One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.175823_2025-05-16.175823_YJjJog/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_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/2025/05/16/peak-motifs.2025-05-16.175823_2025-05-16.175823_YJjJog/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; raATGAATGah ; Alignment reference a 33 41 100 2 2 94 100 0 10 41 31 c 17 16 1 1 5 4 5 1 10 19 29 g 35 25 3 1 99 8 3 6 79 27 20 t 24 27 5 105 3 3 1 102 10 22 29

MA1124.1_rc_shift0 (ZNF24_rc)
; oligos_6nt_mkv2_m3 versus MA1124.1_rc (ZNF24_rc); m=1/5; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.744145; GAATGAATGAA ; cor=; Ncor= a 2685.0 19146.0 19421.0 279.0 789.0 22610.0 22192.0 147.0 723.0 21867.0 19505.0 c 856.0 1045.0 811.0 589.0 93.0 182.0 128.0 501.0 118.0 461.0 739.0 g 17701.0 2128.0 2062.0 402.0 22068.0 330.0 887.0 219.0 22137.0 544.0 2102.0 t 2062.0 985.0 1010.0 22034.0 354.0 182.0 97.0 22437.0 326.0 432.0 958.0

MA0601.2_shift1 (Arid3b)
; oligos_6nt_mkv2_m3 versus MA0601.2 (Arid3b); m=2/5; ncol2=7; w=0; offset=1; strand=D; shift=1; score=0.449203; -waTTAAT--- ; cor=; Ncor= a 0 273.0 609.0 104.0 0.0 1000.0 911.0 89.0 0 0 0 c 0 80.0 119.0 0.0 0.0 0.0 0.0 0.0 0 0 0 g 0 80.0 34.0 0.0 0.0 0.0 0.0 0.0 0 0 0 t 0 566.0 238.0 895.0 1000.0 0.0 89.0 911.0 0 0 0

MA1499.2_rc_shift0 (HOXB4_rc)
; oligos_6nt_mkv2_m3 versus MA1499.2_rc (HOXB4_rc); m=3/5; ncol2=6; w=0; offset=0; strand=R; shift=0; score=0.41158; TAATkA----- ; cor=; Ncor= a 0.0 9080.0 9080.0 0.0 0.0 9080.0 0 0 0 0 0 c 55.0 271.0 0.0 265.0 0.0 0.0 0 0 0 0 0 g 0.0 0.0 0.0 0.0 5459.0 2103.0 0 0 0 0 0 t 9080.0 0.0 0.0 9080.0 3621.0 0.0 0 0 0 0 0

MA1504.2_rc_shift0 (HOXC4_rc)
; oligos_6nt_mkv2_m3 versus MA1504.2_rc (HOXC4_rc); m=4/5; ncol2=6; w=0; offset=0; strand=R; shift=0; score=0.405742; TAATkR----- ; cor=; Ncor= a 0.0 8759.0 8759.0 0.0 0.0 8759.0 0 0 0 0 0 c 825.0 0.0 0.0 583.0 0.0 0.0 0 0 0 0 0 g 0.0 0.0 0.0 0.0 5152.0 3111.0 0 0 0 0 0 t 8759.0 0.0 0.0 8759.0 3607.0 188.0 0 0 0 0 0

MA1114.2_shift3 (PBX3)
; oligos_6nt_mkv2_m3 versus MA1114.2 (PBX3); m=5/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.402183; ---TGAGTGAC ; cor=; Ncor= a 0 0 0 596.0 228.0 6426.0 335.0 247.0 146.0 6164.0 150.0 c 0 0 0 225.0 227.0 125.0 788.0 199.0 242.0 108.0 6524.0 g 0 0 0 503.0 6406.0 214.0 4929.0 285.0 6550.0 604.0 209.0 t 0 0 0 5697.0 160.0 256.0 969.0 6290.0 83.0 145.0 138.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; raATGAATGah ; Alignment reference a 33 41 100 2 2 94 100 0 10 41 31 c 17 16 1 1 5 4 5 1 10 19 29 g 35 25 3 1 99 8 3 6 79 27 20 t 24 27 5 105 3 3 1 102 10 22 29
MA1124.1_rc_shift0 (ZNF24_rc)				; oligos_6nt_mkv2_m3 versus MA1124.1_rc (ZNF24_rc); m=1/5; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.744145; GAATGAATGAA ; cor=; Ncor= a 2685.0 19146.0 19421.0 279.0 789.0 22610.0 22192.0 147.0 723.0 21867.0 19505.0 c 856.0 1045.0 811.0 589.0 93.0 182.0 128.0 501.0 118.0 461.0 739.0 g 17701.0 2128.0 2062.0 402.0 22068.0 330.0 887.0 219.0 22137.0 544.0 2102.0 t 2062.0 985.0 1010.0 22034.0 354.0 182.0 97.0 22437.0 326.0 432.0 958.0
MA0601.2_shift1 (Arid3b)				; oligos_6nt_mkv2_m3 versus MA0601.2 (Arid3b); m=2/5; ncol2=7; w=0; offset=1; strand=D; shift=1; score=0.449203; -waTTAAT--- ; cor=; Ncor= a 0 273.0 609.0 104.0 0.0 1000.0 911.0 89.0 0 0 0 c 0 80.0 119.0 0.0 0.0 0.0 0.0 0.0 0 0 0 g 0 80.0 34.0 0.0 0.0 0.0 0.0 0.0 0 0 0 t 0 566.0 238.0 895.0 1000.0 0.0 89.0 911.0 0 0 0
MA1499.2_rc_shift0 (HOXB4_rc)				; oligos_6nt_mkv2_m3 versus MA1499.2_rc (HOXB4_rc); m=3/5; ncol2=6; w=0; offset=0; strand=R; shift=0; score=0.41158; TAATkA----- ; cor=; Ncor= a 0.0 9080.0 9080.0 0.0 0.0 9080.0 0 0 0 0 0 c 55.0 271.0 0.0 265.0 0.0 0.0 0 0 0 0 0 g 0.0 0.0 0.0 0.0 5459.0 2103.0 0 0 0 0 0 t 9080.0 0.0 0.0 9080.0 3621.0 0.0 0 0 0 0 0
MA1504.2_rc_shift0 (HOXC4_rc)				; oligos_6nt_mkv2_m3 versus MA1504.2_rc (HOXC4_rc); m=4/5; ncol2=6; w=0; offset=0; strand=R; shift=0; score=0.405742; TAATkR----- ; cor=; Ncor= a 0.0 8759.0 8759.0 0.0 0.0 8759.0 0 0 0 0 0 c 825.0 0.0 0.0 583.0 0.0 0.0 0 0 0 0 0 g 0.0 0.0 0.0 0.0 5152.0 3111.0 0 0 0 0 0 t 8759.0 0.0 0.0 8759.0 3607.0 188.0 0 0 0 0 0
MA1114.2_shift3 (PBX3)				; oligos_6nt_mkv2_m3 versus MA1114.2 (PBX3); m=5/5; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.402183; ---TGAGTGAC ; cor=; Ncor= a 0 0 0 596.0 228.0 6426.0 335.0 247.0 146.0 6164.0 150.0 c 0 0 0 225.0 227.0 125.0 788.0 199.0 242.0 108.0 6524.0 g 0 0 0 503.0 6406.0 214.0 4929.0 285.0 6550.0 604.0 209.0 t 0 0 0 5697.0 160.0 256.0 969.0 6290.0 83.0 145.0 138.0