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.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2.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.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift3 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=13; shift=3; ncol=16; ---wwATAAATGTGww ; Alignment reference a 0 0 0 1289 1007 3008 196 3096 2600 3104 126 363 205 349 986 1126 c 0 0 0 501 644 88 130 63 177 91 196 87 103 105 514 639 g 0 0 0 670 588 167 233 152 90 105 90 2819 82 2747 585 764 t 0 0 0 949 1170 146 2850 98 542 109 2997 140 3019 208 1324 880

MA1978.2_shift0 (ZNF354A)
; oligos_6nt_test_vs_ctrl_m2 versus MA1978.2 (ZNF354A); m=1/11; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.486706; wAAwtrTAAAtGrayw ; cor=; Ncor= a 277.0 736.0 682.0 385.0 223.0 574.0 115.0 845.0 845.0 791.0 196.0 115.0 304.0 466.0 142.0 277.0 c 115.0 88.0 142.0 142.0 196.0 88.0 115.0 7.0 34.0 88.0 34.0 34.0 115.0 196.0 520.0 142.0 g 61.0 7.0 34.0 196.0 142.0 277.0 34.0 115.0 61.0 61.0 196.0 845.0 466.0 196.0 34.0 142.0 t 547.0 169.0 142.0 277.0 439.0 61.0 736.0 34.0 61.0 61.0 574.0 7.0 115.0 142.0 304.0 439.0

MA2124.1_rc_shift3 (Hmga1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus MA2124.1_rc (Hmga1_rc); m=2/11; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.462217; ---wTAAAAAT----- ; cor=; Ncor= a 0 0 0 11340.0 542.0 24333.0 24654.0 24779.0 24269.0 24172.0 496.0 0 0 0 0 0 c 0 0 0 2438.0 358.0 294.0 237.0 138.0 303.0 421.0 188.0 0 0 0 0 0 g 0 0 0 2348.0 473.0 409.0 264.0 194.0 200.0 393.0 71.0 0 0 0 0 0 t 0 0 0 9680.0 24433.0 770.0 651.0 695.0 1034.0 820.0 25051.0 0 0 0 0 0

MA0108.3_shift4 (TBP)
; oligos_6nt_test_vs_ctrl_m2 versus MA0108.3 (TBP); m=3/11; ncol2=7; w=0; offset=1; strand=D; shift=4; score=0.457341; ----TATAWAw----- ; cor=; Ncor= a 0 0 0 0 16.0 352.0 3.0 354.0 268.0 360.0 222.0 0 0 0 0 0 c 0 0 0 0 46.0 0.0 10.0 0.0 0.0 3.0 2.0 0 0 0 0 0 g 0 0 0 0 18.0 2.0 2.0 5.0 0.0 20.0 44.0 0 0 0 0 0 t 0 0 0 0 309.0 35.0 374.0 30.0 121.0 6.0 121.0 0 0 0 0 0

MA1473.2_shift2 (CDX4)
; oligos_6nt_test_vs_ctrl_m2 versus MA1473.2 (CDX4); m=4/11; ncol2=9; w=-1; offset=-1; strand=D; shift=2; score=0.443485; --GymATAAAa----- ; cor=; Ncor= a 0 0 2533.0 0.0 12392.0 23367.0 0.0 23367.0 23367.0 23367.0 23367.0 0 0 0 0 0 c 0 0 1064.0 14682.0 10976.0 0.0 0.0 0.0 0.0 57.0 6493.0 0 0 0 0 0 g 0 0 23367.0 0.0 25.0 0.0 0.0 0.0 0.0 0.0 2168.0 0 0 0 0 0 t 0 0 98.0 8686.0 0.0 0.0 23367.0 0.0 0.0 0.0 4827.0 0 0 0 0 0

MA0899.2_shift2 (HOXA10)
; oligos_6nt_test_vs_ctrl_m2 versus MA0899.2 (HOXA10); m=5/11; ncol2=9; w=-1; offset=-1; strand=D; shift=2; score=0.431873; --gymATWAAa----- ; cor=; Ncor= a 0 0 2425.0 153.0 8381.0 8381.0 367.0 5960.0 8381.0 8381.0 8381.0 0 0 0 0 0 c 0 0 1757.0 3867.0 4516.0 455.0 11.0 84.0 36.0 568.0 2082.0 0 0 0 0 0 g 0 0 8381.0 59.0 1022.0 718.0 0.0 121.0 76.0 125.0 1560.0 0 0 0 0 0 t 0 0 1341.0 4515.0 957.0 267.0 8381.0 2422.0 384.0 331.0 2058.0 0 0 0 0 0

MA0650.4_shift2 (Hoxa13)
; oligos_6nt_test_vs_ctrl_m2 versus MA0650.4 (Hoxa13); m=6/11; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.429692; --CCAATAAA------ ; cor=; Ncor= a 0 0 1442.0 1273.0 14069.0 15410.0 105.0 15804.0 16813.0 16550.0 0 0 0 0 0 0 c 0 0 12600.0 14100.0 1594.0 243.0 249.0 205.0 125.0 306.0 0 0 0 0 0 0 g 0 0 1889.0 77.0 146.0 666.0 232.0 407.0 98.0 145.0 0 0 0 0 0 0 t 0 0 1317.0 1798.0 1439.0 929.0 16662.0 832.0 212.0 247.0 0 0 0 0 0 0

MA0465.3_shift2 (CDX2)
; oligos_6nt_test_vs_ctrl_m2 versus MA0465.3 (CDX2); m=7/11; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.426546; --GCAATAAA------ ; cor=; Ncor= a 0 0 3157.0 1226.0 26720.0 29957.0 274.0 29221.0 30645.0 30125.0 0 0 0 0 0 0 c 0 0 2096.0 26587.0 3312.0 414.0 391.0 761.0 349.0 595.0 0 0 0 0 0 0 g 0 0 24214.0 607.0 184.0 1196.0 386.0 999.0 366.0 502.0 0 0 0 0 0 0 t 0 0 2559.0 3606.0 1810.0 459.0 30975.0 1045.0 666.0 804.0 0 0 0 0 0 0

MA0909.4_shift3 (Hoxd13)
; oligos_6nt_test_vs_ctrl_m2 versus MA0909.4 (Hoxd13); m=8/11; ncol2=7; w=0; offset=0; strand=D; shift=3; score=0.424401; ---CAATAAA------ ; cor=; Ncor= a 0 0 0 16.0 5775.0 5923.0 0.0 5955.0 5923.0 4227.0 0 0 0 0 0 0 c 0 0 0 5866.0 5.0 13.0 2.0 4.0 37.0 704.0 0 0 0 0 0 0 g 0 0 0 34.0 148.0 11.0 3.0 7.0 2.0 379.0 0 0 0 0 0 0 t 0 0 0 61.0 49.0 30.0 5972.0 11.0 15.0 667.0 0 0 0 0 0 0

MA0913.3_shift2 (HOXD9)
; oligos_6nt_test_vs_ctrl_m2 versus MA0913.3 (HOXD9); m=9/11; ncol2=9; w=-1; offset=-1; strand=D; shift=2; score=0.420214; --GymATAAAA----- ; cor=; Ncor= a 0 0 1300.0 0.0 16363.0 16363.0 215.0 16363.0 16363.0 16363.0 16363.0 0 0 0 0 0 c 0 0 872.0 9773.0 8643.0 226.0 0.0 8.0 0.0 0.0 2202.0 0 0 0 0 0 g 0 0 16363.0 42.0 675.0 439.0 0.0 0.0 0.0 0.0 1216.0 0 0 0 0 0 t 0 0 655.0 6590.0 927.0 4.0 16363.0 5445.0 123.0 0.0 2194.0 0 0 0 0 0

MA0878.3_shift1 (CDX1)
; oligos_6nt_test_vs_ctrl_m2 versus MA0878.3 (CDX1); m=10/11; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.406964; -GGymATAAAA----- ; cor=; Ncor= a 0 1088.0 527.0 11.0 4822.0 8617.0 0.0 8617.0 8617.0 8617.0 7199.0 0 0 0 0 0 c 0 884.0 355.0 4868.0 3795.0 0.0 0.0 56.0 72.0 0.0 1418.0 0 0 0 0 0 g 0 7528.0 8090.0 0.0 0.0 344.0 0.0 0.0 97.0 0.0 754.0 0 0 0 0 0 t 0 1076.0 131.0 3749.0 355.0 0.0 8617.0 230.0 29.0 0.0 854.0 0 0 0 0 0

MA0635.2_shift6 (BARHL2)
; oligos_6nt_test_vs_ctrl_m2 versus MA0635.2 (BARHL2); m=11/11; ncol2=6; w=0; offset=3; strand=D; shift=6; score=0.401413; ------TAAAyG---- ; cor=; Ncor= a 0 0 0 0 0 0 643.0 12855.0 12855.0 12855.0 443.0 1570.0 0 0 0 0 c 0 0 0 0 0 0 0.0 0.0 0.0 116.0 12855.0 0.0 0 0 0 0 g 0 0 0 0 0 0 0.0 0.0 0.0 1086.0 127.0 12855.0 0 0 0 0 t 0 0 0 0 0 0 12855.0 1969.0 0.0 4032.0 7756.0 1335.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=13; shift=3; ncol=16; ---wwATAAATGTGww ; Alignment reference a 0 0 0 1289 1007 3008 196 3096 2600 3104 126 363 205 349 986 1126 c 0 0 0 501 644 88 130 63 177 91 196 87 103 105 514 639 g 0 0 0 670 588 167 233 152 90 105 90 2819 82 2747 585 764 t 0 0 0 949 1170 146 2850 98 542 109 2997 140 3019 208 1324 880
MA1978.2_shift0 (ZNF354A)				; oligos_6nt_test_vs_ctrl_m2 versus MA1978.2 (ZNF354A); m=1/11; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.486706; wAAwtrTAAAtGrayw ; cor=; Ncor= a 277.0 736.0 682.0 385.0 223.0 574.0 115.0 845.0 845.0 791.0 196.0 115.0 304.0 466.0 142.0 277.0 c 115.0 88.0 142.0 142.0 196.0 88.0 115.0 7.0 34.0 88.0 34.0 34.0 115.0 196.0 520.0 142.0 g 61.0 7.0 34.0 196.0 142.0 277.0 34.0 115.0 61.0 61.0 196.0 845.0 466.0 196.0 34.0 142.0 t 547.0 169.0 142.0 277.0 439.0 61.0 736.0 34.0 61.0 61.0 574.0 7.0 115.0 142.0 304.0 439.0
MA2124.1_rc_shift3 (Hmga1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus MA2124.1_rc (Hmga1_rc); m=2/11; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.462217; ---wTAAAAAT----- ; cor=; Ncor= a 0 0 0 11340.0 542.0 24333.0 24654.0 24779.0 24269.0 24172.0 496.0 0 0 0 0 0 c 0 0 0 2438.0 358.0 294.0 237.0 138.0 303.0 421.0 188.0 0 0 0 0 0 g 0 0 0 2348.0 473.0 409.0 264.0 194.0 200.0 393.0 71.0 0 0 0 0 0 t 0 0 0 9680.0 24433.0 770.0 651.0 695.0 1034.0 820.0 25051.0 0 0 0 0 0
MA0108.3_shift4 (TBP)				; oligos_6nt_test_vs_ctrl_m2 versus MA0108.3 (TBP); m=3/11; ncol2=7; w=0; offset=1; strand=D; shift=4; score=0.457341; ----TATAWAw----- ; cor=; Ncor= a 0 0 0 0 16.0 352.0 3.0 354.0 268.0 360.0 222.0 0 0 0 0 0 c 0 0 0 0 46.0 0.0 10.0 0.0 0.0 3.0 2.0 0 0 0 0 0 g 0 0 0 0 18.0 2.0 2.0 5.0 0.0 20.0 44.0 0 0 0 0 0 t 0 0 0 0 309.0 35.0 374.0 30.0 121.0 6.0 121.0 0 0 0 0 0
MA1473.2_shift2 (CDX4)				; oligos_6nt_test_vs_ctrl_m2 versus MA1473.2 (CDX4); m=4/11; ncol2=9; w=-1; offset=-1; strand=D; shift=2; score=0.443485; --GymATAAAa----- ; cor=; Ncor= a 0 0 2533.0 0.0 12392.0 23367.0 0.0 23367.0 23367.0 23367.0 23367.0 0 0 0 0 0 c 0 0 1064.0 14682.0 10976.0 0.0 0.0 0.0 0.0 57.0 6493.0 0 0 0 0 0 g 0 0 23367.0 0.0 25.0 0.0 0.0 0.0 0.0 0.0 2168.0 0 0 0 0 0 t 0 0 98.0 8686.0 0.0 0.0 23367.0 0.0 0.0 0.0 4827.0 0 0 0 0 0
MA0899.2_shift2 (HOXA10)				; oligos_6nt_test_vs_ctrl_m2 versus MA0899.2 (HOXA10); m=5/11; ncol2=9; w=-1; offset=-1; strand=D; shift=2; score=0.431873; --gymATWAAa----- ; cor=; Ncor= a 0 0 2425.0 153.0 8381.0 8381.0 367.0 5960.0 8381.0 8381.0 8381.0 0 0 0 0 0 c 0 0 1757.0 3867.0 4516.0 455.0 11.0 84.0 36.0 568.0 2082.0 0 0 0 0 0 g 0 0 8381.0 59.0 1022.0 718.0 0.0 121.0 76.0 125.0 1560.0 0 0 0 0 0 t 0 0 1341.0 4515.0 957.0 267.0 8381.0 2422.0 384.0 331.0 2058.0 0 0 0 0 0
MA0650.4_shift2 (Hoxa13)				; oligos_6nt_test_vs_ctrl_m2 versus MA0650.4 (Hoxa13); m=6/11; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.429692; --CCAATAAA------ ; cor=; Ncor= a 0 0 1442.0 1273.0 14069.0 15410.0 105.0 15804.0 16813.0 16550.0 0 0 0 0 0 0 c 0 0 12600.0 14100.0 1594.0 243.0 249.0 205.0 125.0 306.0 0 0 0 0 0 0 g 0 0 1889.0 77.0 146.0 666.0 232.0 407.0 98.0 145.0 0 0 0 0 0 0 t 0 0 1317.0 1798.0 1439.0 929.0 16662.0 832.0 212.0 247.0 0 0 0 0 0 0
MA0465.3_shift2 (CDX2)				; oligos_6nt_test_vs_ctrl_m2 versus MA0465.3 (CDX2); m=7/11; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.426546; --GCAATAAA------ ; cor=; Ncor= a 0 0 3157.0 1226.0 26720.0 29957.0 274.0 29221.0 30645.0 30125.0 0 0 0 0 0 0 c 0 0 2096.0 26587.0 3312.0 414.0 391.0 761.0 349.0 595.0 0 0 0 0 0 0 g 0 0 24214.0 607.0 184.0 1196.0 386.0 999.0 366.0 502.0 0 0 0 0 0 0 t 0 0 2559.0 3606.0 1810.0 459.0 30975.0 1045.0 666.0 804.0 0 0 0 0 0 0
MA0909.4_shift3 (Hoxd13)				; oligos_6nt_test_vs_ctrl_m2 versus MA0909.4 (Hoxd13); m=8/11; ncol2=7; w=0; offset=0; strand=D; shift=3; score=0.424401; ---CAATAAA------ ; cor=; Ncor= a 0 0 0 16.0 5775.0 5923.0 0.0 5955.0 5923.0 4227.0 0 0 0 0 0 0 c 0 0 0 5866.0 5.0 13.0 2.0 4.0 37.0 704.0 0 0 0 0 0 0 g 0 0 0 34.0 148.0 11.0 3.0 7.0 2.0 379.0 0 0 0 0 0 0 t 0 0 0 61.0 49.0 30.0 5972.0 11.0 15.0 667.0 0 0 0 0 0 0
MA0913.3_shift2 (HOXD9)				; oligos_6nt_test_vs_ctrl_m2 versus MA0913.3 (HOXD9); m=9/11; ncol2=9; w=-1; offset=-1; strand=D; shift=2; score=0.420214; --GymATAAAA----- ; cor=; Ncor= a 0 0 1300.0 0.0 16363.0 16363.0 215.0 16363.0 16363.0 16363.0 16363.0 0 0 0 0 0 c 0 0 872.0 9773.0 8643.0 226.0 0.0 8.0 0.0 0.0 2202.0 0 0 0 0 0 g 0 0 16363.0 42.0 675.0 439.0 0.0 0.0 0.0 0.0 1216.0 0 0 0 0 0 t 0 0 655.0 6590.0 927.0 4.0 16363.0 5445.0 123.0 0.0 2194.0 0 0 0 0 0
MA0878.3_shift1 (CDX1)				; oligos_6nt_test_vs_ctrl_m2 versus MA0878.3 (CDX1); m=10/11; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.406964; -GGymATAAAA----- ; cor=; Ncor= a 0 1088.0 527.0 11.0 4822.0 8617.0 0.0 8617.0 8617.0 8617.0 7199.0 0 0 0 0 0 c 0 884.0 355.0 4868.0 3795.0 0.0 0.0 56.0 72.0 0.0 1418.0 0 0 0 0 0 g 0 7528.0 8090.0 0.0 0.0 344.0 0.0 0.0 97.0 0.0 754.0 0 0 0 0 0 t 0 1076.0 131.0 3749.0 355.0 0.0 8617.0 230.0 29.0 0.0 854.0 0 0 0 0 0
MA0635.2_shift6 (BARHL2)				; oligos_6nt_test_vs_ctrl_m2 versus MA0635.2 (BARHL2); m=11/11; ncol2=6; w=0; offset=3; strand=D; shift=6; score=0.401413; ------TAAAyG---- ; cor=; Ncor= a 0 0 0 0 0 0 643.0 12855.0 12855.0 12855.0 443.0 1570.0 0 0 0 0 c 0 0 0 0 0 0 0.0 0.0 0.0 116.0 12855.0 0.0 0 0 0 0 g 0 0 0 0 0 0 0.0 0.0 0.0 1086.0 127.0 12855.0 0 0 0 0 t 0 0 0 0 0 0 12855.0 1969.0 0.0 4032.0 7756.0 1335.0 0 0 0 0