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.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_motifs/peak-motifs_motifs_discovered.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.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_vs_db/peak-motifs_motifs_vs_db_JASPAR2024_CORE_vertebrates_non-redundant.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; drCAGAGAGrv ; Alignment reference a 2 2 0 7 0 7 0 7 0 3 2 c 0 1 7 0 0 0 0 0 0 1 2 g 3 3 0 0 7 0 7 0 6 2 2 t 2 1 0 0 0 0 0 0 1 1 1

MA1731.2_rc_shift2 (ZNF768_rc)
; oligos_7nt_mkv1_m2 versus MA1731.2_rc (ZNF768_rc); m=1/1; ncol2=9; w=0; offset=2; strand=R; shift=2; score=0.772426; --CAGAGAgGs ; cor=; Ncor= a 0 0 1.0 987.0 1.0 945.0 20.0 917.0 123.0 141.0 43.0 c 0 0 973.0 11.0 11.0 43.0 29.0 11.0 179.0 62.0 268.0 g 0 0 25.0 1.0 987.0 6.0 950.0 39.0 655.0 768.0 478.0 t 0 0 1.0 1.0 1.0 6.0 1.0 34.0 43.0 29.0 211.0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift1 ; 44 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -ycATTGTGhg ; Alignment reference a 0 2 2 9 0 0 0 0 0 3 2 c 0 3 3 0 0 0 0 0 0 3 1 g 0 1 2 0 0 0 9 0 9 0 5 t 0 3 2 0 9 9 0 9 0 3 1

MA0078.3_rc_shift1 (Sox17_rc)
; oligos_6nt_mkv1_m3 versus MA0078.3_rc (Sox17_rc); m=1/43; ncol2=10; w=0; offset=0; strand=R; shift=1; score=0.723235; -CCATTGTTct ; cor=; Ncor= a 0 870.0 471.0 10955.0 114.0 136.0 285.0 182.0 907.0 2044.0 1605.0 c 0 9181.0 10241.0 189.0 281.0 105.0 490.0 163.0 1561.0 6638.0 1889.0 g 0 1012.0 251.0 138.0 258.0 140.0 11241.0 124.0 1111.0 885.0 957.0 t 0 1224.0 1324.0 1005.0 11634.0 11906.0 271.0 11818.0 8708.0 2720.0 7836.0

MA0515.1_shift1 (Sox6)
; oligos_6nt_mkv1_m3 versus MA0515.1 (Sox6); m=2/43; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.701703; -cCwTTGTyyy ; cor=; Ncor= a 0 4.0 0.0 161.0 0.0 0.0 0.0 0.0 0.0 4.0 14.0 c 0 139.0 221.0 0.0 0.0 0.0 0.0 0.0 115.0 112.0 76.0 g 0 50.0 0.0 0.0 0.0 0.0 249.0 0.0 5.0 0.0 31.0 t 0 56.0 28.0 88.0 249.0 249.0 0.0 249.0 129.0 133.0 128.0

MA1562.2_rc_shift2 (SOX14_rc)
; oligos_6nt_mkv1_m3 versus MA1562.2_rc (SOX14_rc); m=3/43; ncol2=9; w=0; offset=1; strand=R; shift=2; score=0.684137; --cATTGTTCG ; cor=; Ncor= a 0 0 80.0 594.0 5.0 0.0 17.0 19.0 37.0 70.0 99.0 c 0 0 372.0 16.0 0.0 0.0 10.0 0.0 27.0 594.0 44.0 g 0 0 67.0 2.0 17.0 0.0 594.0 13.0 8.0 18.0 594.0 t 0 0 75.0 0.0 594.0 594.0 4.0 594.0 594.0 44.0 68.0

MA1563.2_rc_shift1 (SOX18_rc)
; oligos_6nt_mkv1_m3 versus MA1563.2_rc (SOX18_rc); m=4/43; ncol2=8; w=0; offset=0; strand=R; shift=1; score=0.657429; -bhATTGTt-- ; cor=; Ncor= a 0 0.0 228.0 447.0 0.0 0.0 2.0 0.0 34.0 0 0 c 0 424.0 221.0 0.0 17.0 0.0 91.0 0.0 170.0 0 0 g 0 551.0 0.0 0.0 35.0 0.0 424.0 0.0 81.0 0 0 t 0 382.0 203.0 0.0 424.0 424.0 0.0 424.0 424.0 0 0

MA1120.2_rc_shift1 (SOX13_rc)
; oligos_6nt_mkv1_m3 versus MA1120.2_rc (SOX13_rc); m=5/43; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.657047; -cCATTGT--- ; cor=; Ncor= a 0 461.0 73.0 4291.0 51.0 118.0 161.0 39.0 0 0 0 c 0 2666.0 3837.0 28.0 63.0 50.0 60.0 40.0 0 0 0 g 0 647.0 57.0 77.0 48.0 55.0 4276.0 22.0 0 0 0 t 0 778.0 585.0 156.0 4390.0 4329.0 55.0 4451.0 0 0 0

MA0514.3_rc_shift1 (Sox3_rc)
; oligos_6nt_mkv1_m3 versus MA0514.3_rc (Sox3_rc); m=6/43; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.65318; -cCATTGT--- ; cor=; Ncor= a 0 973.0 187.0 11151.0 69.0 289.0 525.0 89.0 0 0 0 c 0 7664.0 10041.0 104.0 143.0 93.0 178.0 76.0 0 0 0 g 0 1582.0 133.0 150.0 143.0 312.0 11125.0 52.0 0 0 0 t 0 1759.0 1617.0 573.0 11623.0 11284.0 150.0 11761.0 0 0 0

MA0143.5_rc_shift1 (SOX2_rc)
; oligos_6nt_mkv1_m3 versus MA0143.5_rc (SOX2_rc); m=7/43; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.65193; -cCATTGT--- ; cor=; Ncor= a 0 10304.0 1656.0 79277.0 1185.0 2412.0 4848.0 1385.0 0 0 0 c 0 54414.0 73372.0 930.0 2002.0 550.0 1243.0 418.0 0 0 0 g 0 6264.0 800.0 732.0 1742.0 1205.0 78356.0 436.0 0 0 0 t 0 14772.0 9926.0 4815.0 80825.0 81587.0 1307.0 83515.0 0 0 0

MA1152.2_shift1 (SOX15)
; oligos_6nt_mkv1_m3 versus MA1152.2 (SOX15); m=8/43; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.649596; -yywTTGT--- ; cor=; Ncor= a 0 32.0 62.0 631.0 3.0 3.0 83.0 24.0 0 0 0 c 0 554.0 412.0 3.0 3.0 2.0 21.0 2.0 0 0 0 g 0 147.0 26.0 5.0 6.0 2.0 890.0 3.0 0 0 0 t 0 267.0 501.0 362.0 988.0 994.0 5.0 971.0 0 0 0

MA0077.2_shift1 (SOX9)
; oligos_6nt_mkv1_m3 versus MA0077.2 (SOX9); m=9/43; ncol2=8; w=0; offset=0; strand=D; shift=1; score=0.625036; -CyATTGTT-- ; cor=; Ncor= a 0 3.0 8.0 71.0 2.0 7.0 2.0 13.0 9.0 0 0 c 0 55.0 38.0 1.0 1.0 0.0 2.0 0.0 7.0 0 0 g 0 9.0 6.0 0.0 2.0 4.0 72.0 4.0 6.0 0 0 t 0 9.0 24.0 4.0 71.0 65.0 0.0 59.0 54.0 0 0

MA0087.3_rc_shift1 (Sox5_rc)
; oligos_6nt_mkv1_m3 versus MA0087.3_rc (Sox5_rc); m=10/43; ncol2=8; w=0; offset=0; strand=R; shift=1; score=0.602651; -CCATTGTT-- ; cor=; Ncor= a 0 7.0 3.0 114.0 1.0 0.0 2.0 1.0 4.0 0 0 c 0 90.0 101.0 1.0 4.0 2.0 2.0 1.0 12.0 0 0 g 0 14.0 0.0 3.0 5.0 2.0 120.0 0.0 4.0 0 0 t 0 13.0 20.0 6.0 114.0 120.0 0.0 122.0 104.0 0 0

MA0084.2_rc_shift3 (SRY_rc)
; oligos_6nt_mkv1_m3 versus MA0084.2_rc (SRY_rc); m=11/43; ncol2=7; w=0; offset=2; strand=R; shift=3; score=0.570614; ---wTTGTtw- ; cor=; Ncor= a 0 0 0 19.0 0.0 0.0 2.0 3.0 4.0 10.0 0 c 0 0 0 2.0 1.0 0.0 0.0 0.0 3.0 3.0 0 g 0 0 0 0.0 0.0 0.0 26.0 0.0 3.0 0.0 0 t 0 0 0 7.0 27.0 28.0 0.0 25.0 18.0 15.0 0

MA0868.3_rc_shift2 (SOX8_rc)
; oligos_6nt_mkv1_m3 versus MA0868.3_rc (SOX8_rc); m=12/43; ncol2=7; w=0; offset=1; strand=R; shift=2; score=0.56669; --yATTGTT-- ; cor=; Ncor= a 0 0 287.0 1827.0 36.0 16.0 70.0 45.0 222.0 0 0 c 0 0 1827.0 20.0 0.0 0.0 35.0 0.0 263.0 0 0 g 0 0 208.0 36.0 43.0 0.0 1827.0 0.0 151.0 0 0 t 0 0 1356.0 273.0 1827.0 1827.0 3.0 1827.0 1827.0 0 0

MA0867.3_rc_shift1 (SOX4_rc)
; oligos_6nt_mkv1_m3 versus MA0867.3_rc (SOX4_rc); m=13/43; ncol2=8; w=0; offset=0; strand=R; shift=1; score=0.563373; -yCwTTGTt-- ; cor=; Ncor= a 0 174.0 83.0 2719.0 0.0 0.0 33.0 9.0 431.0 0 0 c 0 3489.0 5582.0 50.0 11.0 6.0 37.0 0.0 2047.0 0 0 g 0 1422.0 64.0 120.0 6.0 1.0 5582.0 0.0 951.0 0 0 t 0 2093.0 1018.0 5582.0 5582.0 5582.0 0.0 5582.0 5582.0 0 0

MA0102.5_rc_shift3 (CEBPA_rc)
; oligos_6nt_mkv1_m3 versus MA0102.5_rc (CEBPA_rc); m=14/43; ncol2=10; w=0; offset=2; strand=R; shift=3; score=0.558287; ---aTTGTGCA ; cor=; Ncor= a 0 0 0 50992.0 1411.0 1092.0 9787.0 6308.0 2053.0 10928.0 75354.0 c 0 0 0 7312.0 1381.0 340.0 1583.0 6751.0 678.0 57887.0 2365.0 g 0 0 0 16193.0 1034.0 5655.0 61538.0 3535.0 75124.0 936.0 282.0 t 0 0 0 4506.0 75177.0 71916.0 6095.0 62409.0 1148.0 9252.0 1002.0

MA0836.3_rc_shift4 (CEBPD_rc)
; oligos_6nt_mkv1_m3 versus MA0836.3_rc (CEBPD_rc); m=15/43; ncol2=8; w=0; offset=3; strand=R; shift=4; score=0.524094; ----TTGTGCA ; cor=; Ncor= a 0 0 0 0 359.0 185.0 2276.0 1831.0 292.0 1977.0 20939.0 c 0 0 0 0 404.0 75.0 377.0 2625.0 214.0 17309.0 233.0 g 0 0 0 0 315.0 652.0 17458.0 1022.0 20683.0 299.0 81.0 t 0 0 0 0 20374.0 20540.0 1341.0 15974.0 263.0 1867.0 199.0

MA0700.3_rc_shift1 (LHX2_rc)
; oligos_6nt_mkv1_m3 versus MA0700.3_rc (LHX2_rc); m=16/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.480426; -TAATTG---- ; cor=; Ncor= a 0 39.0 6256.0 6082.0 133.0 420.0 640.0 0 0 0 0 c 0 6.0 5.0 64.0 77.0 52.0 37.0 0 0 0 0 g 0 13.0 5.0 58.0 101.0 71.0 5612.0 0 0 0 0 t 0 6275.0 67.0 129.0 6022.0 5790.0 44.0 0 0 0 0

MA1561.2_rc_shift3 (SOX12_rc)
; oligos_6nt_mkv1_m3 versus MA1561.2_rc (SOX12_rc); m=17/43; ncol2=10; w=0; offset=2; strand=R; shift=3; score=0.479085; ---ATTGTTCG ; cor=; Ncor= a 0 0 0 854.0 20.0 0.0 3.0 0.0 1.0 48.0 56.0 c 0 0 0 57.0 44.0 0.0 0.0 4.0 2.0 854.0 34.0 g 0 0 0 211.0 91.0 0.0 854.0 2.0 26.0 26.0 854.0 t 0 0 0 129.0 854.0 854.0 0.0 854.0 854.0 47.0 48.0

MA0708.3_rc_shift1 (MSX2_rc)
; oligos_6nt_mkv1_m3 versus MA0708.3_rc (MSX2_rc); m=18/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.478045; -TAATTR---- ; cor=; Ncor= a 0 0.0 6353.0 6353.0 0.0 0.0 2737.0 0 0 0 0 c 0 243.0 0.0 0.0 0.0 259.0 0.0 0 0 0 0 g 0 0.0 600.0 0.0 112.0 175.0 6353.0 0 0 0 0 t 0 6353.0 62.0 0.0 6353.0 6353.0 220.0 0 0 0 0

MA0709.2_rc_shift1 (Msx3_rc)
; oligos_6nt_mkv1_m3 versus MA0709.2_rc (Msx3_rc); m=19/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.472135; -TAATTr---- ; cor=; Ncor= a 0 213.0 8380.0 8380.0 5.0 94.0 2582.0 0 0 0 0 c 0 88.0 105.0 0.0 38.0 237.0 29.0 0 0 0 0 g 0 59.0 215.0 0.0 89.0 160.0 5798.0 0 0 0 0 t 0 8380.0 121.0 0.0 8380.0 8380.0 312.0 0 0 0 0

MA0666.3_rc_shift1 (MSX1_rc)
; oligos_6nt_mkv1_m3 versus MA0666.3_rc (MSX1_rc); m=20/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.470786; -TAATTr---- ; cor=; Ncor= a 0 0.0 5064.0 5064.0 0.0 0.0 2415.0 0 0 0 0 c 0 159.0 0.0 0.0 0.0 146.0 0.0 0 0 0 0 g 0 0.0 280.0 0.0 42.0 125.0 5064.0 0 0 0 0 t 0 5064.0 0.0 0.0 5064.0 5064.0 227.0 0 0 0 0

MA0879.3_rc_shift1 (DLX1_rc)
; oligos_6nt_mkv1_m3 versus MA0879.3_rc (DLX1_rc); m=21/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.460045; -TAATTr---- ; cor=; Ncor= a 0 614.0 6231.0 6231.0 0.0 540.0 2171.0 0 0 0 0 c 0 168.0 155.0 0.0 0.0 954.0 0.0 0 0 0 0 g 0 0.0 639.0 0.0 222.0 1212.0 4059.0 0 0 0 0 t 0 6231.0 0.0 0.0 6231.0 6231.0 265.0 0 0 0 0

MA0881.2_rc_shift1 (Dlx4_rc)
; oligos_6nt_mkv1_m3 versus MA0881.2_rc (Dlx4_rc); m=22/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.453397; -TAATTr---- ; cor=; Ncor= a 0 1127.0 12054.0 12054.0 499.0 883.0 5213.0 0 0 0 0 c 0 134.0 542.0 38.0 55.0 739.0 145.0 0 0 0 0 g 0 316.0 868.0 85.0 744.0 1500.0 6841.0 0 0 0 0 t 0 12054.0 440.0 88.0 12054.0 12054.0 724.0 0 0 0 0

MA0027.3_rc_shift1 (EN1_rc)
; oligos_6nt_mkv1_m3 versus MA0027.3_rc (EN1_rc); m=23/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.453269; -TAATTr---- ; cor=; Ncor= a 0 132.0 2891.0 2891.0 0.0 0.0 1562.0 0 0 0 0 c 0 30.0 162.0 0.0 0.0 71.0 5.0 0 0 0 0 g 0 0.0 483.0 0.0 28.0 99.0 1328.0 0 0 0 0 t 0 2891.0 57.0 0.0 2891.0 2891.0 104.0 0 0 0 0

MA0890.2_rc_shift1 (GBX2_rc)
; oligos_6nt_mkv1_m3 versus MA0890.2_rc (GBX2_rc); m=24/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.453154; -TAATTr---- ; cor=; Ncor= a 0 650.0 27366.0 27366.0 25.0 227.0 11855.0 0 0 0 0 c 0 30.0 673.0 65.0 114.0 1113.0 106.0 0 0 0 0 g 0 73.0 570.0 61.0 250.0 570.0 15511.0 0 0 0 0 t 0 27366.0 318.0 0.0 27366.0 27366.0 699.0 0 0 0 0

MA0717.2_rc_shift1 (RAX2_rc)
; oligos_6nt_mkv1_m3 versus MA0717.2_rc (RAX2_rc); m=25/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.451769; -TAATTr---- ; cor=; Ncor= a 0 4258.0 38860.0 38860.0 1030.0 2421.0 19215.0 0 0 0 0 c 0 360.0 2513.0 125.0 757.0 4490.0 1688.0 0 0 0 0 g 0 2644.0 4232.0 738.0 1523.0 3060.0 19645.0 0 0 0 0 t 0 38860.0 2167.0 270.0 38860.0 38860.0 3558.0 0 0 0 0

MA0880.2_rc_shift1 (Dlx3_rc)
; oligos_6nt_mkv1_m3 versus MA0880.2_rc (Dlx3_rc); m=26/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.451424; -TAATTr---- ; cor=; Ncor= a 0 691.0 7323.0 7323.0 299.0 643.0 3190.0 0 0 0 0 c 0 101.0 452.0 60.0 62.0 587.0 164.0 0 0 0 0 g 0 202.0 535.0 66.0 536.0 995.0 4133.0 0 0 0 0 t 0 7323.0 399.0 173.0 7323.0 7323.0 572.0 0 0 0 0

MA0699.2_rc_shift1 (LBX2_rc)
; oligos_6nt_mkv1_m3 versus MA0699.2_rc (LBX2_rc); m=27/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.450569; -TAATTr---- ; cor=; Ncor= a 0 148.0 2996.0 2996.0 89.0 57.0 1362.0 0 0 0 0 c 0 106.0 293.0 118.0 130.0 325.0 109.0 0 0 0 0 g 0 34.0 258.0 29.0 290.0 338.0 1634.0 0 0 0 0 t 0 2996.0 150.0 0.0 2996.0 2996.0 157.0 0 0 0 0

MA0894.2_shift1 (HESX1)
; oligos_6nt_mkv1_m3 versus MA0894.2 (HESX1); m=28/43; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.450317; -TAATTr---- ; cor=; Ncor= a 0 187.0 4072.0 4072.0 0.0 0.0 1892.0 0 0 0 0 c 0 0.0 0.0 7.0 0.0 15.0 38.0 0 0 0 0 g 0 34.0 53.0 9.0 15.0 0.0 2180.0 0 0 0 0 t 0 4072.0 31.0 0.0 4072.0 4072.0 97.0 0 0 0 0

MA0718.2_rc_shift1 (RAX_rc)
; oligos_6nt_mkv1_m3 versus MA0718.2_rc (RAX_rc); m=29/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.44881; -TAATTr---- ; cor=; Ncor= a 0 126.0 2412.0 2412.0 24.0 40.0 1131.0 0 0 0 0 c 0 20.0 49.0 0.0 12.0 3.0 25.0 0 0 0 0 g 0 0.0 71.0 0.0 38.0 17.0 1281.0 0 0 0 0 t 0 2412.0 71.0 123.0 2412.0 2412.0 214.0 0 0 0 0

MA0909.4_rc_shift0 (Hoxd13_rc)
; oligos_6nt_mkv1_m3 versus MA0909.4_rc (Hoxd13_rc); m=30/43; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.44838; TTTATTG---- ; cor=; Ncor= a 667.0 15.0 11.0 5972.0 30.0 49.0 61.0 0 0 0 0 c 379.0 2.0 7.0 3.0 11.0 148.0 34.0 0 0 0 0 g 704.0 37.0 4.0 2.0 13.0 5.0 5866.0 0 0 0 0 t 4227.0 5923.0 5955.0 0.0 5923.0 5775.0 16.0 0 0 0 0

MA0720.2_rc_shift1 (Shox2_rc)
; oligos_6nt_mkv1_m3 versus MA0720.2_rc (Shox2_rc); m=31/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.447118; -TAATTr---- ; cor=; Ncor= a 0 895.0 18179.0 18179.0 79.0 766.0 9152.0 0 0 0 0 c 0 36.0 870.0 0.0 3.0 426.0 228.0 0 0 0 0 g 0 193.0 545.0 12.0 138.0 626.0 9027.0 0 0 0 0 t 0 18179.0 597.0 29.0 18179.0 18179.0 979.0 0 0 0 0

MA0125.2_shift1 (Nobox)
; oligos_6nt_mkv1_m3 versus MA0125.2 (Nobox); m=32/43; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.444393; -TAATTr---- ; cor=; Ncor= a 0 0.0 36.0 38.0 1.0 2.0 15.0 0 0 0 0 c 0 1.0 0.0 0.0 1.0 0.0 0.0 0 0 0 0 g 0 0.0 0.0 0.0 2.0 4.0 22.0 0 0 0 0 t 0 37.0 2.0 0.0 34.0 32.0 1.0 0 0 0 0

MA0882.2_rc_shift1 (DLX6_rc)
; oligos_6nt_mkv1_m3 versus MA0882.2_rc (DLX6_rc); m=33/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.444327; -TAATTr---- ; cor=; Ncor= a 0 193.0 2623.0 2623.0 56.0 184.0 1212.0 0 0 0 0 c 0 16.0 68.0 0.0 0.0 143.0 21.0 0 0 0 0 g 0 30.0 140.0 0.0 124.0 273.0 1410.0 0 0 0 0 t 0 2623.0 48.0 12.0 2623.0 2623.0 137.0 0 0 0 0

MA0716.2_rc_shift1 (PRRX1_rc)
; oligos_6nt_mkv1_m3 versus MA0716.2_rc (PRRX1_rc); m=34/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.44302; -TAATTr---- ; cor=; Ncor= a 0 1229.0 23897.0 23897.0 209.0 810.0 12775.0 0 0 0 0 c 0 136.0 1004.0 0.0 202.0 1776.0 1121.0 0 0 0 0 g 0 644.0 2302.0 3.0 503.0 1088.0 11122.0 0 0 0 0 t 0 23897.0 1264.0 0.0 23897.0 23897.0 2373.0 0 0 0 0

MA0721.2_rc_shift1 (UNCX_rc)
; oligos_6nt_mkv1_m3 versus MA0721.2_rc (UNCX_rc); m=35/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.442158; -TAATTr---- ; cor=; Ncor= a 0 3885.0 36926.0 36926.0 890.0 2629.0 20126.0 0 0 0 0 c 0 731.0 1782.0 117.0 420.0 4582.0 2086.0 0 0 0 0 g 0 2211.0 3958.0 806.0 1302.0 2540.0 16800.0 0 0 0 0 t 0 36926.0 3111.0 481.0 36926.0 36926.0 3975.0 0 0 0 0

MA0662.2_rc_shift1 (MIXL1_rc)
; oligos_6nt_mkv1_m3 versus MA0662.2_rc (MIXL1_rc); m=36/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.442057; -TAATTr---- ; cor=; Ncor= a 0 2895.0 27042.0 27042.0 736.0 1038.0 15403.0 0 0 0 0 c 0 115.0 2031.0 181.0 556.0 3660.0 1245.0 0 0 0 0 g 0 1903.0 4270.0 510.0 662.0 1911.0 11639.0 0 0 0 0 t 0 27042.0 1385.0 0.0 27042.0 27042.0 2635.0 0 0 0 0

MA0630.2_shift1 (SHOX)
; oligos_6nt_mkv1_m3 versus MA0630.2 (SHOX); m=37/43; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.441534; -TAATTr---- ; cor=; Ncor= a 0 74.0 852.0 991.0 15.0 98.0 416.0 0 0 0 0 c 0 30.0 48.0 2.0 15.0 50.0 48.0 0 0 0 0 g 0 9.0 55.0 5.0 27.0 84.0 424.0 0 0 0 0 t 0 886.0 45.0 2.0 943.0 768.0 111.0 0 0 0 0

MA1505.2_rc_shift1 (HOXC8_rc)
; oligos_6nt_mkv1_m3 versus MA1505.2_rc (HOXC8_rc); m=38/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.43948; -YAATTr---- ; cor=; Ncor= a 0 0.0 9273.0 9273.0 0.0 983.0 9273.0 0 0 0 0 c 0 4325.0 2656.0 211.0 0.0 19.0 0.0 0 0 0 0 g 0 0.0 99.0 0.0 20.0 2727.0 4555.0 0 0 0 0 t 0 9273.0 961.0 0.0 9273.0 9273.0 0.0 0 0 0 0

MA0654.2_rc_shift1 (ISX_rc)
; oligos_6nt_mkv1_m3 versus MA0654.2_rc (ISX_rc); m=39/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.437345; -TAATTr---- ; cor=; Ncor= a 0 49.0 2065.0 2065.0 10.0 24.0 1061.0 0 0 0 0 c 0 0.0 24.0 0.0 0.0 5.0 0.0 0 0 0 0 g 0 0.0 0.0 0.0 16.0 48.0 1003.0 0 0 0 0 t 0 2065.0 0.0 0.0 2065.0 2065.0 10.0 0 0 0 0

MA0634.2_rc_shift1 (ALX3_rc)
; oligos_6nt_mkv1_m3 versus MA0634.2_rc (ALX3_rc); m=40/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.435389; -TAATTr---- ; cor=; Ncor= a 0 977.0 7877.0 7877.0 231.0 629.0 4510.0 0 0 0 0 c 0 87.0 239.0 8.0 141.0 885.0 345.0 0 0 0 0 g 0 449.0 729.0 72.0 317.0 506.0 3367.0 0 0 0 0 t 0 7877.0 697.0 76.0 7877.0 7877.0 794.0 0 0 0 0

MA1577.2_rc_shift1 (TLX2_rc)
; oligos_6nt_mkv1_m3 versus MA1577.2_rc (TLX2_rc); m=41/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.431779; -TAATTr---- ; cor=; Ncor= a 0 0.0 7799.0 7799.0 0.0 0.0 8156.0 0 0 0 0 c 0 0.0 0.0 0.0 0.0 80.0 1112.0 0 0 0 0 g 0 0.0 0.0 0.0 0.0 0.0 7799.0 0 0 0 0 t 0 7799.0 0.0 0.0 7799.0 7799.0 1435.0 0 0 0 0

MA1481.2_rc_shift1 (DRGX_rc)
; oligos_6nt_mkv1_m3 versus MA1481.2_rc (DRGX_rc); m=42/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.422285; -TAATTr---- ; cor=; Ncor= a 0 144.0 14867.0 14867.0 0.0 0.0 8870.0 0 0 0 0 c 0 962.0 209.0 0.0 0.0 2037.0 1111.0 0 0 0 0 g 0 17.0 813.0 0.0 0.0 501.0 5997.0 0 0 0 0 t 0 14867.0 0.0 0.0 14867.0 14867.0 1079.0 0 0 0 0

MA0705.2_rc_shift1 (Lhx8_rc)
; oligos_6nt_mkv1_m3 versus MA0705.2_rc (Lhx8_rc); m=43/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.421045; -YRATTR---- ; cor=; Ncor= a 0 0.0 5092.0 5092.0 0.0 0.0 5092.0 0 0 0 0 c 0 1929.0 88.0 0.0 0.0 1670.0 0.0 0 0 0 0 g 0 0.0 2083.0 0.0 0.0 160.0 1996.0 0 0 0 0 t 0 5092.0 0.0 0.0 5092.0 5092.0 0.0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift2 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --dgCAGAGAgw ; Alignment reference a 0 0 4 2 0 10 0 10 0 10 1 4 c 0 0 0 2 10 0 0 0 0 0 2 1 g 0 0 3 5 0 0 10 0 10 0 6 2 t 0 0 3 1 0 0 0 0 0 0 1 3

MA1731.2_rc_shift4 (ZNF768_rc)
; oligos_6nt_mkv1_m4 versus MA1731.2_rc (ZNF768_rc); m=1/4; ncol2=9; w=0; offset=2; strand=R; shift=4; score=0.689009; ----CAGAGAgG ; cor=; Ncor= a 0 0 0 0 1.0 987.0 1.0 945.0 20.0 917.0 123.0 141.0 c 0 0 0 0 973.0 11.0 11.0 43.0 29.0 11.0 179.0 62.0 g 0 0 0 0 25.0 1.0 987.0 6.0 950.0 39.0 655.0 768.0 t 0 0 0 0 1.0 1.0 1.0 6.0 1.0 34.0 43.0 29.0

MA1593.2_shift0 (ZNF317)
; oligos_6nt_mkv1_m4 versus MA1593.2 (ZNF317); m=2/4; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.449161; ACAGCAGA---- ; cor=; Ncor= a 9381.0 281.0 10344.0 691.0 395.0 9323.0 284.0 10825.0 0 0 0 0 c 357.0 10821.0 85.0 192.0 10608.0 250.0 186.0 208.0 0 0 0 0 g 480.0 183.0 317.0 10374.0 223.0 289.0 10730.0 206.0 0 0 0 0 t 1245.0 178.0 717.0 206.0 237.0 1601.0 263.0 224.0 0 0 0 0

MA0508.4_rc_shift6 (PRDM1_rc)
; oligos_6nt_mkv1_m4 versus MA0508.4_rc (PRDM1_rc); m=3/4; ncol2=7; w=0; offset=4; strand=R; shift=6; score=0.430944; ------GAGAAA ; cor=; Ncor= a 0 0 0 0 0 0 660.0 49466.0 432.0 52619.0 50943.0 52905.0 c 0 0 0 0 0 0 290.0 1390.0 207.0 561.0 1011.0 826.0 g 0 0 0 0 0 0 52821.0 1076.0 53465.0 488.0 1346.0 467.0 t 0 0 0 0 0 0 1710.0 3549.0 1377.0 1813.0 2181.0 1283.0

MA0092.2_rc_shift0 (Hand1::Tcf3_rc)
; oligos_6nt_mkv1_m4 versus MA0092.2_rc (Hand1::Tcf3_rc); m=4/4; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.411895; awkCCAGAy--- ; cor=; Ncor= a 16.0 10.0 5.0 1.0 0.0 29.0 1.0 24.0 4.0 0 0 0 c 4.0 3.0 1.0 25.0 29.0 0.0 0.0 1.0 15.0 0 0 0 g 4.0 0.0 14.0 3.0 0.0 0.0 28.0 2.0 0.0 0 0 0 t 5.0 16.0 9.0 0.0 0.0 0.0 0.0 2.0 10.0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; mAGCCAGCCAGCC ; Alignment reference a 32 59 1 1 1 63 1 0 0 62 1 2 3 c 33 0 8 62 63 1 8 65 63 0 0 58 58 g 0 5 56 1 0 0 56 0 1 3 64 4 3 t 0 1 0 1 1 1 0 0 1 0 0 1 1

MA2341.1_shift2 (FEZF2)
; oligos_6nt_mkv1_m1 versus MA2341.1 (FEZF2); m=1/1; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.432688; --CCCAGCCT--- ; cor=; Ncor= a 0 0 17.0 5.0 4.0 231.0 6.0 8.0 7.0 14.0 0 0 0 c 0 0 202.0 206.0 258.0 15.0 8.0 224.0 247.0 10.0 0 0 0 g 0 0 10.0 9.0 0.0 14.0 251.0 28.0 2.0 8.0 0 0 0 t 0 0 36.0 45.0 3.0 5.0 0.0 5.0 9.0 233.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -ycATTGTGhg ; Alignment reference a 0 2 2 9 0 0 0 0 0 3 2 c 0 3 3 0 0 0 0 0 0 3 1 g 0 1 2 0 0 0 9 0 9 0 5 t 0 3 2 0 9 9 0 9 0 3 1
MA0078.3_rc_shift1 (Sox17_rc)				; oligos_6nt_mkv1_m3 versus MA0078.3_rc (Sox17_rc); m=1/43; ncol2=10; w=0; offset=0; strand=R; shift=1; score=0.723235; -CCATTGTTct ; cor=; Ncor= a 0 870.0 471.0 10955.0 114.0 136.0 285.0 182.0 907.0 2044.0 1605.0 c 0 9181.0 10241.0 189.0 281.0 105.0 490.0 163.0 1561.0 6638.0 1889.0 g 0 1012.0 251.0 138.0 258.0 140.0 11241.0 124.0 1111.0 885.0 957.0 t 0 1224.0 1324.0 1005.0 11634.0 11906.0 271.0 11818.0 8708.0 2720.0 7836.0
MA0515.1_shift1 (Sox6)				; oligos_6nt_mkv1_m3 versus MA0515.1 (Sox6); m=2/43; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.701703; -cCwTTGTyyy ; cor=; Ncor= a 0 4.0 0.0 161.0 0.0 0.0 0.0 0.0 0.0 4.0 14.0 c 0 139.0 221.0 0.0 0.0 0.0 0.0 0.0 115.0 112.0 76.0 g 0 50.0 0.0 0.0 0.0 0.0 249.0 0.0 5.0 0.0 31.0 t 0 56.0 28.0 88.0 249.0 249.0 0.0 249.0 129.0 133.0 128.0
MA1562.2_rc_shift2 (SOX14_rc)				; oligos_6nt_mkv1_m3 versus MA1562.2_rc (SOX14_rc); m=3/43; ncol2=9; w=0; offset=1; strand=R; shift=2; score=0.684137; --cATTGTTCG ; cor=; Ncor= a 0 0 80.0 594.0 5.0 0.0 17.0 19.0 37.0 70.0 99.0 c 0 0 372.0 16.0 0.0 0.0 10.0 0.0 27.0 594.0 44.0 g 0 0 67.0 2.0 17.0 0.0 594.0 13.0 8.0 18.0 594.0 t 0 0 75.0 0.0 594.0 594.0 4.0 594.0 594.0 44.0 68.0
MA1563.2_rc_shift1 (SOX18_rc)				; oligos_6nt_mkv1_m3 versus MA1563.2_rc (SOX18_rc); m=4/43; ncol2=8; w=0; offset=0; strand=R; shift=1; score=0.657429; -bhATTGTt-- ; cor=; Ncor= a 0 0.0 228.0 447.0 0.0 0.0 2.0 0.0 34.0 0 0 c 0 424.0 221.0 0.0 17.0 0.0 91.0 0.0 170.0 0 0 g 0 551.0 0.0 0.0 35.0 0.0 424.0 0.0 81.0 0 0 t 0 382.0 203.0 0.0 424.0 424.0 0.0 424.0 424.0 0 0
MA1120.2_rc_shift1 (SOX13_rc)				; oligos_6nt_mkv1_m3 versus MA1120.2_rc (SOX13_rc); m=5/43; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.657047; -cCATTGT--- ; cor=; Ncor= a 0 461.0 73.0 4291.0 51.0 118.0 161.0 39.0 0 0 0 c 0 2666.0 3837.0 28.0 63.0 50.0 60.0 40.0 0 0 0 g 0 647.0 57.0 77.0 48.0 55.0 4276.0 22.0 0 0 0 t 0 778.0 585.0 156.0 4390.0 4329.0 55.0 4451.0 0 0 0
MA0514.3_rc_shift1 (Sox3_rc)				; oligos_6nt_mkv1_m3 versus MA0514.3_rc (Sox3_rc); m=6/43; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.65318; -cCATTGT--- ; cor=; Ncor= a 0 973.0 187.0 11151.0 69.0 289.0 525.0 89.0 0 0 0 c 0 7664.0 10041.0 104.0 143.0 93.0 178.0 76.0 0 0 0 g 0 1582.0 133.0 150.0 143.0 312.0 11125.0 52.0 0 0 0 t 0 1759.0 1617.0 573.0 11623.0 11284.0 150.0 11761.0 0 0 0
MA0143.5_rc_shift1 (SOX2_rc)				; oligos_6nt_mkv1_m3 versus MA0143.5_rc (SOX2_rc); m=7/43; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.65193; -cCATTGT--- ; cor=; Ncor= a 0 10304.0 1656.0 79277.0 1185.0 2412.0 4848.0 1385.0 0 0 0 c 0 54414.0 73372.0 930.0 2002.0 550.0 1243.0 418.0 0 0 0 g 0 6264.0 800.0 732.0 1742.0 1205.0 78356.0 436.0 0 0 0 t 0 14772.0 9926.0 4815.0 80825.0 81587.0 1307.0 83515.0 0 0 0
MA1152.2_shift1 (SOX15)				; oligos_6nt_mkv1_m3 versus MA1152.2 (SOX15); m=8/43; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.649596; -yywTTGT--- ; cor=; Ncor= a 0 32.0 62.0 631.0 3.0 3.0 83.0 24.0 0 0 0 c 0 554.0 412.0 3.0 3.0 2.0 21.0 2.0 0 0 0 g 0 147.0 26.0 5.0 6.0 2.0 890.0 3.0 0 0 0 t 0 267.0 501.0 362.0 988.0 994.0 5.0 971.0 0 0 0
MA0077.2_shift1 (SOX9)				; oligos_6nt_mkv1_m3 versus MA0077.2 (SOX9); m=9/43; ncol2=8; w=0; offset=0; strand=D; shift=1; score=0.625036; -CyATTGTT-- ; cor=; Ncor= a 0 3.0 8.0 71.0 2.0 7.0 2.0 13.0 9.0 0 0 c 0 55.0 38.0 1.0 1.0 0.0 2.0 0.0 7.0 0 0 g 0 9.0 6.0 0.0 2.0 4.0 72.0 4.0 6.0 0 0 t 0 9.0 24.0 4.0 71.0 65.0 0.0 59.0 54.0 0 0
MA0087.3_rc_shift1 (Sox5_rc)				; oligos_6nt_mkv1_m3 versus MA0087.3_rc (Sox5_rc); m=10/43; ncol2=8; w=0; offset=0; strand=R; shift=1; score=0.602651; -CCATTGTT-- ; cor=; Ncor= a 0 7.0 3.0 114.0 1.0 0.0 2.0 1.0 4.0 0 0 c 0 90.0 101.0 1.0 4.0 2.0 2.0 1.0 12.0 0 0 g 0 14.0 0.0 3.0 5.0 2.0 120.0 0.0 4.0 0 0 t 0 13.0 20.0 6.0 114.0 120.0 0.0 122.0 104.0 0 0
MA0084.2_rc_shift3 (SRY_rc)				; oligos_6nt_mkv1_m3 versus MA0084.2_rc (SRY_rc); m=11/43; ncol2=7; w=0; offset=2; strand=R; shift=3; score=0.570614; ---wTTGTtw- ; cor=; Ncor= a 0 0 0 19.0 0.0 0.0 2.0 3.0 4.0 10.0 0 c 0 0 0 2.0 1.0 0.0 0.0 0.0 3.0 3.0 0 g 0 0 0 0.0 0.0 0.0 26.0 0.0 3.0 0.0 0 t 0 0 0 7.0 27.0 28.0 0.0 25.0 18.0 15.0 0
MA0868.3_rc_shift2 (SOX8_rc)				; oligos_6nt_mkv1_m3 versus MA0868.3_rc (SOX8_rc); m=12/43; ncol2=7; w=0; offset=1; strand=R; shift=2; score=0.56669; --yATTGTT-- ; cor=; Ncor= a 0 0 287.0 1827.0 36.0 16.0 70.0 45.0 222.0 0 0 c 0 0 1827.0 20.0 0.0 0.0 35.0 0.0 263.0 0 0 g 0 0 208.0 36.0 43.0 0.0 1827.0 0.0 151.0 0 0 t 0 0 1356.0 273.0 1827.0 1827.0 3.0 1827.0 1827.0 0 0
MA0867.3_rc_shift1 (SOX4_rc)				; oligos_6nt_mkv1_m3 versus MA0867.3_rc (SOX4_rc); m=13/43; ncol2=8; w=0; offset=0; strand=R; shift=1; score=0.563373; -yCwTTGTt-- ; cor=; Ncor= a 0 174.0 83.0 2719.0 0.0 0.0 33.0 9.0 431.0 0 0 c 0 3489.0 5582.0 50.0 11.0 6.0 37.0 0.0 2047.0 0 0 g 0 1422.0 64.0 120.0 6.0 1.0 5582.0 0.0 951.0 0 0 t 0 2093.0 1018.0 5582.0 5582.0 5582.0 0.0 5582.0 5582.0 0 0
MA0102.5_rc_shift3 (CEBPA_rc)				; oligos_6nt_mkv1_m3 versus MA0102.5_rc (CEBPA_rc); m=14/43; ncol2=10; w=0; offset=2; strand=R; shift=3; score=0.558287; ---aTTGTGCA ; cor=; Ncor= a 0 0 0 50992.0 1411.0 1092.0 9787.0 6308.0 2053.0 10928.0 75354.0 c 0 0 0 7312.0 1381.0 340.0 1583.0 6751.0 678.0 57887.0 2365.0 g 0 0 0 16193.0 1034.0 5655.0 61538.0 3535.0 75124.0 936.0 282.0 t 0 0 0 4506.0 75177.0 71916.0 6095.0 62409.0 1148.0 9252.0 1002.0
MA0836.3_rc_shift4 (CEBPD_rc)				; oligos_6nt_mkv1_m3 versus MA0836.3_rc (CEBPD_rc); m=15/43; ncol2=8; w=0; offset=3; strand=R; shift=4; score=0.524094; ----TTGTGCA ; cor=; Ncor= a 0 0 0 0 359.0 185.0 2276.0 1831.0 292.0 1977.0 20939.0 c 0 0 0 0 404.0 75.0 377.0 2625.0 214.0 17309.0 233.0 g 0 0 0 0 315.0 652.0 17458.0 1022.0 20683.0 299.0 81.0 t 0 0 0 0 20374.0 20540.0 1341.0 15974.0 263.0 1867.0 199.0
MA0700.3_rc_shift1 (LHX2_rc)				; oligos_6nt_mkv1_m3 versus MA0700.3_rc (LHX2_rc); m=16/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.480426; -TAATTG---- ; cor=; Ncor= a 0 39.0 6256.0 6082.0 133.0 420.0 640.0 0 0 0 0 c 0 6.0 5.0 64.0 77.0 52.0 37.0 0 0 0 0 g 0 13.0 5.0 58.0 101.0 71.0 5612.0 0 0 0 0 t 0 6275.0 67.0 129.0 6022.0 5790.0 44.0 0 0 0 0
MA1561.2_rc_shift3 (SOX12_rc)				; oligos_6nt_mkv1_m3 versus MA1561.2_rc (SOX12_rc); m=17/43; ncol2=10; w=0; offset=2; strand=R; shift=3; score=0.479085; ---ATTGTTCG ; cor=; Ncor= a 0 0 0 854.0 20.0 0.0 3.0 0.0 1.0 48.0 56.0 c 0 0 0 57.0 44.0 0.0 0.0 4.0 2.0 854.0 34.0 g 0 0 0 211.0 91.0 0.0 854.0 2.0 26.0 26.0 854.0 t 0 0 0 129.0 854.0 854.0 0.0 854.0 854.0 47.0 48.0
MA0708.3_rc_shift1 (MSX2_rc)				; oligos_6nt_mkv1_m3 versus MA0708.3_rc (MSX2_rc); m=18/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.478045; -TAATTR---- ; cor=; Ncor= a 0 0.0 6353.0 6353.0 0.0 0.0 2737.0 0 0 0 0 c 0 243.0 0.0 0.0 0.0 259.0 0.0 0 0 0 0 g 0 0.0 600.0 0.0 112.0 175.0 6353.0 0 0 0 0 t 0 6353.0 62.0 0.0 6353.0 6353.0 220.0 0 0 0 0
MA0709.2_rc_shift1 (Msx3_rc)				; oligos_6nt_mkv1_m3 versus MA0709.2_rc (Msx3_rc); m=19/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.472135; -TAATTr---- ; cor=; Ncor= a 0 213.0 8380.0 8380.0 5.0 94.0 2582.0 0 0 0 0 c 0 88.0 105.0 0.0 38.0 237.0 29.0 0 0 0 0 g 0 59.0 215.0 0.0 89.0 160.0 5798.0 0 0 0 0 t 0 8380.0 121.0 0.0 8380.0 8380.0 312.0 0 0 0 0
MA0666.3_rc_shift1 (MSX1_rc)				; oligos_6nt_mkv1_m3 versus MA0666.3_rc (MSX1_rc); m=20/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.470786; -TAATTr---- ; cor=; Ncor= a 0 0.0 5064.0 5064.0 0.0 0.0 2415.0 0 0 0 0 c 0 159.0 0.0 0.0 0.0 146.0 0.0 0 0 0 0 g 0 0.0 280.0 0.0 42.0 125.0 5064.0 0 0 0 0 t 0 5064.0 0.0 0.0 5064.0 5064.0 227.0 0 0 0 0
MA0879.3_rc_shift1 (DLX1_rc)				; oligos_6nt_mkv1_m3 versus MA0879.3_rc (DLX1_rc); m=21/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.460045; -TAATTr---- ; cor=; Ncor= a 0 614.0 6231.0 6231.0 0.0 540.0 2171.0 0 0 0 0 c 0 168.0 155.0 0.0 0.0 954.0 0.0 0 0 0 0 g 0 0.0 639.0 0.0 222.0 1212.0 4059.0 0 0 0 0 t 0 6231.0 0.0 0.0 6231.0 6231.0 265.0 0 0 0 0
MA0881.2_rc_shift1 (Dlx4_rc)				; oligos_6nt_mkv1_m3 versus MA0881.2_rc (Dlx4_rc); m=22/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.453397; -TAATTr---- ; cor=; Ncor= a 0 1127.0 12054.0 12054.0 499.0 883.0 5213.0 0 0 0 0 c 0 134.0 542.0 38.0 55.0 739.0 145.0 0 0 0 0 g 0 316.0 868.0 85.0 744.0 1500.0 6841.0 0 0 0 0 t 0 12054.0 440.0 88.0 12054.0 12054.0 724.0 0 0 0 0
MA0027.3_rc_shift1 (EN1_rc)				; oligos_6nt_mkv1_m3 versus MA0027.3_rc (EN1_rc); m=23/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.453269; -TAATTr---- ; cor=; Ncor= a 0 132.0 2891.0 2891.0 0.0 0.0 1562.0 0 0 0 0 c 0 30.0 162.0 0.0 0.0 71.0 5.0 0 0 0 0 g 0 0.0 483.0 0.0 28.0 99.0 1328.0 0 0 0 0 t 0 2891.0 57.0 0.0 2891.0 2891.0 104.0 0 0 0 0
MA0890.2_rc_shift1 (GBX2_rc)				; oligos_6nt_mkv1_m3 versus MA0890.2_rc (GBX2_rc); m=24/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.453154; -TAATTr---- ; cor=; Ncor= a 0 650.0 27366.0 27366.0 25.0 227.0 11855.0 0 0 0 0 c 0 30.0 673.0 65.0 114.0 1113.0 106.0 0 0 0 0 g 0 73.0 570.0 61.0 250.0 570.0 15511.0 0 0 0 0 t 0 27366.0 318.0 0.0 27366.0 27366.0 699.0 0 0 0 0
MA0717.2_rc_shift1 (RAX2_rc)				; oligos_6nt_mkv1_m3 versus MA0717.2_rc (RAX2_rc); m=25/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.451769; -TAATTr---- ; cor=; Ncor= a 0 4258.0 38860.0 38860.0 1030.0 2421.0 19215.0 0 0 0 0 c 0 360.0 2513.0 125.0 757.0 4490.0 1688.0 0 0 0 0 g 0 2644.0 4232.0 738.0 1523.0 3060.0 19645.0 0 0 0 0 t 0 38860.0 2167.0 270.0 38860.0 38860.0 3558.0 0 0 0 0
MA0880.2_rc_shift1 (Dlx3_rc)				; oligos_6nt_mkv1_m3 versus MA0880.2_rc (Dlx3_rc); m=26/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.451424; -TAATTr---- ; cor=; Ncor= a 0 691.0 7323.0 7323.0 299.0 643.0 3190.0 0 0 0 0 c 0 101.0 452.0 60.0 62.0 587.0 164.0 0 0 0 0 g 0 202.0 535.0 66.0 536.0 995.0 4133.0 0 0 0 0 t 0 7323.0 399.0 173.0 7323.0 7323.0 572.0 0 0 0 0
MA0699.2_rc_shift1 (LBX2_rc)				; oligos_6nt_mkv1_m3 versus MA0699.2_rc (LBX2_rc); m=27/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.450569; -TAATTr---- ; cor=; Ncor= a 0 148.0 2996.0 2996.0 89.0 57.0 1362.0 0 0 0 0 c 0 106.0 293.0 118.0 130.0 325.0 109.0 0 0 0 0 g 0 34.0 258.0 29.0 290.0 338.0 1634.0 0 0 0 0 t 0 2996.0 150.0 0.0 2996.0 2996.0 157.0 0 0 0 0
MA0894.2_shift1 (HESX1)				; oligos_6nt_mkv1_m3 versus MA0894.2 (HESX1); m=28/43; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.450317; -TAATTr---- ; cor=; Ncor= a 0 187.0 4072.0 4072.0 0.0 0.0 1892.0 0 0 0 0 c 0 0.0 0.0 7.0 0.0 15.0 38.0 0 0 0 0 g 0 34.0 53.0 9.0 15.0 0.0 2180.0 0 0 0 0 t 0 4072.0 31.0 0.0 4072.0 4072.0 97.0 0 0 0 0
MA0718.2_rc_shift1 (RAX_rc)				; oligos_6nt_mkv1_m3 versus MA0718.2_rc (RAX_rc); m=29/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.44881; -TAATTr---- ; cor=; Ncor= a 0 126.0 2412.0 2412.0 24.0 40.0 1131.0 0 0 0 0 c 0 20.0 49.0 0.0 12.0 3.0 25.0 0 0 0 0 g 0 0.0 71.0 0.0 38.0 17.0 1281.0 0 0 0 0 t 0 2412.0 71.0 123.0 2412.0 2412.0 214.0 0 0 0 0
MA0909.4_rc_shift0 (Hoxd13_rc)				; oligos_6nt_mkv1_m3 versus MA0909.4_rc (Hoxd13_rc); m=30/43; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.44838; TTTATTG---- ; cor=; Ncor= a 667.0 15.0 11.0 5972.0 30.0 49.0 61.0 0 0 0 0 c 379.0 2.0 7.0 3.0 11.0 148.0 34.0 0 0 0 0 g 704.0 37.0 4.0 2.0 13.0 5.0 5866.0 0 0 0 0 t 4227.0 5923.0 5955.0 0.0 5923.0 5775.0 16.0 0 0 0 0
MA0720.2_rc_shift1 (Shox2_rc)				; oligos_6nt_mkv1_m3 versus MA0720.2_rc (Shox2_rc); m=31/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.447118; -TAATTr---- ; cor=; Ncor= a 0 895.0 18179.0 18179.0 79.0 766.0 9152.0 0 0 0 0 c 0 36.0 870.0 0.0 3.0 426.0 228.0 0 0 0 0 g 0 193.0 545.0 12.0 138.0 626.0 9027.0 0 0 0 0 t 0 18179.0 597.0 29.0 18179.0 18179.0 979.0 0 0 0 0
MA0125.2_shift1 (Nobox)				; oligos_6nt_mkv1_m3 versus MA0125.2 (Nobox); m=32/43; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.444393; -TAATTr---- ; cor=; Ncor= a 0 0.0 36.0 38.0 1.0 2.0 15.0 0 0 0 0 c 0 1.0 0.0 0.0 1.0 0.0 0.0 0 0 0 0 g 0 0.0 0.0 0.0 2.0 4.0 22.0 0 0 0 0 t 0 37.0 2.0 0.0 34.0 32.0 1.0 0 0 0 0
MA0882.2_rc_shift1 (DLX6_rc)				; oligos_6nt_mkv1_m3 versus MA0882.2_rc (DLX6_rc); m=33/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.444327; -TAATTr---- ; cor=; Ncor= a 0 193.0 2623.0 2623.0 56.0 184.0 1212.0 0 0 0 0 c 0 16.0 68.0 0.0 0.0 143.0 21.0 0 0 0 0 g 0 30.0 140.0 0.0 124.0 273.0 1410.0 0 0 0 0 t 0 2623.0 48.0 12.0 2623.0 2623.0 137.0 0 0 0 0
MA0716.2_rc_shift1 (PRRX1_rc)				; oligos_6nt_mkv1_m3 versus MA0716.2_rc (PRRX1_rc); m=34/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.44302; -TAATTr---- ; cor=; Ncor= a 0 1229.0 23897.0 23897.0 209.0 810.0 12775.0 0 0 0 0 c 0 136.0 1004.0 0.0 202.0 1776.0 1121.0 0 0 0 0 g 0 644.0 2302.0 3.0 503.0 1088.0 11122.0 0 0 0 0 t 0 23897.0 1264.0 0.0 23897.0 23897.0 2373.0 0 0 0 0
MA0721.2_rc_shift1 (UNCX_rc)				; oligos_6nt_mkv1_m3 versus MA0721.2_rc (UNCX_rc); m=35/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.442158; -TAATTr---- ; cor=; Ncor= a 0 3885.0 36926.0 36926.0 890.0 2629.0 20126.0 0 0 0 0 c 0 731.0 1782.0 117.0 420.0 4582.0 2086.0 0 0 0 0 g 0 2211.0 3958.0 806.0 1302.0 2540.0 16800.0 0 0 0 0 t 0 36926.0 3111.0 481.0 36926.0 36926.0 3975.0 0 0 0 0
MA0662.2_rc_shift1 (MIXL1_rc)				; oligos_6nt_mkv1_m3 versus MA0662.2_rc (MIXL1_rc); m=36/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.442057; -TAATTr---- ; cor=; Ncor= a 0 2895.0 27042.0 27042.0 736.0 1038.0 15403.0 0 0 0 0 c 0 115.0 2031.0 181.0 556.0 3660.0 1245.0 0 0 0 0 g 0 1903.0 4270.0 510.0 662.0 1911.0 11639.0 0 0 0 0 t 0 27042.0 1385.0 0.0 27042.0 27042.0 2635.0 0 0 0 0
MA0630.2_shift1 (SHOX)				; oligos_6nt_mkv1_m3 versus MA0630.2 (SHOX); m=37/43; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.441534; -TAATTr---- ; cor=; Ncor= a 0 74.0 852.0 991.0 15.0 98.0 416.0 0 0 0 0 c 0 30.0 48.0 2.0 15.0 50.0 48.0 0 0 0 0 g 0 9.0 55.0 5.0 27.0 84.0 424.0 0 0 0 0 t 0 886.0 45.0 2.0 943.0 768.0 111.0 0 0 0 0
MA1505.2_rc_shift1 (HOXC8_rc)				; oligos_6nt_mkv1_m3 versus MA1505.2_rc (HOXC8_rc); m=38/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.43948; -YAATTr---- ; cor=; Ncor= a 0 0.0 9273.0 9273.0 0.0 983.0 9273.0 0 0 0 0 c 0 4325.0 2656.0 211.0 0.0 19.0 0.0 0 0 0 0 g 0 0.0 99.0 0.0 20.0 2727.0 4555.0 0 0 0 0 t 0 9273.0 961.0 0.0 9273.0 9273.0 0.0 0 0 0 0
MA0654.2_rc_shift1 (ISX_rc)				; oligos_6nt_mkv1_m3 versus MA0654.2_rc (ISX_rc); m=39/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.437345; -TAATTr---- ; cor=; Ncor= a 0 49.0 2065.0 2065.0 10.0 24.0 1061.0 0 0 0 0 c 0 0.0 24.0 0.0 0.0 5.0 0.0 0 0 0 0 g 0 0.0 0.0 0.0 16.0 48.0 1003.0 0 0 0 0 t 0 2065.0 0.0 0.0 2065.0 2065.0 10.0 0 0 0 0
MA0634.2_rc_shift1 (ALX3_rc)				; oligos_6nt_mkv1_m3 versus MA0634.2_rc (ALX3_rc); m=40/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.435389; -TAATTr---- ; cor=; Ncor= a 0 977.0 7877.0 7877.0 231.0 629.0 4510.0 0 0 0 0 c 0 87.0 239.0 8.0 141.0 885.0 345.0 0 0 0 0 g 0 449.0 729.0 72.0 317.0 506.0 3367.0 0 0 0 0 t 0 7877.0 697.0 76.0 7877.0 7877.0 794.0 0 0 0 0
MA1577.2_rc_shift1 (TLX2_rc)				; oligos_6nt_mkv1_m3 versus MA1577.2_rc (TLX2_rc); m=41/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.431779; -TAATTr---- ; cor=; Ncor= a 0 0.0 7799.0 7799.0 0.0 0.0 8156.0 0 0 0 0 c 0 0.0 0.0 0.0 0.0 80.0 1112.0 0 0 0 0 g 0 0.0 0.0 0.0 0.0 0.0 7799.0 0 0 0 0 t 0 7799.0 0.0 0.0 7799.0 7799.0 1435.0 0 0 0 0
MA1481.2_rc_shift1 (DRGX_rc)				; oligos_6nt_mkv1_m3 versus MA1481.2_rc (DRGX_rc); m=42/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.422285; -TAATTr---- ; cor=; Ncor= a 0 144.0 14867.0 14867.0 0.0 0.0 8870.0 0 0 0 0 c 0 962.0 209.0 0.0 0.0 2037.0 1111.0 0 0 0 0 g 0 17.0 813.0 0.0 0.0 501.0 5997.0 0 0 0 0 t 0 14867.0 0.0 0.0 14867.0 14867.0 1079.0 0 0 0 0
MA0705.2_rc_shift1 (Lhx8_rc)				; oligos_6nt_mkv1_m3 versus MA0705.2_rc (Lhx8_rc); m=43/43; ncol2=6; w=0; offset=0; strand=R; shift=1; score=0.421045; -YRATTR---- ; cor=; Ncor= a 0 0.0 5092.0 5092.0 0.0 0.0 5092.0 0 0 0 0 c 0 1929.0 88.0 0.0 0.0 1670.0 0.0 0 0 0 0 g 0 0.0 2083.0 0.0 0.0 160.0 1996.0 0 0 0 0 t 0 5092.0 0.0 0.0 5092.0 5092.0 0.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m4_shift2 (oligos_6nt_mkv1_m4)				; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --dgCAGAGAgw ; Alignment reference a 0 0 4 2 0 10 0 10 0 10 1 4 c 0 0 0 2 10 0 0 0 0 0 2 1 g 0 0 3 5 0 0 10 0 10 0 6 2 t 0 0 3 1 0 0 0 0 0 0 1 3
MA1731.2_rc_shift4 (ZNF768_rc)				; oligos_6nt_mkv1_m4 versus MA1731.2_rc (ZNF768_rc); m=1/4; ncol2=9; w=0; offset=2; strand=R; shift=4; score=0.689009; ----CAGAGAgG ; cor=; Ncor= a 0 0 0 0 1.0 987.0 1.0 945.0 20.0 917.0 123.0 141.0 c 0 0 0 0 973.0 11.0 11.0 43.0 29.0 11.0 179.0 62.0 g 0 0 0 0 25.0 1.0 987.0 6.0 950.0 39.0 655.0 768.0 t 0 0 0 0 1.0 1.0 1.0 6.0 1.0 34.0 43.0 29.0
MA1593.2_shift0 (ZNF317)				; oligos_6nt_mkv1_m4 versus MA1593.2 (ZNF317); m=2/4; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.449161; ACAGCAGA---- ; cor=; Ncor= a 9381.0 281.0 10344.0 691.0 395.0 9323.0 284.0 10825.0 0 0 0 0 c 357.0 10821.0 85.0 192.0 10608.0 250.0 186.0 208.0 0 0 0 0 g 480.0 183.0 317.0 10374.0 223.0 289.0 10730.0 206.0 0 0 0 0 t 1245.0 178.0 717.0 206.0 237.0 1601.0 263.0 224.0 0 0 0 0
MA0508.4_rc_shift6 (PRDM1_rc)				; oligos_6nt_mkv1_m4 versus MA0508.4_rc (PRDM1_rc); m=3/4; ncol2=7; w=0; offset=4; strand=R; shift=6; score=0.430944; ------GAGAAA ; cor=; Ncor= a 0 0 0 0 0 0 660.0 49466.0 432.0 52619.0 50943.0 52905.0 c 0 0 0 0 0 0 290.0 1390.0 207.0 561.0 1011.0 826.0 g 0 0 0 0 0 0 52821.0 1076.0 53465.0 488.0 1346.0 467.0 t 0 0 0 0 0 0 1710.0 3549.0 1377.0 1813.0 2181.0 1283.0
MA0092.2_rc_shift0 (Hand1::Tcf3_rc)				; oligos_6nt_mkv1_m4 versus MA0092.2_rc (Hand1::Tcf3_rc); m=4/4; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.411895; awkCCAGAy--- ; cor=; Ncor= a 16.0 10.0 5.0 1.0 0.0 29.0 1.0 24.0 4.0 0 0 0 c 4.0 3.0 1.0 25.0 29.0 0.0 0.0 1.0 15.0 0 0 0 g 4.0 0.0 14.0 3.0 0.0 0.0 28.0 2.0 0.0 0 0 0 t 5.0 16.0 9.0 0.0 0.0 0.0 0.0 2.0 10.0 0 0 0