One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_non-redundant_pfms_transfac.txt -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/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4_vs_db_JASPAR2024_CORE_plants_non-redundant

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m4_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m4_shift0 (oligos_8nt_mkv1_m4)
; oligos_8nt_mkv1_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; wAAAAGCTCCTry ; Alignment reference a 1 2 2 2 2 0 0 0 0 0 0 1 0 c 0 0 0 0 0 0 2 0 2 2 0 0 1 g 0 0 0 0 0 2 0 0 0 0 0 1 0 t 1 0 0 0 0 0 0 2 0 0 2 0 1

MA1747.2_rc_shift1 (DOF4.3_rc)
; oligos_8nt_mkv1_m4 versus MA1747.2_rc (DOF4.3_rc); m=1/7; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.61216; -wAAAGcywCTTT ; cor=; Ncor= a 0 424.0 998.0 998.0 995.0 2.0 95.0 76.0 429.0 0.0 0.0 0.0 0.0 c 0 103.0 0.0 0.0 0.0 0.0 571.0 345.0 91.0 1000.0 0.0 0.0 0.0 g 0 66.0 2.0 0.0 5.0 995.0 147.0 2.0 178.0 0.0 0.0 0.0 0.0 t 0 407.0 0.0 2.0 0.0 3.0 188.0 578.0 302.0 0.0 1000.0 1000.0 1000.0

MA2029.2_shift3 (MYB88)
; oligos_8nt_mkv1_m4 versus MA2029.2 (MYB88); m=2/7; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.508175; ---ACGCTCCTC- ; cor=; Ncor= a 0 0 0 150.0 3.0 1.0 0.0 1.0 1.0 0.0 18.0 7.0 0 c 0 0 0 15.0 159.0 1.0 167.0 1.0 165.0 152.0 6.0 138.0 0 g 0 0 0 3.0 6.0 165.0 1.0 27.0 2.0 3.0 3.0 6.0 0 t 0 0 0 0.0 0.0 1.0 0.0 139.0 0.0 13.0 141.0 17.0 0

MA0973.2_shift0 (CDF2)
; oligos_8nt_mkv1_m4 versus MA0973.2 (CDF2); m=3/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.471427; aWAAAGy------ ; cor=; Ncor= a 608.0 693.0 980.0 979.0 868.0 17.0 53.0 0 0 0 0 0 0 c 92.0 16.0 10.0 10.0 29.0 7.0 295.0 0 0 0 0 0 0 g 150.0 41.0 4.0 2.0 81.0 969.0 154.0 0 0 0 0 0 0 t 150.0 250.0 5.0 9.0 22.0 6.0 498.0 0 0 0 0 0 0

MA1815.2_rc_shift5 (GRF4_rc)
; oligos_8nt_mkv1_m4 versus MA1815.2_rc (GRF4_rc); m=4/7; ncol2=8; w=0; offset=5; strand=R; shift=5; score=0.441764; -----GCTGCTGC ; cor=; Ncor= a 0 0 0 0 0 0.0 1.0 10.0 2.0 1.0 3.0 0.0 3.0 c 0 0 0 0 0 4.0 59.0 0.0 0.0 61.0 5.0 3.0 54.0 g 0 0 0 0 0 59.0 3.0 2.0 60.0 1.0 1.0 59.0 1.0 t 0 0 0 0 0 2.0 2.0 53.0 3.0 2.0 56.0 3.0 7.0

MA1272.3_shift0 (DOF2.2)
; oligos_8nt_mkv1_m4 versus MA1272.3 (DOF2.2); m=5/7; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.435014; AAAAAG------- ; cor=; Ncor= a 1086.0 1077.0 1086.0 1084.0 1086.0 0.0 0 0 0 0 0 0 0 c 0.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 g 0.0 0.0 0.0 0.0 0.0 1086.0 0 0 0 0 0 0 0 t 0.0 9.0 0.0 2.0 0.0 0.0 0 0 0 0 0 0 0

MA1280.2_shift0 (DOF5.4)
; oligos_8nt_mkv1_m4 versus MA1280.2 (DOF5.4); m=6/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.430692; AAAAAGk------ ; cor=; Ncor= a 529.0 456.0 599.0 600.0 600.0 0.0 22.0 0 0 0 0 0 0 c 17.0 0.0 0.0 0.0 0.0 0.0 37.0 0 0 0 0 0 0 g 34.0 3.0 0.0 0.0 0.0 600.0 209.0 0 0 0 0 0 0 t 20.0 141.0 1.0 0.0 0.0 0.0 332.0 0 0 0 0 0 0

MA1276.2_shift0 (DOF3.5)
; oligos_8nt_mkv1_m4 versus MA1276.2 (DOF3.5); m=7/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.405671; AwAAAGk------ ; cor=; Ncor= a 467.0 348.0 599.0 599.0 599.0 0.0 2.0 0 0 0 0 0 0 c 4.0 0.0 0.0 0.0 0.0 0.0 6.0 0 0 0 0 0 0 g 103.0 0.0 0.0 0.0 0.0 599.0 219.0 0 0 0 0 0 0 t 25.0 251.0 0.0 0.0 0.0 0.0 372.0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv1_m4_shift0 (oligos_8nt_mkv1_m4)				; oligos_8nt_mkv1_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; wAAAAGCTCCTry ; Alignment reference a 1 2 2 2 2 0 0 0 0 0 0 1 0 c 0 0 0 0 0 0 2 0 2 2 0 0 1 g 0 0 0 0 0 2 0 0 0 0 0 1 0 t 1 0 0 0 0 0 0 2 0 0 2 0 1
MA1747.2_rc_shift1 (DOF4.3_rc)				; oligos_8nt_mkv1_m4 versus MA1747.2_rc (DOF4.3_rc); m=1/7; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.61216; -wAAAGcywCTTT ; cor=; Ncor= a 0 424.0 998.0 998.0 995.0 2.0 95.0 76.0 429.0 0.0 0.0 0.0 0.0 c 0 103.0 0.0 0.0 0.0 0.0 571.0 345.0 91.0 1000.0 0.0 0.0 0.0 g 0 66.0 2.0 0.0 5.0 995.0 147.0 2.0 178.0 0.0 0.0 0.0 0.0 t 0 407.0 0.0 2.0 0.0 3.0 188.0 578.0 302.0 0.0 1000.0 1000.0 1000.0
MA2029.2_shift3 (MYB88)				; oligos_8nt_mkv1_m4 versus MA2029.2 (MYB88); m=2/7; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.508175; ---ACGCTCCTC- ; cor=; Ncor= a 0 0 0 150.0 3.0 1.0 0.0 1.0 1.0 0.0 18.0 7.0 0 c 0 0 0 15.0 159.0 1.0 167.0 1.0 165.0 152.0 6.0 138.0 0 g 0 0 0 3.0 6.0 165.0 1.0 27.0 2.0 3.0 3.0 6.0 0 t 0 0 0 0.0 0.0 1.0 0.0 139.0 0.0 13.0 141.0 17.0 0
MA0973.2_shift0 (CDF2)				; oligos_8nt_mkv1_m4 versus MA0973.2 (CDF2); m=3/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.471427; aWAAAGy------ ; cor=; Ncor= a 608.0 693.0 980.0 979.0 868.0 17.0 53.0 0 0 0 0 0 0 c 92.0 16.0 10.0 10.0 29.0 7.0 295.0 0 0 0 0 0 0 g 150.0 41.0 4.0 2.0 81.0 969.0 154.0 0 0 0 0 0 0 t 150.0 250.0 5.0 9.0 22.0 6.0 498.0 0 0 0 0 0 0
MA1815.2_rc_shift5 (GRF4_rc)				; oligos_8nt_mkv1_m4 versus MA1815.2_rc (GRF4_rc); m=4/7; ncol2=8; w=0; offset=5; strand=R; shift=5; score=0.441764; -----GCTGCTGC ; cor=; Ncor= a 0 0 0 0 0 0.0 1.0 10.0 2.0 1.0 3.0 0.0 3.0 c 0 0 0 0 0 4.0 59.0 0.0 0.0 61.0 5.0 3.0 54.0 g 0 0 0 0 0 59.0 3.0 2.0 60.0 1.0 1.0 59.0 1.0 t 0 0 0 0 0 2.0 2.0 53.0 3.0 2.0 56.0 3.0 7.0
MA1272.3_shift0 (DOF2.2)				; oligos_8nt_mkv1_m4 versus MA1272.3 (DOF2.2); m=5/7; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.435014; AAAAAG------- ; cor=; Ncor= a 1086.0 1077.0 1086.0 1084.0 1086.0 0.0 0 0 0 0 0 0 0 c 0.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 g 0.0 0.0 0.0 0.0 0.0 1086.0 0 0 0 0 0 0 0 t 0.0 9.0 0.0 2.0 0.0 0.0 0 0 0 0 0 0 0
MA1280.2_shift0 (DOF5.4)				; oligos_8nt_mkv1_m4 versus MA1280.2 (DOF5.4); m=6/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.430692; AAAAAGk------ ; cor=; Ncor= a 529.0 456.0 599.0 600.0 600.0 0.0 22.0 0 0 0 0 0 0 c 17.0 0.0 0.0 0.0 0.0 0.0 37.0 0 0 0 0 0 0 g 34.0 3.0 0.0 0.0 0.0 600.0 209.0 0 0 0 0 0 0 t 20.0 141.0 1.0 0.0 0.0 0.0 332.0 0 0 0 0 0 0
MA1276.2_shift0 (DOF3.5)				; oligos_8nt_mkv1_m4 versus MA1276.2 (DOF3.5); m=7/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.405671; AwAAAGk------ ; cor=; Ncor= a 467.0 348.0 599.0 599.0 599.0 0.0 2.0 0 0 0 0 0 0 c 4.0 0.0 0.0 0.0 0.0 0.0 6.0 0 0 0 0 0 0 g 103.0 0.0 0.0 0.0 0.0 599.0 219.0 0 0 0 0 0 0 t 25.0 251.0 0.0 0.0 0.0 0.0 372.0 0 0 0 0 0 0