1 1 0 0 0 t 0 0 0 0 36 9 23 86 74 23 15 34

7183_AHL12_ArabidopsisPBM_20140210__rc_shift0 (7183_AHL12_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv2_m3 versus 7183_AHL12_ArabidopsisPBM_20140210__rc; m=7/9; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.514619; wAAwwwwTTw-- ; cor=; Ncor= a 37 77 84 49 33 66 50 10 6 42 0 0 c 13 2 4 1 1 0 0 2 15 13 0 0 g 11 15 2 0 0 1 2 4 2 8 0 0 t 39 6 10 50 66 33 48 84 77 37 0 0

7205_ATHB51_ArabidopsisPBM_20140210__rc_shift0 (7205_ATHB51_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv2_m3 versus 7205_ATHB51_ArabidopsisPBM_20140210__rc; m=8/9; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.504544; kCAATwATKr-- ; cor=; Ncor= a 21 10 96 99 0 58 99 2 6 32 0 0 c 21 78 1 0 1 0 0 0 0 16 0 0 g 26 2 3 0 0 1 1 0 25 38 0 0 t 32 10 0 1 99 41 0 98 69 14 0 0

7191_AHL25_3_ArabidopsisPBM_20140210__shift0 (7191_AHL25_3_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv2_m3 versus 7191_AHL25_3_ArabidopsisPBM_20140210_; m=9/9; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.486321; waWwWwAwTw-- ; cor=; Ncor= a 37 54 74 39 29 49 83 37 8 28 0 0 c 18 9 0 1 0 0 0 1 3 9 0 0 g 16 15 1 0 0 0 1 0 6 7 0 0 t 29 22 25 60 71 51 16 62 83 56 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=2; ncol=12; --wwTAATTAww ; Alignment reference a 0 0 36 29 0 84 84 0 0 84 29 26 c 0 0 11 14 0 0 0 0 0 0 12 11 g 0 0 11 12 0 0 0 0 0 0 14 11 t 0 0 26 29 84 0 0 84 84 0 29 36
7278_WOX13_2_ArabidopsisPBM_20140210__shift2 (7278_WOX13_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv2_m3 versus 7278_WOX13_2_ArabidopsisPBM_20140210_; m=1/9; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.907285; --tttAATTaam ; cor=; Ncor= a 0 0 22 16 20 81 81 8 10 59 57 27 c 0 0 22 15 17 6 2 9 3 4 11 34 g 0 0 19 11 4 3 9 2 6 17 16 20 t 0 0 37 58 59 10 8 81 81 20 16 19
7184_AHL12_2_ArabidopsisPBM_20140210__shift2 (7184_AHL12_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv2_m3 versus 7184_AHL12_2_ArabidopsisPBM_20140210_; m=2/9; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.826396; --rwwAWWTwwT ; cor=; Ncor= a 0 0 34 56 37 79 74 25 20 59 40 5 c 0 0 9 2 2 0 0 1 1 2 2 18 g 0 0 42 2 2 1 1 0 0 2 3 3 t 0 0 15 40 59 20 25 74 79 37 55 74
7231_ICU4_ArabidopsisPBM_20140210__rc_shift1 (7231_ICU4_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv2_m3 versus 7231_ICU4_ArabidopsisPBM_20140210__rc; m=3/9; ncol2=10; w=-1; offset=-1; strand=R; shift=1; score=0.642993; -TAAThATTAc- ; cor=; Ncor= a 0 9 72 93 4 38 93 3 3 68 9 0 c 0 17 19 3 1 28 2 1 6 6 64 0 g 0 6 6 1 2 7 1 3 19 17 7 0 t 0 68 3 3 93 27 4 93 72 9 20 0
7284_YAB5_ArabidopsisPBM_20140210__shift1 (7284_YAB5_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv2_m3 versus 7284_YAB5_ArabidopsisPBM_20140210_; m=4/9; ncol2=10; w=-1; offset=-1; strand=D; shift=1; score=0.634603; -waATgAtTAh- ; cor=; Ncor= a 0 28 53 78 7 18 78 10 15 73 29 0 c 0 23 8 9 16 24 5 18 4 17 26 0 g 0 22 18 5 3 53 2 5 10 6 16 0 t 0 27 21 8 74 5 15 67 71 4 29 0
7189_AHL25_ArabidopsisPBM_20140210__shift0 (7189_AHL25_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv2_m3 versus 7189_AHL25_ArabidopsisPBM_20140210_; m=5/9; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.549813; dAwTTAAwTw-- ; cor=; Ncor= a 30 87 62 21 23 77 79 38 5 39 0 0 c 17 3 0 0 0 0 0 0 5 16 0 0 g 28 5 1 0 0 0 0 0 3 9 0 0 t 25 5 37 79 77 23 21 62 87 36 0 0
7187_AHL20_2_ArabidopsisPBM_20140210__shift4 (7187_AHL20_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv2_m3 versus 7187_AHL20_2_ArabidopsisPBM_20140210_; m=6/9; ncol2=10; w=0; offset=2; strand=D; shift=4; score=0.547395; ----hAATTAAw ; cor=; Ncor= a 0 0 0 0 28 77 75 13 24 77 84 65 c 0 0 0 0 27 7 1 0 1 0 1 1 g 0 0 0 0 9 7 1 1 1 0 0 0 t 0 0 0 0 36 9 23 86 74 23 15 34
7183_AHL12_ArabidopsisPBM_20140210__rc_shift0 (7183_AHL12_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv2_m3 versus 7183_AHL12_ArabidopsisPBM_20140210__rc; m=7/9; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.514619; wAAwwwwTTw-- ; cor=; Ncor= a 37 77 84 49 33 66 50 10 6 42 0 0 c 13 2 4 1 1 0 0 2 15 13 0 0 g 11 15 2 0 0 1 2 4 2 8 0 0 t 39 6 10 50 66 33 48 84 77 37 0 0
7205_ATHB51_ArabidopsisPBM_20140210__rc_shift0 (7205_ATHB51_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv2_m3 versus 7205_ATHB51_ArabidopsisPBM_20140210__rc; m=8/9; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.504544; kCAATwATKr-- ; cor=; Ncor= a 21 10 96 99 0 58 99 2 6 32 0 0 c 21 78 1 0 1 0 0 0 0 16 0 0 g 26 2 3 0 0 1 1 0 25 38 0 0 t 32 10 0 1 99 41 0 98 69 14 0 0
7191_AHL25_3_ArabidopsisPBM_20140210__shift0 (7191_AHL25_3_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv2_m3 versus 7191_AHL25_3_ArabidopsisPBM_20140210_; m=9/9; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.486321; waWwWwAwTw-- ; cor=; Ncor= a 37 54 74 39 29 49 83 37 8 28 0 0 c 18 9 0 1 0 0 0 1 3 9 0 0 g 16 15 1 0 0 0 1 0 6 7 0 0 t 29 22 25 60 71 51 16 62 83 56 0 0