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_m3/peak-motifs_oligos_8nt_mkv1_m3.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_m3/peak-motifs_oligos_8nt_mkv1_m3_vs_db_JASPAR2024_CORE_plants_non-redundant

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m3_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m3_shift1 (oligos_8nt_mkv1_m3)
; oligos_8nt_mkv1_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -rvCmCTATrGhT ; Alignment reference a 0 2 1 0 2 0 0 3 0 1 0 1 0 c 0 0 1 3 1 3 0 0 0 0 0 1 0 g 0 1 1 0 0 0 0 0 0 2 3 0 0 t 0 0 0 0 0 0 3 0 3 0 0 1 3

MA1368.3_shift2 (GT-4)
; oligos_8nt_mkv1_m3 versus MA1368.3 (GT-4); m=1/4; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.603419; --TAACYATGGTT ; cor=; Ncor= a 0 0 111.0 516.0 621.0 10.0 8.0 571.0 20.0 87.0 20.0 9.0 63.0 c 0 0 55.0 20.0 6.0 612.0 181.0 24.0 26.0 1.0 5.0 5.0 36.0 g 0 0 37.0 44.0 4.0 9.0 2.0 28.0 33.0 552.0 618.0 3.0 11.0 t 0 0 443.0 66.0 15.0 15.0 455.0 23.0 567.0 6.0 3.0 629.0 536.0

MA2404.1_shift1 (OsTRBF3)
; oligos_8nt_mkv1_m3 versus MA2404.1 (OsTRBF3); m=2/4; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.439256; -wrmCCTA----- ; cor=; Ncor= a 0 415.0 534.0 416.0 25.0 41.0 10.0 831.0 0 0 0 0 0 c 0 113.0 24.0 562.0 962.0 928.0 0.0 31.0 0 0 0 0 0 g 0 59.0 369.0 6.0 1.0 26.0 0.0 82.0 0 0 0 0 0 t 0 411.0 71.0 14.0 11.0 3.0 988.0 53.0 0 0 0 0 0

MA1030.2_shift1 (P0510F09.23)
; oligos_8nt_mkv1_m3 versus MA1030.2 (P0510F09.23); m=3/4; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.439233; -wrmCCTA----- ; cor=; Ncor= a 0 416.0 535.0 416.0 26.0 41.0 10.0 832.0 0 0 0 0 0 c 0 113.0 24.0 562.0 962.0 928.0 1.0 32.0 0 0 0 0 0 g 0 60.0 369.0 7.0 1.0 27.0 0.0 83.0 0 0 0 0 0 t 0 411.0 72.0 15.0 11.0 4.0 989.0 54.0 0 0 0 0 0

MA2032.2_shift0 (TRB1)
; oligos_8nt_mkv1_m3 versus MA2032.2 (TRB1); m=4/4; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.434271; aAACCCTAr---- ; cor=; Ncor= a 2956.0 4615.0 4355.0 138.0 86.0 71.0 108.0 4824.0 2829.0 0 0 0 0 c 451.0 128.0 40.0 4706.0 4755.0 4767.0 44.0 34.0 372.0 0 0 0 0 g 682.0 96.0 443.0 35.0 36.0 55.0 57.0 44.0 1303.0 0 0 0 0 t 854.0 104.0 105.0 64.0 66.0 50.0 4734.0 41.0 439.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv1_m3_shift1 (oligos_8nt_mkv1_m3)				; oligos_8nt_mkv1_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -rvCmCTATrGhT ; Alignment reference a 0 2 1 0 2 0 0 3 0 1 0 1 0 c 0 0 1 3 1 3 0 0 0 0 0 1 0 g 0 1 1 0 0 0 0 0 0 2 3 0 0 t 0 0 0 0 0 0 3 0 3 0 0 1 3
MA1368.3_shift2 (GT-4)				; oligos_8nt_mkv1_m3 versus MA1368.3 (GT-4); m=1/4; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.603419; --TAACYATGGTT ; cor=; Ncor= a 0 0 111.0 516.0 621.0 10.0 8.0 571.0 20.0 87.0 20.0 9.0 63.0 c 0 0 55.0 20.0 6.0 612.0 181.0 24.0 26.0 1.0 5.0 5.0 36.0 g 0 0 37.0 44.0 4.0 9.0 2.0 28.0 33.0 552.0 618.0 3.0 11.0 t 0 0 443.0 66.0 15.0 15.0 455.0 23.0 567.0 6.0 3.0 629.0 536.0
MA2404.1_shift1 (OsTRBF3)				; oligos_8nt_mkv1_m3 versus MA2404.1 (OsTRBF3); m=2/4; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.439256; -wrmCCTA----- ; cor=; Ncor= a 0 415.0 534.0 416.0 25.0 41.0 10.0 831.0 0 0 0 0 0 c 0 113.0 24.0 562.0 962.0 928.0 0.0 31.0 0 0 0 0 0 g 0 59.0 369.0 6.0 1.0 26.0 0.0 82.0 0 0 0 0 0 t 0 411.0 71.0 14.0 11.0 3.0 988.0 53.0 0 0 0 0 0
MA1030.2_shift1 (P0510F09.23)				; oligos_8nt_mkv1_m3 versus MA1030.2 (P0510F09.23); m=3/4; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.439233; -wrmCCTA----- ; cor=; Ncor= a 0 416.0 535.0 416.0 26.0 41.0 10.0 832.0 0 0 0 0 0 c 0 113.0 24.0 562.0 962.0 928.0 1.0 32.0 0 0 0 0 0 g 0 60.0 369.0 7.0 1.0 27.0 0.0 83.0 0 0 0 0 0 t 0 411.0 72.0 15.0 11.0 4.0 989.0 54.0 0 0 0 0 0
MA2032.2_shift0 (TRB1)				; oligos_8nt_mkv1_m3 versus MA2032.2 (TRB1); m=4/4; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.434271; aAACCCTAr---- ; cor=; Ncor= a 2956.0 4615.0 4355.0 138.0 86.0 71.0 108.0 4824.0 2829.0 0 0 0 0 c 451.0 128.0 40.0 4706.0 4755.0 4767.0 44.0 34.0 372.0 0 0 0 0 g 682.0 96.0 443.0 35.0 36.0 55.0 57.0 44.0 1303.0 0 0 0 0 t 854.0 104.0 105.0 64.0 66.0 50.0 4734.0 41.0 439.0 0 0 0 0