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.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_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.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift4 ; 28 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift4 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=10; shift=4; ncol=14; ----wtATTTAAww ; Alignment reference a 0 0 0 0 9973 5592 26183 960 4053 989 25397 21809 9547 9082 c 0 0 0 0 4145 5185 76 479 520 102 164 1423 4827 4536 g 0 0 0 0 5742 3536 517 486 1822 74 99 470 3538 4670 t 0 0 0 0 7203 12750 287 25138 20668 25898 1403 3361 9151 8775

MA0845.1_rc_shift4 (FOXB1_rc)
; positions_6nt_m3 versus MA0845.1_rc (FOXB1_rc); m=1/27; ncol2=11; w=0; offset=0; strand=R; shift=4; score=0.641046; ----aTrTTKACwT ; cor=; Ncor= a 0 0 0 0 4008.0 147.0 4589.0 216.0 381.0 73.0 6841.0 124.0 4858.0 561.0 c 0 0 0 0 556.0 157.0 104.0 47.0 0.0 75.0 113.0 6841.0 409.0 1498.0 g 0 0 0 0 573.0 0.0 2252.0 47.0 213.0 1950.0 240.0 54.0 218.0 263.0 t 0 0 0 0 1704.0 6841.0 28.0 6841.0 6841.0 4891.0 180.0 1159.0 1983.0 5343.0

MA0135.2_rc_shift3 (Lhx3_rc)
; positions_6nt_m3 versus MA0135.2_rc (Lhx3_rc); m=2/27; ncol2=12; w=-1; offset=-1; strand=R; shift=3; score=0.618525; ---rwTAATTAATT ; cor=; Ncor= a 0 0 0 10.0 8.0 3.0 19.0 16.0 0.0 1.0 20.0 20.0 1.0 0.0 c 0 0 0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 g 0 0 0 8.0 0.0 1.0 1.0 2.0 0.0 0.0 0.0 0.0 0.0 2.0 t 0 0 0 2.0 9.0 16.0 0.0 2.0 20.0 19.0 0.0 0.0 19.0 16.0

MA0703.3_rc_shift4 (LMX1B_rc)
; positions_6nt_m3 versus MA0703.3_rc (LMX1B_rc); m=3/27; ncol2=8; w=0; offset=0; strand=R; shift=4; score=0.582174; ----tTAATTAA-- ; cor=; Ncor= a 0 0 0 0 609.0 0.0 4064.0 4064.0 0.0 0.0 4064.0 3465.0 0 0 c 0 0 0 0 350.0 0.0 0.0 0.0 0.0 0.0 0.0 190.0 0 0 g 0 0 0 0 785.0 12.0 0.0 0.0 0.0 0.0 0.0 599.0 0 0 t 0 0 0 0 2319.0 4064.0 0.0 0.0 4064.0 4064.0 0.0 0.0 0 0

MA0619.2_rc_shift6 (LIN54_rc)
; positions_6nt_m3 versus MA0619.2_rc (LIN54_rc); m=4/27; ncol2=7; w=0; offset=2; strand=R; shift=6; score=0.558442; ------ATTyAAA- ; cor=; Ncor= a 0 0 0 0 0 0 685.0 0.0 0.0 0.0 788.0 999.0 999.0 0 c 0 0 0 0 0 0 0.0 0.0 0.0 562.0 0.0 0.0 0.0 0 g 0 0 0 0 0 0 211.0 0.0 0.0 0.0 212.0 0.0 0.0 0 t 0 0 0 0 0 0 104.0 999.0 999.0 438.0 0.0 0.0 0.0 0

MA0601.2_rc_shift7 (Arid3b_rc)
; positions_6nt_m3 versus MA0601.2_rc (Arid3b_rc); m=5/27; ncol2=7; w=0; offset=3; strand=R; shift=7; score=0.516573; -------ATTAAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 911.0 89.0 0.0 1000.0 895.0 238.0 566.0 c 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 34.0 80.0 g 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 119.0 80.0 t 0 0 0 0 0 0 0 89.0 911.0 1000.0 0.0 104.0 609.0 273.0

MA0621.2_rc_shift5 (mix-a_rc)
; positions_6nt_m3 versus MA0621.2_rc (mix-a_rc); m=6/27; ncol2=7; w=0; offset=1; strand=R; shift=5; score=0.513697; -----TAATTAa-- ; cor=; Ncor= a 0 0 0 0 0 21.0 1000.0 1000.0 0.0 0.0 1000.0 679.0 0 0 c 0 0 0 0 0 21.0 0.0 0.0 0.0 0.0 0.0 46.0 0 0 g 0 0 0 0 0 21.0 0.0 0.0 0.0 0.0 0.0 146.0 0 0 t 0 0 0 0 0 938.0 0.0 0.0 1000.0 1000.0 0.0 130.0 0 0

MA0108.3_shift7 (TBP)
; positions_6nt_m3 versus MA0108.3 (TBP); m=7/27; ncol2=7; w=0; offset=3; strand=D; shift=7; score=0.511634; -------TATAWAw ; cor=; Ncor= a 0 0 0 0 0 0 0 16.0 352.0 3.0 354.0 268.0 360.0 222.0 c 0 0 0 0 0 0 0 46.0 0.0 10.0 0.0 0.0 3.0 2.0 g 0 0 0 0 0 0 0 18.0 2.0 2.0 5.0 0.0 20.0 44.0 t 0 0 0 0 0 0 0 309.0 35.0 374.0 30.0 121.0 6.0 121.0

MA0702.3_rc_shift5 (LMX1A_rc)
; positions_6nt_m3 versus MA0702.3_rc (LMX1A_rc); m=8/27; ncol2=7; w=0; offset=1; strand=R; shift=5; score=0.508914; -----TAATTAr-- ; cor=; Ncor= a 0 0 0 0 0 0.0 7355.0 7355.0 0.0 0.0 7355.0 5133.0 0 0 c 0 0 0 0 0 501.0 0.0 0.0 0.0 0.0 19.0 305.0 0 0 g 0 0 0 0 0 102.0 0.0 50.0 9.0 0.0 31.0 2222.0 0 0 t 0 0 0 0 0 7355.0 0.0 0.0 7355.0 7355.0 0.0 90.0 0 0

MA0151.1_rc_shift7 (Arid3a_rc)
; positions_6nt_m3 versus MA0151.1_rc (Arid3a_rc); m=9/27; ncol2=6; w=0; offset=3; strand=R; shift=7; score=0.50747; -------TTTrAT- ; cor=; Ncor= a 0 0 0 0 0 0 0 6.0 0.0 0.0 17.0 27.0 0.0 0 c 0 0 0 0 0 0 0 1.0 0.0 0.0 0.0 0.0 0.0 0 g 0 0 0 0 0 0 0 0.0 0.0 0.0 9.0 0.0 0.0 0 t 0 0 0 0 0 0 0 20.0 27.0 27.0 1.0 0.0 27.0 0

MA0674.2_rc_shift8 (NKX6-1_rc)
; positions_6nt_m3 versus MA0674.2_rc (NKX6-1_rc); m=10/27; ncol2=7; w=0; offset=4; strand=R; shift=8; score=0.47571; --------tTAATk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 327.0 17.0 2212.0 2212.0 40.0 195.0 c 0 0 0 0 0 0 0 0 142.0 132.0 0.0 0.0 12.0 0.0 g 0 0 0 0 0 0 0 0 294.0 27.0 45.0 0.0 200.0 805.0 t 0 0 0 0 0 0 0 0 1450.0 2212.0 58.0 0.0 2212.0 1407.0

MA0683.2_shift1 (POU4F2)
; positions_6nt_m3 versus MA0683.2 (POU4F2); m=11/27; ncol2=15; w=-3; offset=-3; strand=D; shift=1; score=0.475199; -TGmATAATTAATk ; cor=; Ncor= a 0 110.0 193.0 1160.0 3079.0 1.0 2990.0 2621.0 76.0 304.0 3098.0 3187.0 19.0 130.0 c 0 121.0 34.0 2471.0 6.0 0.0 9.0 82.0 54.0 9.0 26.0 4.0 30.0 168.0 g 0 53.0 3440.0 2.0 4.0 0.0 14.0 53.0 28.0 8.0 234.0 9.0 69.0 2193.0 t 0 2757.0 81.0 5.0 11.0 2829.0 258.0 737.0 2735.0 2669.0 57.0 0.0 2761.0 1072.0

MA0635.2_rc_shift5 (BARHL2_rc)
; positions_6nt_m3 versus MA0635.2_rc (BARHL2_rc); m=12/27; ncol2=6; w=0; offset=1; strand=R; shift=5; score=0.453727; -----CrTTTA--- ; cor=; Ncor= a 0 0 0 0 0 1335.0 7756.0 4032.0 0.0 1969.0 12855.0 0 0 0 c 0 0 0 0 0 12855.0 127.0 1086.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0 0.0 12855.0 116.0 0.0 0.0 0.0 0 0 0 t 0 0 0 0 0 1570.0 443.0 12855.0 12855.0 12855.0 643.0 0 0 0

MA0650.4_rc_shift7 (Hoxa13_rc)
; positions_6nt_m3 versus MA0650.4_rc (Hoxa13_rc); m=13/27; ncol2=8; w=0; offset=3; strand=R; shift=7; score=0.446839; -------TTTATTG ; cor=; Ncor= a 0 0 0 0 0 0 0 247.0 212.0 832.0 16662.0 929.0 1439.0 1798.0 c 0 0 0 0 0 0 0 145.0 98.0 407.0 232.0 666.0 146.0 77.0 g 0 0 0 0 0 0 0 306.0 125.0 205.0 249.0 243.0 1594.0 14100.0 t 0 0 0 0 0 0 0 16550.0 16813.0 15804.0 105.0 15410.0 14069.0 1273.0

MA0847.4_rc_shift1 (FOXD2_rc)
; positions_6nt_m3 versus MA0847.4_rc (FOXD2_rc); m=14/27; ncol2=11; w=-3; offset=-3; strand=R; shift=1; score=0.437077; -TGTTTryTTAr-- ; cor=; Ncor= a 0 232.0 768.0 2.0 1.0 79.0 1141.0 4.0 262.0 0.0 2004.0 1578.0 0 0 c 0 34.0 0.0 5.0 18.0 0.0 3.0 1615.0 292.0 137.0 0.0 131.0 0 0 g 0 24.0 2484.0 0.0 23.0 81.0 1342.0 23.0 285.0 16.0 19.0 906.0 0 0 t 0 2484.0 0.0 2484.0 2484.0 2484.0 84.0 2484.0 2484.0 2484.0 480.0 219.0 0 0

MA1577.2_shift5 (TLX2)
; positions_6nt_m3 versus MA1577.2 (TLX2); m=15/27; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.432284; -----yAATTA--- ; cor=; Ncor= a 0 0 0 0 0 1435.0 7799.0 7799.0 0.0 0.0 7799.0 0 0 0 c 0 0 0 0 0 7799.0 0.0 0.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0 1112.0 80.0 0.0 0.0 0.0 0.0 0 0 0 t 0 0 0 0 0 8156.0 0.0 0.0 7799.0 7799.0 0.0 0 0 0

MA0654.2_shift5 (ISX)
; positions_6nt_m3 versus MA0654.2 (ISX); m=16/27; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.428616; -----yAATTA--- ; cor=; Ncor= a 0 0 0 0 0 10.0 2065.0 2065.0 0.0 0.0 2065.0 0 0 0 c 0 0 0 0 0 1003.0 48.0 16.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0 0.0 5.0 0.0 0.0 24.0 0.0 0 0 0 t 0 0 0 0 0 1061.0 24.0 10.0 2065.0 2065.0 49.0 0 0 0

MA0718.2_shift5 (RAX)
; positions_6nt_m3 versus MA0718.2 (RAX); m=17/27; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.426787; -----yAATTA--- ; cor=; Ncor= a 0 0 0 0 0 214.0 2412.0 2412.0 123.0 71.0 2412.0 0 0 0 c 0 0 0 0 0 1281.0 17.0 38.0 0.0 71.0 0.0 0 0 0 g 0 0 0 0 0 25.0 3.0 12.0 0.0 49.0 20.0 0 0 0 t 0 0 0 0 0 1131.0 40.0 24.0 2412.0 2412.0 126.0 0 0 0

MA0894.2_rc_shift5 (HESX1_rc)
; positions_6nt_m3 versus MA0894.2_rc (HESX1_rc); m=18/27; ncol2=6; w=0; offset=1; strand=R; shift=5; score=0.425089; -----yAATTA--- ; cor=; Ncor= a 0 0 0 0 0 97.0 4072.0 4072.0 0.0 31.0 4072.0 0 0 0 c 0 0 0 0 0 2180.0 0.0 15.0 9.0 53.0 34.0 0 0 0 g 0 0 0 0 0 38.0 15.0 0.0 7.0 0.0 0.0 0 0 0 t 0 0 0 0 0 1892.0 0.0 0.0 4072.0 4072.0 187.0 0 0 0

MA0125.2_rc_shift5 (Nobox_rc)
; positions_6nt_m3 versus MA0125.2_rc (Nobox_rc); m=19/27; ncol2=6; w=0; offset=1; strand=R; shift=5; score=0.424687; -----yAATTA--- ; cor=; Ncor= a 0 0 0 0 0 1.0 32.0 34.0 0.0 2.0 37.0 0 0 0 c 0 0 0 0 0 22.0 4.0 2.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0 0.0 0.0 1.0 0.0 0.0 1.0 0 0 0 t 0 0 0 0 0 15.0 2.0 1.0 38.0 36.0 0.0 0 0 0

MA1487.3_rc_shift0 (FOXE1_rc)
; positions_6nt_m3 versus MA1487.3_rc (FOXE1_rc); m=20/27; ncol2=12; w=-4; offset=-4; strand=R; shift=0; score=0.423904; tTGTTTrYTTAr-- ; cor=; Ncor= a 450.0 110.0 85.0 9.0 53.0 20.0 2064.0 27.0 579.0 43.0 2545.0 1479.0 0 0 c 258.0 18.0 0.0 23.0 0.0 0.0 17.0 871.0 116.0 402.0 0.0 57.0 0 0 g 392.0 32.0 3126.0 0.0 90.0 362.0 1062.0 117.0 113.0 28.0 43.0 1646.0 0 0 t 2026.0 3126.0 0.0 3126.0 3126.0 3126.0 587.0 2255.0 2547.0 3126.0 581.0 86.0 0 0

MA0628.2_shift5 (POU6F1)
; positions_6nt_m3 versus MA0628.2 (POU6F1); m=21/27; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.42194; -----TAATTA--- ; cor=; Ncor= a 0 0 0 0 0 32.0 905.0 938.0 14.0 18.0 950.0 0 0 0 c 0 0 0 0 0 10.0 70.0 34.0 14.0 8.0 8.0 0 0 0 g 0 0 0 0 0 8.0 8.0 14.0 34.0 70.0 10.0 0 0 0 t 0 0 0 0 0 950.0 18.0 14.0 938.0 905.0 32.0 0 0 0

MA0899.2_rc_shift7 (HOXA10_rc)
; positions_6nt_m3 versus MA0899.2_rc (HOXA10_rc); m=22/27; ncol2=9; w=0; offset=3; strand=R; shift=7; score=0.42093; -------tTTWATk ; cor=; Ncor= a 0 0 0 0 0 0 0 2058.0 331.0 384.0 2422.0 8381.0 267.0 957.0 c 0 0 0 0 0 0 0 1560.0 125.0 76.0 121.0 0.0 718.0 1022.0 g 0 0 0 0 0 0 0 2082.0 568.0 36.0 84.0 11.0 455.0 4516.0 t 0 0 0 0 0 0 0 8381.0 8381.0 8381.0 5960.0 367.0 8381.0 8381.0

MA0612.3_shift5 (EMX1)
; positions_6nt_m3 versus MA0612.3 (EMX1); m=23/27; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.420829; -----TAATTA--- ; cor=; Ncor= a 0 0 0 0 0 19.0 9544.0 9544.0 0.0 0.0 9544.0 0 0 0 c 0 0 0 0 0 2263.0 1235.0 0.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0 0.0 0.0 0.0 0.0 933.0 0.0 0 0 0 t 0 0 0 0 0 7281.0 0.0 0.0 9544.0 9544.0 0.0 0 0 0

MA0913.3_rc_shift7 (HOXD9_rc)
; positions_6nt_m3 versus MA0913.3_rc (HOXD9_rc); m=24/27; ncol2=9; w=0; offset=3; strand=R; shift=7; score=0.41956; -------TTTTATk ; cor=; Ncor= a 0 0 0 0 0 0 0 2194.0 0.0 123.0 5445.0 16363.0 4.0 927.0 c 0 0 0 0 0 0 0 1216.0 0.0 0.0 0.0 0.0 439.0 675.0 g 0 0 0 0 0 0 0 2202.0 0.0 0.0 8.0 0.0 226.0 8643.0 t 0 0 0 0 0 0 0 16363.0 16363.0 16363.0 16363.0 215.0 16363.0 16363.0

MA0722.2_shift8 (VAX1)
; positions_6nt_m3 versus MA0722.2 (VAX1); m=25/27; ncol2=7; w=0; offset=4; strand=D; shift=8; score=0.410902; --------yTAATt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 447.0 679.0 5253.0 5253.0 297.0 508.0 c 0 0 0 0 0 0 0 0 2775.0 995.0 863.0 153.0 86.0 321.0 g 0 0 0 0 0 0 0 0 455.0 101.0 189.0 46.0 213.0 1951.0 t 0 0 0 0 0 0 0 0 2479.0 5253.0 302.0 133.0 5253.0 5253.0

MA0876.2_rc_shift9 (BSX_rc)
; positions_6nt_m3 versus MA0876.2_rc (BSX_rc); m=26/27; ncol2=6; w=0; offset=5; strand=R; shift=9; score=0.404191; ---------TAATk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0.0 8832.0 8832.0 66.0 116.0 c 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 1078.0 2197.0 g 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 194.0 2483.0 t 0 0 0 0 0 0 0 0 0 8832.0 96.0 0.0 8832.0 4036.0

MA0892.2_rc_shift9 (GSX1_rc)
; positions_6nt_m3 versus MA0892.2_rc (GSX1_rc); m=27/27; ncol2=6; w=0; offset=5; strand=R; shift=9; score=0.400015; ---------TAATk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 103.0 1183.0 1183.0 50.0 177.0 c 0 0 0 0 0 0 0 0 0 9.0 0.0 3.0 123.0 60.0 g 0 0 0 0 0 0 0 0 0 0.0 106.0 79.0 106.0 402.0 t 0 0 0 0 0 0 0 0 0 1183.0 106.0 90.0 1183.0 781.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift4 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=10; shift=4; ncol=14; ----wtATTTAAww ; Alignment reference a 0 0 0 0 9973 5592 26183 960 4053 989 25397 21809 9547 9082 c 0 0 0 0 4145 5185 76 479 520 102 164 1423 4827 4536 g 0 0 0 0 5742 3536 517 486 1822 74 99 470 3538 4670 t 0 0 0 0 7203 12750 287 25138 20668 25898 1403 3361 9151 8775
MA0845.1_rc_shift4 (FOXB1_rc)				; positions_6nt_m3 versus MA0845.1_rc (FOXB1_rc); m=1/27; ncol2=11; w=0; offset=0; strand=R; shift=4; score=0.641046; ----aTrTTKACwT ; cor=; Ncor= a 0 0 0 0 4008.0 147.0 4589.0 216.0 381.0 73.0 6841.0 124.0 4858.0 561.0 c 0 0 0 0 556.0 157.0 104.0 47.0 0.0 75.0 113.0 6841.0 409.0 1498.0 g 0 0 0 0 573.0 0.0 2252.0 47.0 213.0 1950.0 240.0 54.0 218.0 263.0 t 0 0 0 0 1704.0 6841.0 28.0 6841.0 6841.0 4891.0 180.0 1159.0 1983.0 5343.0
MA0135.2_rc_shift3 (Lhx3_rc)				; positions_6nt_m3 versus MA0135.2_rc (Lhx3_rc); m=2/27; ncol2=12; w=-1; offset=-1; strand=R; shift=3; score=0.618525; ---rwTAATTAATT ; cor=; Ncor= a 0 0 0 10.0 8.0 3.0 19.0 16.0 0.0 1.0 20.0 20.0 1.0 0.0 c 0 0 0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 g 0 0 0 8.0 0.0 1.0 1.0 2.0 0.0 0.0 0.0 0.0 0.0 2.0 t 0 0 0 2.0 9.0 16.0 0.0 2.0 20.0 19.0 0.0 0.0 19.0 16.0
MA0703.3_rc_shift4 (LMX1B_rc)				; positions_6nt_m3 versus MA0703.3_rc (LMX1B_rc); m=3/27; ncol2=8; w=0; offset=0; strand=R; shift=4; score=0.582174; ----tTAATTAA-- ; cor=; Ncor= a 0 0 0 0 609.0 0.0 4064.0 4064.0 0.0 0.0 4064.0 3465.0 0 0 c 0 0 0 0 350.0 0.0 0.0 0.0 0.0 0.0 0.0 190.0 0 0 g 0 0 0 0 785.0 12.0 0.0 0.0 0.0 0.0 0.0 599.0 0 0 t 0 0 0 0 2319.0 4064.0 0.0 0.0 4064.0 4064.0 0.0 0.0 0 0
MA0619.2_rc_shift6 (LIN54_rc)				; positions_6nt_m3 versus MA0619.2_rc (LIN54_rc); m=4/27; ncol2=7; w=0; offset=2; strand=R; shift=6; score=0.558442; ------ATTyAAA- ; cor=; Ncor= a 0 0 0 0 0 0 685.0 0.0 0.0 0.0 788.0 999.0 999.0 0 c 0 0 0 0 0 0 0.0 0.0 0.0 562.0 0.0 0.0 0.0 0 g 0 0 0 0 0 0 211.0 0.0 0.0 0.0 212.0 0.0 0.0 0 t 0 0 0 0 0 0 104.0 999.0 999.0 438.0 0.0 0.0 0.0 0
MA0601.2_rc_shift7 (Arid3b_rc)				; positions_6nt_m3 versus MA0601.2_rc (Arid3b_rc); m=5/27; ncol2=7; w=0; offset=3; strand=R; shift=7; score=0.516573; -------ATTAAtw ; cor=; Ncor= a 0 0 0 0 0 0 0 911.0 89.0 0.0 1000.0 895.0 238.0 566.0 c 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 34.0 80.0 g 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 119.0 80.0 t 0 0 0 0 0 0 0 89.0 911.0 1000.0 0.0 104.0 609.0 273.0
MA0621.2_rc_shift5 (mix-a_rc)				; positions_6nt_m3 versus MA0621.2_rc (mix-a_rc); m=6/27; ncol2=7; w=0; offset=1; strand=R; shift=5; score=0.513697; -----TAATTAa-- ; cor=; Ncor= a 0 0 0 0 0 21.0 1000.0 1000.0 0.0 0.0 1000.0 679.0 0 0 c 0 0 0 0 0 21.0 0.0 0.0 0.0 0.0 0.0 46.0 0 0 g 0 0 0 0 0 21.0 0.0 0.0 0.0 0.0 0.0 146.0 0 0 t 0 0 0 0 0 938.0 0.0 0.0 1000.0 1000.0 0.0 130.0 0 0
MA0108.3_shift7 (TBP)				; positions_6nt_m3 versus MA0108.3 (TBP); m=7/27; ncol2=7; w=0; offset=3; strand=D; shift=7; score=0.511634; -------TATAWAw ; cor=; Ncor= a 0 0 0 0 0 0 0 16.0 352.0 3.0 354.0 268.0 360.0 222.0 c 0 0 0 0 0 0 0 46.0 0.0 10.0 0.0 0.0 3.0 2.0 g 0 0 0 0 0 0 0 18.0 2.0 2.0 5.0 0.0 20.0 44.0 t 0 0 0 0 0 0 0 309.0 35.0 374.0 30.0 121.0 6.0 121.0
MA0702.3_rc_shift5 (LMX1A_rc)				; positions_6nt_m3 versus MA0702.3_rc (LMX1A_rc); m=8/27; ncol2=7; w=0; offset=1; strand=R; shift=5; score=0.508914; -----TAATTAr-- ; cor=; Ncor= a 0 0 0 0 0 0.0 7355.0 7355.0 0.0 0.0 7355.0 5133.0 0 0 c 0 0 0 0 0 501.0 0.0 0.0 0.0 0.0 19.0 305.0 0 0 g 0 0 0 0 0 102.0 0.0 50.0 9.0 0.0 31.0 2222.0 0 0 t 0 0 0 0 0 7355.0 0.0 0.0 7355.0 7355.0 0.0 90.0 0 0
MA0151.1_rc_shift7 (Arid3a_rc)				; positions_6nt_m3 versus MA0151.1_rc (Arid3a_rc); m=9/27; ncol2=6; w=0; offset=3; strand=R; shift=7; score=0.50747; -------TTTrAT- ; cor=; Ncor= a 0 0 0 0 0 0 0 6.0 0.0 0.0 17.0 27.0 0.0 0 c 0 0 0 0 0 0 0 1.0 0.0 0.0 0.0 0.0 0.0 0 g 0 0 0 0 0 0 0 0.0 0.0 0.0 9.0 0.0 0.0 0 t 0 0 0 0 0 0 0 20.0 27.0 27.0 1.0 0.0 27.0 0
MA0674.2_rc_shift8 (NKX6-1_rc)				; positions_6nt_m3 versus MA0674.2_rc (NKX6-1_rc); m=10/27; ncol2=7; w=0; offset=4; strand=R; shift=8; score=0.47571; --------tTAATk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 327.0 17.0 2212.0 2212.0 40.0 195.0 c 0 0 0 0 0 0 0 0 142.0 132.0 0.0 0.0 12.0 0.0 g 0 0 0 0 0 0 0 0 294.0 27.0 45.0 0.0 200.0 805.0 t 0 0 0 0 0 0 0 0 1450.0 2212.0 58.0 0.0 2212.0 1407.0
MA0683.2_shift1 (POU4F2)				; positions_6nt_m3 versus MA0683.2 (POU4F2); m=11/27; ncol2=15; w=-3; offset=-3; strand=D; shift=1; score=0.475199; -TGmATAATTAATk ; cor=; Ncor= a 0 110.0 193.0 1160.0 3079.0 1.0 2990.0 2621.0 76.0 304.0 3098.0 3187.0 19.0 130.0 c 0 121.0 34.0 2471.0 6.0 0.0 9.0 82.0 54.0 9.0 26.0 4.0 30.0 168.0 g 0 53.0 3440.0 2.0 4.0 0.0 14.0 53.0 28.0 8.0 234.0 9.0 69.0 2193.0 t 0 2757.0 81.0 5.0 11.0 2829.0 258.0 737.0 2735.0 2669.0 57.0 0.0 2761.0 1072.0
MA0635.2_rc_shift5 (BARHL2_rc)				; positions_6nt_m3 versus MA0635.2_rc (BARHL2_rc); m=12/27; ncol2=6; w=0; offset=1; strand=R; shift=5; score=0.453727; -----CrTTTA--- ; cor=; Ncor= a 0 0 0 0 0 1335.0 7756.0 4032.0 0.0 1969.0 12855.0 0 0 0 c 0 0 0 0 0 12855.0 127.0 1086.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0 0.0 12855.0 116.0 0.0 0.0 0.0 0 0 0 t 0 0 0 0 0 1570.0 443.0 12855.0 12855.0 12855.0 643.0 0 0 0
MA0650.4_rc_shift7 (Hoxa13_rc)				; positions_6nt_m3 versus MA0650.4_rc (Hoxa13_rc); m=13/27; ncol2=8; w=0; offset=3; strand=R; shift=7; score=0.446839; -------TTTATTG ; cor=; Ncor= a 0 0 0 0 0 0 0 247.0 212.0 832.0 16662.0 929.0 1439.0 1798.0 c 0 0 0 0 0 0 0 145.0 98.0 407.0 232.0 666.0 146.0 77.0 g 0 0 0 0 0 0 0 306.0 125.0 205.0 249.0 243.0 1594.0 14100.0 t 0 0 0 0 0 0 0 16550.0 16813.0 15804.0 105.0 15410.0 14069.0 1273.0
MA0847.4_rc_shift1 (FOXD2_rc)				; positions_6nt_m3 versus MA0847.4_rc (FOXD2_rc); m=14/27; ncol2=11; w=-3; offset=-3; strand=R; shift=1; score=0.437077; -TGTTTryTTAr-- ; cor=; Ncor= a 0 232.0 768.0 2.0 1.0 79.0 1141.0 4.0 262.0 0.0 2004.0 1578.0 0 0 c 0 34.0 0.0 5.0 18.0 0.0 3.0 1615.0 292.0 137.0 0.0 131.0 0 0 g 0 24.0 2484.0 0.0 23.0 81.0 1342.0 23.0 285.0 16.0 19.0 906.0 0 0 t 0 2484.0 0.0 2484.0 2484.0 2484.0 84.0 2484.0 2484.0 2484.0 480.0 219.0 0 0
MA1577.2_shift5 (TLX2)				; positions_6nt_m3 versus MA1577.2 (TLX2); m=15/27; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.432284; -----yAATTA--- ; cor=; Ncor= a 0 0 0 0 0 1435.0 7799.0 7799.0 0.0 0.0 7799.0 0 0 0 c 0 0 0 0 0 7799.0 0.0 0.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0 1112.0 80.0 0.0 0.0 0.0 0.0 0 0 0 t 0 0 0 0 0 8156.0 0.0 0.0 7799.0 7799.0 0.0 0 0 0
MA0654.2_shift5 (ISX)				; positions_6nt_m3 versus MA0654.2 (ISX); m=16/27; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.428616; -----yAATTA--- ; cor=; Ncor= a 0 0 0 0 0 10.0 2065.0 2065.0 0.0 0.0 2065.0 0 0 0 c 0 0 0 0 0 1003.0 48.0 16.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0 0.0 5.0 0.0 0.0 24.0 0.0 0 0 0 t 0 0 0 0 0 1061.0 24.0 10.0 2065.0 2065.0 49.0 0 0 0
MA0718.2_shift5 (RAX)				; positions_6nt_m3 versus MA0718.2 (RAX); m=17/27; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.426787; -----yAATTA--- ; cor=; Ncor= a 0 0 0 0 0 214.0 2412.0 2412.0 123.0 71.0 2412.0 0 0 0 c 0 0 0 0 0 1281.0 17.0 38.0 0.0 71.0 0.0 0 0 0 g 0 0 0 0 0 25.0 3.0 12.0 0.0 49.0 20.0 0 0 0 t 0 0 0 0 0 1131.0 40.0 24.0 2412.0 2412.0 126.0 0 0 0
MA0894.2_rc_shift5 (HESX1_rc)				; positions_6nt_m3 versus MA0894.2_rc (HESX1_rc); m=18/27; ncol2=6; w=0; offset=1; strand=R; shift=5; score=0.425089; -----yAATTA--- ; cor=; Ncor= a 0 0 0 0 0 97.0 4072.0 4072.0 0.0 31.0 4072.0 0 0 0 c 0 0 0 0 0 2180.0 0.0 15.0 9.0 53.0 34.0 0 0 0 g 0 0 0 0 0 38.0 15.0 0.0 7.0 0.0 0.0 0 0 0 t 0 0 0 0 0 1892.0 0.0 0.0 4072.0 4072.0 187.0 0 0 0
MA0125.2_rc_shift5 (Nobox_rc)				; positions_6nt_m3 versus MA0125.2_rc (Nobox_rc); m=19/27; ncol2=6; w=0; offset=1; strand=R; shift=5; score=0.424687; -----yAATTA--- ; cor=; Ncor= a 0 0 0 0 0 1.0 32.0 34.0 0.0 2.0 37.0 0 0 0 c 0 0 0 0 0 22.0 4.0 2.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0 0.0 0.0 1.0 0.0 0.0 1.0 0 0 0 t 0 0 0 0 0 15.0 2.0 1.0 38.0 36.0 0.0 0 0 0
MA1487.3_rc_shift0 (FOXE1_rc)				; positions_6nt_m3 versus MA1487.3_rc (FOXE1_rc); m=20/27; ncol2=12; w=-4; offset=-4; strand=R; shift=0; score=0.423904; tTGTTTrYTTAr-- ; cor=; Ncor= a 450.0 110.0 85.0 9.0 53.0 20.0 2064.0 27.0 579.0 43.0 2545.0 1479.0 0 0 c 258.0 18.0 0.0 23.0 0.0 0.0 17.0 871.0 116.0 402.0 0.0 57.0 0 0 g 392.0 32.0 3126.0 0.0 90.0 362.0 1062.0 117.0 113.0 28.0 43.0 1646.0 0 0 t 2026.0 3126.0 0.0 3126.0 3126.0 3126.0 587.0 2255.0 2547.0 3126.0 581.0 86.0 0 0
MA0628.2_shift5 (POU6F1)				; positions_6nt_m3 versus MA0628.2 (POU6F1); m=21/27; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.42194; -----TAATTA--- ; cor=; Ncor= a 0 0 0 0 0 32.0 905.0 938.0 14.0 18.0 950.0 0 0 0 c 0 0 0 0 0 10.0 70.0 34.0 14.0 8.0 8.0 0 0 0 g 0 0 0 0 0 8.0 8.0 14.0 34.0 70.0 10.0 0 0 0 t 0 0 0 0 0 950.0 18.0 14.0 938.0 905.0 32.0 0 0 0
MA0899.2_rc_shift7 (HOXA10_rc)				; positions_6nt_m3 versus MA0899.2_rc (HOXA10_rc); m=22/27; ncol2=9; w=0; offset=3; strand=R; shift=7; score=0.42093; -------tTTWATk ; cor=; Ncor= a 0 0 0 0 0 0 0 2058.0 331.0 384.0 2422.0 8381.0 267.0 957.0 c 0 0 0 0 0 0 0 1560.0 125.0 76.0 121.0 0.0 718.0 1022.0 g 0 0 0 0 0 0 0 2082.0 568.0 36.0 84.0 11.0 455.0 4516.0 t 0 0 0 0 0 0 0 8381.0 8381.0 8381.0 5960.0 367.0 8381.0 8381.0
MA0612.3_shift5 (EMX1)				; positions_6nt_m3 versus MA0612.3 (EMX1); m=23/27; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.420829; -----TAATTA--- ; cor=; Ncor= a 0 0 0 0 0 19.0 9544.0 9544.0 0.0 0.0 9544.0 0 0 0 c 0 0 0 0 0 2263.0 1235.0 0.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0 0.0 0.0 0.0 0.0 933.0 0.0 0 0 0 t 0 0 0 0 0 7281.0 0.0 0.0 9544.0 9544.0 0.0 0 0 0
MA0913.3_rc_shift7 (HOXD9_rc)				; positions_6nt_m3 versus MA0913.3_rc (HOXD9_rc); m=24/27; ncol2=9; w=0; offset=3; strand=R; shift=7; score=0.41956; -------TTTTATk ; cor=; Ncor= a 0 0 0 0 0 0 0 2194.0 0.0 123.0 5445.0 16363.0 4.0 927.0 c 0 0 0 0 0 0 0 1216.0 0.0 0.0 0.0 0.0 439.0 675.0 g 0 0 0 0 0 0 0 2202.0 0.0 0.0 8.0 0.0 226.0 8643.0 t 0 0 0 0 0 0 0 16363.0 16363.0 16363.0 16363.0 215.0 16363.0 16363.0
MA0722.2_shift8 (VAX1)				; positions_6nt_m3 versus MA0722.2 (VAX1); m=25/27; ncol2=7; w=0; offset=4; strand=D; shift=8; score=0.410902; --------yTAATt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 447.0 679.0 5253.0 5253.0 297.0 508.0 c 0 0 0 0 0 0 0 0 2775.0 995.0 863.0 153.0 86.0 321.0 g 0 0 0 0 0 0 0 0 455.0 101.0 189.0 46.0 213.0 1951.0 t 0 0 0 0 0 0 0 0 2479.0 5253.0 302.0 133.0 5253.0 5253.0
MA0876.2_rc_shift9 (BSX_rc)				; positions_6nt_m3 versus MA0876.2_rc (BSX_rc); m=26/27; ncol2=6; w=0; offset=5; strand=R; shift=9; score=0.404191; ---------TAATk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0.0 8832.0 8832.0 66.0 116.0 c 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 1078.0 2197.0 g 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 194.0 2483.0 t 0 0 0 0 0 0 0 0 0 8832.0 96.0 0.0 8832.0 4036.0
MA0892.2_rc_shift9 (GSX1_rc)				; positions_6nt_m3 versus MA0892.2_rc (GSX1_rc); m=27/27; ncol2=6; w=0; offset=5; strand=R; shift=9; score=0.400015; ---------TAATk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 103.0 1183.0 1183.0 50.0 177.0 c 0 0 0 0 0 0 0 0 0 9.0 0.0 3.0 123.0 60.0 g 0 0 0 0 0 0 0 0 0 0.0 106.0 79.0 106.0 402.0 t 0 0 0 0 0 0 0 0 0 1183.0 106.0 90.0 1183.0 781.0