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_6nt_mkv1_m1/peak-motifs_oligos_6nt_mkv1_m1.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_6nt_mkv1_m1/peak-motifs_oligos_6nt_mkv1_m1_vs_db_JASPAR2024_CORE_plants_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --swAGTGmArw ; Alignment reference a 0 0 1 3 6 0 0 0 2 6 3 3 c 0 0 2 0 0 0 0 0 4 0 0 1 g 0 0 3 1 0 6 0 6 0 0 2 0 t 0 0 0 2 0 0 6 0 0 0 1 2

MA2420.1_shift3 (SBP6)
; oligos_6nt_mkv1_m1 versus MA2420.1 (SBP6); m=1/6; ncol2=8; w=0; offset=1; strand=D; shift=3; score=0.567971; ---AAGTACAA- ; cor=; Ncor= a 0 0 0 11102.0 11189.0 127.0 121.0 12984.0 132.0 12012.0 10537.0 0 c 0 0 0 376.0 290.0 62.0 55.0 51.0 12922.0 339.0 891.0 0 g 0 0 0 1080.0 1425.0 12390.0 479.0 66.0 42.0 330.0 490.0 0 t 0 0 0 607.0 261.0 586.0 12510.0 64.0 69.0 484.0 1247.0 0

MA1381.2_rc_shift2 (AT3G46070_rc)
; oligos_6nt_mkv1_m1 versus MA1381.2_rc (AT3G46070_rc); m=2/6; ncol2=7; w=0; offset=0; strand=R; shift=2; score=0.553548; --agAGTGA--- ; cor=; Ncor= a 0 0 106.0 35.0 202.0 0.0 2.0 0.0 193.0 0 0 0 c 0 0 10.0 22.0 0.0 0.0 0.0 0.0 0.0 0 0 0 g 0 0 44.0 131.0 0.0 200.0 0.0 202.0 0.0 0 0 0 t 0 0 42.0 14.0 0.0 2.0 200.0 0.0 9.0 0 0 0

MA1372.2_rc_shift4 (ZAT10_rc)
; oligos_6nt_mkv1_m1 versus MA1372.2_rc (ZAT10_rc); m=3/6; ncol2=10; w=0; offset=2; strand=R; shift=4; score=0.481435; ----ASTGddas ; cor=; Ncor= a 0 0 0 0 557.0 0.0 0.0 114.0 285.0 159.0 366.0 84.0 c 0 0 0 0 0.0 156.0 0.0 0.0 1.0 128.0 0.0 157.0 g 0 0 0 0 13.0 444.0 0.0 486.0 153.0 155.0 102.0 325.0 t 0 0 0 0 30.0 0.0 600.0 0.0 161.0 158.0 132.0 34.0

MA2372.1_rc_shift0 (AZF1_rc)
; oligos_6nt_mkv1_m1 versus MA2372.1_rc (AZF1_rc); m=4/6; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.456797; wGwsAGTGw--- ; cor=; Ncor= a 350.0 142.0 412.0 104.0 998.0 0.0 0.0 11.0 468.0 0 0 0 c 21.0 33.0 65.0 270.0 0.0 119.0 0.0 0.0 0.0 0 0 0 g 130.0 703.0 83.0 377.0 1.0 880.0 0.0 988.0 109.0 0 0 0 t 496.0 120.0 437.0 248.0 0.0 0.0 1000.0 0.0 422.0 0 0 0

MA1736.2_rc_shift4 (AT5G04390_rc)
; oligos_6nt_mkv1_m1 versus MA1736.2_rc (AT5G04390_rc); m=5/6; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.453164; ----AGTGw--- ; cor=; Ncor= a 0 0 0 0 1000.0 0.0 0.0 15.0 559.0 0 0 0 c 0 0 0 0 0.0 37.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0.0 963.0 0.0 985.0 170.0 0 0 0 t 0 0 0 0 0.0 0.0 1000.0 0.0 270.0 0 0 0

MA0974.3_shift0 (CDF3)
; oligos_6nt_mkv1_m1 versus MA0974.3 (CDF3); m=6/6; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.40469; AAAAAGTG---- ; cor=; Ncor= a 879.0 964.0 1143.0 1133.0 1125.0 1.0 29.0 86.0 0 0 0 0 c 63.0 24.0 2.0 4.0 3.0 0.0 44.0 7.0 0 0 0 0 g 79.0 29.0 7.0 11.0 19.0 1154.0 37.0 1038.0 0 0 0 0 t 136.0 140.0 5.0 9.0 10.0 2.0 1047.0 26.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --swAGTGmArw ; Alignment reference a 0 0 1 3 6 0 0 0 2 6 3 3 c 0 0 2 0 0 0 0 0 4 0 0 1 g 0 0 3 1 0 6 0 6 0 0 2 0 t 0 0 0 2 0 0 6 0 0 0 1 2
MA2420.1_shift3 (SBP6)				; oligos_6nt_mkv1_m1 versus MA2420.1 (SBP6); m=1/6; ncol2=8; w=0; offset=1; strand=D; shift=3; score=0.567971; ---AAGTACAA- ; cor=; Ncor= a 0 0 0 11102.0 11189.0 127.0 121.0 12984.0 132.0 12012.0 10537.0 0 c 0 0 0 376.0 290.0 62.0 55.0 51.0 12922.0 339.0 891.0 0 g 0 0 0 1080.0 1425.0 12390.0 479.0 66.0 42.0 330.0 490.0 0 t 0 0 0 607.0 261.0 586.0 12510.0 64.0 69.0 484.0 1247.0 0
MA1381.2_rc_shift2 (AT3G46070_rc)				; oligos_6nt_mkv1_m1 versus MA1381.2_rc (AT3G46070_rc); m=2/6; ncol2=7; w=0; offset=0; strand=R; shift=2; score=0.553548; --agAGTGA--- ; cor=; Ncor= a 0 0 106.0 35.0 202.0 0.0 2.0 0.0 193.0 0 0 0 c 0 0 10.0 22.0 0.0 0.0 0.0 0.0 0.0 0 0 0 g 0 0 44.0 131.0 0.0 200.0 0.0 202.0 0.0 0 0 0 t 0 0 42.0 14.0 0.0 2.0 200.0 0.0 9.0 0 0 0
MA1372.2_rc_shift4 (ZAT10_rc)				; oligos_6nt_mkv1_m1 versus MA1372.2_rc (ZAT10_rc); m=3/6; ncol2=10; w=0; offset=2; strand=R; shift=4; score=0.481435; ----ASTGddas ; cor=; Ncor= a 0 0 0 0 557.0 0.0 0.0 114.0 285.0 159.0 366.0 84.0 c 0 0 0 0 0.0 156.0 0.0 0.0 1.0 128.0 0.0 157.0 g 0 0 0 0 13.0 444.0 0.0 486.0 153.0 155.0 102.0 325.0 t 0 0 0 0 30.0 0.0 600.0 0.0 161.0 158.0 132.0 34.0
MA2372.1_rc_shift0 (AZF1_rc)				; oligos_6nt_mkv1_m1 versus MA2372.1_rc (AZF1_rc); m=4/6; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.456797; wGwsAGTGw--- ; cor=; Ncor= a 350.0 142.0 412.0 104.0 998.0 0.0 0.0 11.0 468.0 0 0 0 c 21.0 33.0 65.0 270.0 0.0 119.0 0.0 0.0 0.0 0 0 0 g 130.0 703.0 83.0 377.0 1.0 880.0 0.0 988.0 109.0 0 0 0 t 496.0 120.0 437.0 248.0 0.0 0.0 1000.0 0.0 422.0 0 0 0
MA1736.2_rc_shift4 (AT5G04390_rc)				; oligos_6nt_mkv1_m1 versus MA1736.2_rc (AT5G04390_rc); m=5/6; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.453164; ----AGTGw--- ; cor=; Ncor= a 0 0 0 0 1000.0 0.0 0.0 15.0 559.0 0 0 0 c 0 0 0 0 0.0 37.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0.0 963.0 0.0 985.0 170.0 0 0 0 t 0 0 0 0 0.0 0.0 1000.0 0.0 270.0 0 0 0
MA0974.3_shift0 (CDF3)				; oligos_6nt_mkv1_m1 versus MA0974.3 (CDF3); m=6/6; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.40469; AAAAAGTG---- ; cor=; Ncor= a 879.0 964.0 1143.0 1133.0 1125.0 1.0 29.0 86.0 0 0 0 0 c 63.0 24.0 2.0 4.0 3.0 0.0 44.0 7.0 0 0 0 0 g 79.0 29.0 7.0 11.0 19.0 1154.0 37.0 1038.0 0 0 0 0 t 136.0 140.0 5.0 9.0 10.0 2.0 1047.0 26.0 0 0 0 0