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_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4.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_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift3 ; 14 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=12; shift=3; ncol=15; ---waCAAAGAAAaa ; Alignment reference a 0 0 0 252 231 69 572 542 564 35 508 547 547 220 249 c 0 0 0 86 114 446 13 22 7 55 51 21 16 104 85 g 0 0 0 110 136 47 3 25 18 474 30 24 20 137 140 t 0 0 0 150 117 36 10 9 9 34 9 6 15 137 124

MA0041.3_shift1 (FOXD3)
; oligos_6nt_mkv3_m4 versus MA0041.3 (FOXD3); m=1/13; ncol2=14; w=-2; offset=-2; strand=D; shift=1; score=0.624851; -wawrhAAAYAAACa ; cor=; Ncor= a 0 86.0 120.0 91.0 56.0 99.0 171.0 171.0 171.0 0.0 171.0 171.0 171.0 13.0 125.0 c 0 22.0 17.0 45.0 17.0 109.0 37.0 8.0 1.0 43.0 4.0 11.0 17.0 171.0 20.0 g 0 13.0 52.0 45.0 115.0 8.0 1.0 0.0 7.0 0.0 2.0 8.0 20.0 13.0 30.0 t 0 85.0 22.0 81.0 10.0 171.0 2.0 7.0 2.0 128.0 7.0 11.0 35.0 30.0 47.0

MA0867.3_shift3 (SOX4)
; oligos_6nt_mkv3_m4 versus MA0867.3 (SOX4); m=2/13; ncol2=8; w=0; offset=0; strand=D; shift=3; score=0.541858; ---aACAAwGr---- ; cor=; Ncor= a 0 0 0 5582.0 5582.0 0.0 5582.0 5582.0 5582.0 1018.0 2093.0 0 0 0 0 c 0 0 0 951.0 0.0 5582.0 1.0 6.0 120.0 64.0 1422.0 0 0 0 0 g 0 0 0 2047.0 0.0 37.0 6.0 11.0 50.0 5582.0 3489.0 0 0 0 0 t 0 0 0 431.0 9.0 33.0 0.0 0.0 2719.0 83.0 174.0 0 0 0 0

MA1125.2_shift6 (ZNF384)
; oligos_6nt_mkv3_m4 versus MA1125.2 (ZNF384); m=3/13; ncol2=8; w=0; offset=3; strand=D; shift=6; score=0.537408; ------AAAAAAaa- ; cor=; Ncor= a 0 0 0 0 0 0 30354.0 30191.0 30072.0 30252.0 30202.0 30406.0 20322.0 18916.0 0 c 0 0 0 0 0 0 7.0 35.0 21.0 13.0 26.0 6.0 2908.0 3963.0 0 g 0 0 0 0 0 0 13.0 19.0 26.0 15.0 14.0 0.0 2767.0 2898.0 0 t 0 0 0 0 0 0 59.0 188.0 314.0 153.0 191.0 21.0 4436.0 4656.0 0

MA0769.3_rc_shift3 (TCF7_rc)
; oligos_6nt_mkv3_m4 versus MA0769.3_rc (TCF7_rc); m=4/13; ncol2=7; w=0; offset=0; strand=R; shift=3; score=0.51448; ---wTCAAAG----- ; cor=; Ncor= a 0 0 0 8498.0 239.0 478.0 14489.0 14178.0 14556.0 157.0 0 0 0 0 0 c 0 0 0 1220.0 115.0 13972.0 83.0 266.0 67.0 206.0 0 0 0 0 0 g 0 0 0 855.0 63.0 278.0 62.0 248.0 125.0 14379.0 0 0 0 0 0 t 0 0 0 4421.0 14577.0 266.0 360.0 302.0 246.0 252.0 0 0 0 0 0

MA0869.3_shift2 (Sox11)
; oligos_6nt_mkv3_m4 versus MA0869.3 (Sox11); m=5/13; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.495536; --GAACAAAG----- ; cor=; Ncor= a 0 0 1014.0 7912.0 9856.0 119.0 10020.0 9676.0 9276.0 506.0 0 0 0 0 0 c 0 0 764.0 766.0 100.0 9471.0 108.0 264.0 61.0 148.0 0 0 0 0 0 g 0 0 8063.0 1298.0 211.0 501.0 49.0 248.0 233.0 9486.0 0 0 0 0 0 t 0 0 407.0 272.0 81.0 157.0 71.0 60.0 678.0 108.0 0 0 0 0 0

MA0768.3_rc_shift3 (Lef1_rc)
; oligos_6nt_mkv3_m4 versus MA0768.3_rc (Lef1_rc); m=6/13; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.492282; ---ATCAAAGG---- ; cor=; Ncor= a 0 0 0 872.0 41.0 51.0 1030.0 976.0 1036.0 45.0 90.0 0 0 0 0 c 0 0 0 51.0 25.0 882.0 15.0 39.0 14.0 21.0 130.0 0 0 0 0 g 0 0 0 28.0 28.0 75.0 18.0 47.0 19.0 989.0 788.0 0 0 0 0 t 0 0 0 130.0 987.0 73.0 18.0 19.0 12.0 26.0 73.0 0 0 0 0

MA2098.1_shift7 (ZNF766)
; oligos_6nt_mkv3_m4 versus MA2098.1 (ZNF766); m=7/13; ncol2=9; w=0; offset=4; strand=D; shift=7; score=0.479571; -------AAkAAACC ; cor=; Ncor= a 0 0 0 0 0 0 0 6635.0 7378.0 51.0 7935.0 8002.0 7986.0 67.0 326.0 c 0 0 0 0 0 0 0 373.0 20.0 67.0 95.0 26.0 15.0 7904.0 7492.0 g 0 0 0 0 0 0 0 831.0 431.0 5092.0 20.0 21.0 47.0 35.0 56.0 t 0 0 0 0 0 0 0 230.0 240.0 2859.0 19.0 20.0 21.0 63.0 195.0

MA0442.3_shift4 (SOX10)
; oligos_6nt_mkv3_m4 versus MA0442.3 (SOX10); m=8/13; ncol2=6; w=0; offset=1; strand=D; shift=4; score=0.467955; ----ACAAAG----- ; cor=; Ncor= a 0 0 0 0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 0 0 0 0 0 c 0 0 0 0 4.0 1989.0 7.0 28.0 23.0 13.0 0 0 0 0 0 g 0 0 0 0 3.0 11.0 7.0 20.0 12.0 2012.0 0 0 0 0 0 t 0 0 0 0 25.0 52.0 12.0 39.0 61.0 20.0 0 0 0 0 0

MA0523.2_shift1 (TCF7L2)
; oligos_6nt_mkv3_m4 versus MA0523.2 (TCF7L2); m=9/13; ncol2=9; w=-2; offset=-2; strand=D; shift=1; score=0.438951; -AswTCAAAG----- ; cor=; Ncor= a 0 3070.0 85.0 2795.0 138.0 155.0 4188.0 4103.0 4169.0 303.0 0 0 0 0 0 c 0 136.0 1947.0 26.0 0.0 3304.0 0.0 15.0 0.0 37.0 0 0 0 0 0 g 0 559.0 2008.0 0.0 0.0 729.0 0.0 70.0 19.0 3848.0 0 0 0 0 0 t 0 423.0 148.0 1367.0 4050.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0

MA1991.2_rc_shift1 (Hnf1A_rc)
; oligos_6nt_mkv3_m4 versus MA1991.2_rc (Hnf1A_rc); m=10/13; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.438136; -asATCAAAGg---- ; cor=; Ncor= a 0 784.0 98.0 1092.0 73.0 68.0 1210.0 1122.0 1193.0 62.0 198.0 0 0 0 0 c 0 99.0 377.0 31.0 16.0 1033.0 12.0 60.0 7.0 39.0 204.0 0 0 0 0 g 0 210.0 689.0 21.0 35.0 118.0 11.0 51.0 30.0 1130.0 744.0 0 0 0 0 t 0 156.0 85.0 105.0 1125.0 30.0 16.0 16.0 19.0 18.0 103.0 0 0 0 0

MA1487.3_shift0 (FOXE1)
; oligos_6nt_mkv3_m4 versus MA1487.3 (FOXE1); m=11/13; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.42923; yTAARyAAACAa--- ; cor=; Ncor= a 86.0 581.0 3126.0 2547.0 2255.0 587.0 3126.0 3126.0 3126.0 0.0 3126.0 2026.0 0 0 0 c 1646.0 43.0 28.0 113.0 117.0 1062.0 362.0 90.0 0.0 3126.0 32.0 392.0 0 0 0 g 57.0 0.0 402.0 116.0 871.0 17.0 0.0 0.0 23.0 0.0 18.0 258.0 0 0 0 t 1479.0 2545.0 43.0 579.0 27.0 2064.0 20.0 53.0 9.0 85.0 110.0 450.0 0 0 0

MA0847.4_shift0 (FOXD2)
; oligos_6nt_mkv3_m4 versus MA0847.4 (FOXD2); m=12/13; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.410277; yTAAryAAACA---- ; cor=; Ncor= a 219.0 480.0 2484.0 2484.0 2484.0 84.0 2484.0 2484.0 2484.0 0.0 2484.0 0 0 0 0 c 906.0 19.0 16.0 285.0 23.0 1342.0 81.0 23.0 0.0 2484.0 24.0 0 0 0 0 g 131.0 0.0 137.0 292.0 1615.0 3.0 0.0 18.0 5.0 0.0 34.0 0 0 0 0 t 1578.0 2004.0 0.0 262.0 4.0 1141.0 79.0 1.0 2.0 768.0 232.0 0 0 0 0

MA0515.1_rc_shift1 (Sox6_rc)
; oligos_6nt_mkv3_m4 versus MA0515.1_rc (Sox6_rc); m=13/13; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.405238; -rrrACAAwGg---- ; cor=; Ncor= a 0 128.0 133.0 129.0 249.0 0.0 249.0 249.0 88.0 28.0 56.0 0 0 0 0 c 0 31.0 0.0 5.0 0.0 249.0 0.0 0.0 0.0 0.0 50.0 0 0 0 0 g 0 76.0 112.0 115.0 0.0 0.0 0.0 0.0 0.0 221.0 139.0 0 0 0 0 t 0 14.0 4.0 0.0 0.0 0.0 0.0 0.0 161.0 0.0 4.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift3 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=12; shift=3; ncol=15; ---waCAAAGAAAaa ; Alignment reference a 0 0 0 252 231 69 572 542 564 35 508 547 547 220 249 c 0 0 0 86 114 446 13 22 7 55 51 21 16 104 85 g 0 0 0 110 136 47 3 25 18 474 30 24 20 137 140 t 0 0 0 150 117 36 10 9 9 34 9 6 15 137 124
MA0041.3_shift1 (FOXD3)				; oligos_6nt_mkv3_m4 versus MA0041.3 (FOXD3); m=1/13; ncol2=14; w=-2; offset=-2; strand=D; shift=1; score=0.624851; -wawrhAAAYAAACa ; cor=; Ncor= a 0 86.0 120.0 91.0 56.0 99.0 171.0 171.0 171.0 0.0 171.0 171.0 171.0 13.0 125.0 c 0 22.0 17.0 45.0 17.0 109.0 37.0 8.0 1.0 43.0 4.0 11.0 17.0 171.0 20.0 g 0 13.0 52.0 45.0 115.0 8.0 1.0 0.0 7.0 0.0 2.0 8.0 20.0 13.0 30.0 t 0 85.0 22.0 81.0 10.0 171.0 2.0 7.0 2.0 128.0 7.0 11.0 35.0 30.0 47.0
MA0867.3_shift3 (SOX4)				; oligos_6nt_mkv3_m4 versus MA0867.3 (SOX4); m=2/13; ncol2=8; w=0; offset=0; strand=D; shift=3; score=0.541858; ---aACAAwGr---- ; cor=; Ncor= a 0 0 0 5582.0 5582.0 0.0 5582.0 5582.0 5582.0 1018.0 2093.0 0 0 0 0 c 0 0 0 951.0 0.0 5582.0 1.0 6.0 120.0 64.0 1422.0 0 0 0 0 g 0 0 0 2047.0 0.0 37.0 6.0 11.0 50.0 5582.0 3489.0 0 0 0 0 t 0 0 0 431.0 9.0 33.0 0.0 0.0 2719.0 83.0 174.0 0 0 0 0
MA1125.2_shift6 (ZNF384)				; oligos_6nt_mkv3_m4 versus MA1125.2 (ZNF384); m=3/13; ncol2=8; w=0; offset=3; strand=D; shift=6; score=0.537408; ------AAAAAAaa- ; cor=; Ncor= a 0 0 0 0 0 0 30354.0 30191.0 30072.0 30252.0 30202.0 30406.0 20322.0 18916.0 0 c 0 0 0 0 0 0 7.0 35.0 21.0 13.0 26.0 6.0 2908.0 3963.0 0 g 0 0 0 0 0 0 13.0 19.0 26.0 15.0 14.0 0.0 2767.0 2898.0 0 t 0 0 0 0 0 0 59.0 188.0 314.0 153.0 191.0 21.0 4436.0 4656.0 0
MA0769.3_rc_shift3 (TCF7_rc)				; oligos_6nt_mkv3_m4 versus MA0769.3_rc (TCF7_rc); m=4/13; ncol2=7; w=0; offset=0; strand=R; shift=3; score=0.51448; ---wTCAAAG----- ; cor=; Ncor= a 0 0 0 8498.0 239.0 478.0 14489.0 14178.0 14556.0 157.0 0 0 0 0 0 c 0 0 0 1220.0 115.0 13972.0 83.0 266.0 67.0 206.0 0 0 0 0 0 g 0 0 0 855.0 63.0 278.0 62.0 248.0 125.0 14379.0 0 0 0 0 0 t 0 0 0 4421.0 14577.0 266.0 360.0 302.0 246.0 252.0 0 0 0 0 0
MA0869.3_shift2 (Sox11)				; oligos_6nt_mkv3_m4 versus MA0869.3 (Sox11); m=5/13; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.495536; --GAACAAAG----- ; cor=; Ncor= a 0 0 1014.0 7912.0 9856.0 119.0 10020.0 9676.0 9276.0 506.0 0 0 0 0 0 c 0 0 764.0 766.0 100.0 9471.0 108.0 264.0 61.0 148.0 0 0 0 0 0 g 0 0 8063.0 1298.0 211.0 501.0 49.0 248.0 233.0 9486.0 0 0 0 0 0 t 0 0 407.0 272.0 81.0 157.0 71.0 60.0 678.0 108.0 0 0 0 0 0
MA0768.3_rc_shift3 (Lef1_rc)				; oligos_6nt_mkv3_m4 versus MA0768.3_rc (Lef1_rc); m=6/13; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.492282; ---ATCAAAGG---- ; cor=; Ncor= a 0 0 0 872.0 41.0 51.0 1030.0 976.0 1036.0 45.0 90.0 0 0 0 0 c 0 0 0 51.0 25.0 882.0 15.0 39.0 14.0 21.0 130.0 0 0 0 0 g 0 0 0 28.0 28.0 75.0 18.0 47.0 19.0 989.0 788.0 0 0 0 0 t 0 0 0 130.0 987.0 73.0 18.0 19.0 12.0 26.0 73.0 0 0 0 0
MA2098.1_shift7 (ZNF766)				; oligos_6nt_mkv3_m4 versus MA2098.1 (ZNF766); m=7/13; ncol2=9; w=0; offset=4; strand=D; shift=7; score=0.479571; -------AAkAAACC ; cor=; Ncor= a 0 0 0 0 0 0 0 6635.0 7378.0 51.0 7935.0 8002.0 7986.0 67.0 326.0 c 0 0 0 0 0 0 0 373.0 20.0 67.0 95.0 26.0 15.0 7904.0 7492.0 g 0 0 0 0 0 0 0 831.0 431.0 5092.0 20.0 21.0 47.0 35.0 56.0 t 0 0 0 0 0 0 0 230.0 240.0 2859.0 19.0 20.0 21.0 63.0 195.0
MA0442.3_shift4 (SOX10)				; oligos_6nt_mkv3_m4 versus MA0442.3 (SOX10); m=8/13; ncol2=6; w=0; offset=1; strand=D; shift=4; score=0.467955; ----ACAAAG----- ; cor=; Ncor= a 0 0 0 0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 0 0 0 0 0 c 0 0 0 0 4.0 1989.0 7.0 28.0 23.0 13.0 0 0 0 0 0 g 0 0 0 0 3.0 11.0 7.0 20.0 12.0 2012.0 0 0 0 0 0 t 0 0 0 0 25.0 52.0 12.0 39.0 61.0 20.0 0 0 0 0 0
MA0523.2_shift1 (TCF7L2)				; oligos_6nt_mkv3_m4 versus MA0523.2 (TCF7L2); m=9/13; ncol2=9; w=-2; offset=-2; strand=D; shift=1; score=0.438951; -AswTCAAAG----- ; cor=; Ncor= a 0 3070.0 85.0 2795.0 138.0 155.0 4188.0 4103.0 4169.0 303.0 0 0 0 0 0 c 0 136.0 1947.0 26.0 0.0 3304.0 0.0 15.0 0.0 37.0 0 0 0 0 0 g 0 559.0 2008.0 0.0 0.0 729.0 0.0 70.0 19.0 3848.0 0 0 0 0 0 t 0 423.0 148.0 1367.0 4050.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0
MA1991.2_rc_shift1 (Hnf1A_rc)				; oligos_6nt_mkv3_m4 versus MA1991.2_rc (Hnf1A_rc); m=10/13; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.438136; -asATCAAAGg---- ; cor=; Ncor= a 0 784.0 98.0 1092.0 73.0 68.0 1210.0 1122.0 1193.0 62.0 198.0 0 0 0 0 c 0 99.0 377.0 31.0 16.0 1033.0 12.0 60.0 7.0 39.0 204.0 0 0 0 0 g 0 210.0 689.0 21.0 35.0 118.0 11.0 51.0 30.0 1130.0 744.0 0 0 0 0 t 0 156.0 85.0 105.0 1125.0 30.0 16.0 16.0 19.0 18.0 103.0 0 0 0 0
MA1487.3_shift0 (FOXE1)				; oligos_6nt_mkv3_m4 versus MA1487.3 (FOXE1); m=11/13; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.42923; yTAARyAAACAa--- ; cor=; Ncor= a 86.0 581.0 3126.0 2547.0 2255.0 587.0 3126.0 3126.0 3126.0 0.0 3126.0 2026.0 0 0 0 c 1646.0 43.0 28.0 113.0 117.0 1062.0 362.0 90.0 0.0 3126.0 32.0 392.0 0 0 0 g 57.0 0.0 402.0 116.0 871.0 17.0 0.0 0.0 23.0 0.0 18.0 258.0 0 0 0 t 1479.0 2545.0 43.0 579.0 27.0 2064.0 20.0 53.0 9.0 85.0 110.0 450.0 0 0 0
MA0847.4_shift0 (FOXD2)				; oligos_6nt_mkv3_m4 versus MA0847.4 (FOXD2); m=12/13; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.410277; yTAAryAAACA---- ; cor=; Ncor= a 219.0 480.0 2484.0 2484.0 2484.0 84.0 2484.0 2484.0 2484.0 0.0 2484.0 0 0 0 0 c 906.0 19.0 16.0 285.0 23.0 1342.0 81.0 23.0 0.0 2484.0 24.0 0 0 0 0 g 131.0 0.0 137.0 292.0 1615.0 3.0 0.0 18.0 5.0 0.0 34.0 0 0 0 0 t 1578.0 2004.0 0.0 262.0 4.0 1141.0 79.0 1.0 2.0 768.0 232.0 0 0 0 0
MA0515.1_rc_shift1 (Sox6_rc)				; oligos_6nt_mkv3_m4 versus MA0515.1_rc (Sox6_rc); m=13/13; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.405238; -rrrACAAwGg---- ; cor=; Ncor= a 0 128.0 133.0 129.0 249.0 0.0 249.0 249.0 88.0 28.0 56.0 0 0 0 0 c 0 31.0 0.0 5.0 0.0 249.0 0.0 0.0 0.0 0.0 50.0 0 0 0 0 g 0 76.0 112.0 115.0 0.0 0.0 0.0 0.0 0.0 221.0 139.0 0 0 0 0 t 0 14.0 4.0 0.0 0.0 0.0 0.0 0.0 161.0 0.0 4.0 0 0 0 0