One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.052000_2026-01-05.052000_2qIqyX/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_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/2026/01/05/peak-motifs.2026-01-05.052000_2026-01-05.052000_2qIqyX/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift8 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift8 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=8; ncol=20; --------yrGACAAGTCyv ; Alignment reference a 0 0 0 0 0 0 0 0 97 172 26 353 7 433 316 4 8 10 97 119 c 0 0 0 0 0 0 0 0 148 38 19 14 429 6 22 1 40 415 182 126 g 0 0 0 0 0 0 0 0 75 177 389 79 11 9 8 442 12 7 27 132 t 0 0 0 0 0 0 0 0 131 64 17 5 4 3 105 4 391 19 145 74

MA0844.2_shift10 (XBP1)
; oligos_7nt_mkv4_m3 versus MA0844.2 (XBP1); m=1/5; ncol2=11; w=0; offset=2; strand=D; shift=10; score=0.547156; ----------GmCACGTCAk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 974.0 3699.0 167.0 7840.0 9.0 52.0 0.0 380.0 8004.0 230.0 c 0 0 0 0 0 0 0 0 0 0 367.0 3809.0 7169.0 17.0 7356.0 0.0 16.0 7264.0 48.0 2273.0 g 0 0 0 0 0 0 0 0 0 0 9168.0 59.0 222.0 276.0 2.0 11353.0 8.0 47.0 173.0 3157.0 t 0 0 0 0 0 0 0 0 0 0 2321.0 247.0 442.0 118.0 10.0 10.0 9107.0 35.0 92.0 6389.0

MA0775.2_shift8 (MEIS3)
; oligos_7nt_mkv4_m3 versus MA0775.2 (MEIS3); m=2/5; ncol2=7; w=0; offset=0; strand=D; shift=8; score=0.431482; --------wTGACAg----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1866.0 465.0 0.0 7165.0 53.0 7165.0 1690.0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 60.0 383.0 6.0 20.0 7165.0 8.0 1889.0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1788.0 260.0 7165.0 455.0 8.0 468.0 7165.0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 3451.0 7165.0 0.0 53.0 160.0 145.0 2094.0 0 0 0 0 0

MA0861.2_shift11 (TP73)
; oligos_7nt_mkv4_m3 versus MA0861.2 (TP73); m=3/5; ncol2=16; w=0; offset=3; strand=D; shift=11; score=0.430271; -----------rCATGTcyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 6206.0 0.0 8760.0 3837.0 8.0 130.0 1377.0 2166.0 3488.0 c 0 0 0 0 0 0 0 0 0 0 0 429.0 10829.0 124.0 293.0 28.0 2591.0 8161.0 2940.0 2418.0 g 0 0 0 0 0 0 0 0 0 0 0 3304.0 0.0 557.0 806.0 11787.0 91.0 783.0 2230.0 3558.0 t 0 0 0 0 0 0 0 0 0 0 0 208.0 0.0 198.0 11480.0 1.0 11892.0 2749.0 4242.0 2457.0

MA0525.2_rc_shift10 (TP63_rc)
; oligos_7nt_mkv4_m3 versus MA0525.2_rc (TP63_rc); m=4/5; ncol2=18; w=0; offset=2; strand=R; shift=10; score=0.414371; ----------gACATGTymc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 606.0 3126.0 0.0 2823.0 192.0 0.0 45.0 47.0 829.0 13.0 c 0 0 0 0 0 0 0 0 0 0 198.0 1.0 3532.0 8.0 1.0 0.0 48.0 2132.0 1656.0 2070.0 g 0 0 0 0 0 0 0 0 0 0 2099.0 202.0 0.0 617.0 0.0 2788.0 0.0 1.0 681.0 478.0 t 0 0 0 0 0 0 0 0 0 0 701.0 49.0 0.0 75.0 2151.0 0.0 2192.0 993.0 112.0 649.0

MA0106.3_shift0 (TP53)
; oligos_7nt_mkv4_m3 versus MA0106.3 (TP53); m=5/5; ncol2=18; w=-8; offset=-8; strand=D; shift=0; score=0.40136; rACATGyCcgGrCATGTy-- ; cor=; Ncor= a 7544.0 10514.0 45.0 11931.0 1710.0 8.0 244.0 1228.0 1145.0 3851.0 3584.0 7104.0 0.0 12925.0 1825.0 327.0 879.0 1472.0 0 0 c 1037.0 116.0 19689.0 204.0 374.0 2.0 12014.0 17286.0 11875.0 1474.0 756.0 26.0 19350.0 250.0 118.0 33.0 3338.0 9183.0 0 0 g 6563.0 2433.0 13.0 653.0 137.0 20393.0 109.0 417.0 2151.0 9954.0 17846.0 8821.0 4.0 157.0 89.0 20549.0 116.0 825.0 0 0 t 2268.0 735.0 837.0 739.0 18893.0 0.0 7106.0 2642.0 3774.0 2118.0 1546.0 190.0 1.0 1155.0 17864.0 68.0 17859.0 9120.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift8 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=8; ncol=20; --------yrGACAAGTCyv ; Alignment reference a 0 0 0 0 0 0 0 0 97 172 26 353 7 433 316 4 8 10 97 119 c 0 0 0 0 0 0 0 0 148 38 19 14 429 6 22 1 40 415 182 126 g 0 0 0 0 0 0 0 0 75 177 389 79 11 9 8 442 12 7 27 132 t 0 0 0 0 0 0 0 0 131 64 17 5 4 3 105 4 391 19 145 74
MA0844.2_shift10 (XBP1)				; oligos_7nt_mkv4_m3 versus MA0844.2 (XBP1); m=1/5; ncol2=11; w=0; offset=2; strand=D; shift=10; score=0.547156; ----------GmCACGTCAk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 974.0 3699.0 167.0 7840.0 9.0 52.0 0.0 380.0 8004.0 230.0 c 0 0 0 0 0 0 0 0 0 0 367.0 3809.0 7169.0 17.0 7356.0 0.0 16.0 7264.0 48.0 2273.0 g 0 0 0 0 0 0 0 0 0 0 9168.0 59.0 222.0 276.0 2.0 11353.0 8.0 47.0 173.0 3157.0 t 0 0 0 0 0 0 0 0 0 0 2321.0 247.0 442.0 118.0 10.0 10.0 9107.0 35.0 92.0 6389.0
MA0775.2_shift8 (MEIS3)				; oligos_7nt_mkv4_m3 versus MA0775.2 (MEIS3); m=2/5; ncol2=7; w=0; offset=0; strand=D; shift=8; score=0.431482; --------wTGACAg----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1866.0 465.0 0.0 7165.0 53.0 7165.0 1690.0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 60.0 383.0 6.0 20.0 7165.0 8.0 1889.0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1788.0 260.0 7165.0 455.0 8.0 468.0 7165.0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 3451.0 7165.0 0.0 53.0 160.0 145.0 2094.0 0 0 0 0 0
MA0861.2_shift11 (TP73)				; oligos_7nt_mkv4_m3 versus MA0861.2 (TP73); m=3/5; ncol2=16; w=0; offset=3; strand=D; shift=11; score=0.430271; -----------rCATGTcyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 6206.0 0.0 8760.0 3837.0 8.0 130.0 1377.0 2166.0 3488.0 c 0 0 0 0 0 0 0 0 0 0 0 429.0 10829.0 124.0 293.0 28.0 2591.0 8161.0 2940.0 2418.0 g 0 0 0 0 0 0 0 0 0 0 0 3304.0 0.0 557.0 806.0 11787.0 91.0 783.0 2230.0 3558.0 t 0 0 0 0 0 0 0 0 0 0 0 208.0 0.0 198.0 11480.0 1.0 11892.0 2749.0 4242.0 2457.0
MA0525.2_rc_shift10 (TP63_rc)				; oligos_7nt_mkv4_m3 versus MA0525.2_rc (TP63_rc); m=4/5; ncol2=18; w=0; offset=2; strand=R; shift=10; score=0.414371; ----------gACATGTymc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 606.0 3126.0 0.0 2823.0 192.0 0.0 45.0 47.0 829.0 13.0 c 0 0 0 0 0 0 0 0 0 0 198.0 1.0 3532.0 8.0 1.0 0.0 48.0 2132.0 1656.0 2070.0 g 0 0 0 0 0 0 0 0 0 0 2099.0 202.0 0.0 617.0 0.0 2788.0 0.0 1.0 681.0 478.0 t 0 0 0 0 0 0 0 0 0 0 701.0 49.0 0.0 75.0 2151.0 0.0 2192.0 993.0 112.0 649.0
MA0106.3_shift0 (TP53)				; oligos_7nt_mkv4_m3 versus MA0106.3 (TP53); m=5/5; ncol2=18; w=-8; offset=-8; strand=D; shift=0; score=0.40136; rACATGyCcgGrCATGTy-- ; cor=; Ncor= a 7544.0 10514.0 45.0 11931.0 1710.0 8.0 244.0 1228.0 1145.0 3851.0 3584.0 7104.0 0.0 12925.0 1825.0 327.0 879.0 1472.0 0 0 c 1037.0 116.0 19689.0 204.0 374.0 2.0 12014.0 17286.0 11875.0 1474.0 756.0 26.0 19350.0 250.0 118.0 33.0 3338.0 9183.0 0 0 g 6563.0 2433.0 13.0 653.0 137.0 20393.0 109.0 417.0 2151.0 9954.0 17846.0 8821.0 4.0 157.0 89.0 20549.0 116.0 825.0 0 0 t 2268.0 735.0 837.0 739.0 18893.0 0.0 7106.0 2642.0 3774.0 2118.0 1546.0 190.0 1.0 1155.0 17864.0 68.0 17859.0 9120.0 0 0