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. 2020 Dec 23;11:610395. doi: 10.3389/fmicb.2020.610395

TABLE 1.

Motifs identified in the genome of C. jejuni YH002 with various Modification QV (modQV) parametersa.

modQV cutoff Motif string Typeb Fraction (%) Occurrence in genome Partner motif Mean IPD ratioc Objective score
30 RAATTY m6A 99.0 30,196 RAATTY 5.839 11290815.0
CCYGA m6A 99.3 2,085 − 5.604 752000.4
GKAAYG m6A 99.1 1,555 − 5.950 613870.3
ACNNNNNCTC m6A 99.5 1,226 GAGNNNNNGT 5.449 446525.9
GAGNNNNNGT m6A 99.4 1,226 ACNNNNNCTC 5.992 439943.8
TAAYNNNNNTGC m6A 99.7 618 GCANNNNNRTTA 5.407 225513.5
GCANNNNNRTTA m6A 99.0 618 TAAYNNNNNTGC 5.725 216201.3
HNNNNNARGTAAYG m6A 57.9 164 − 3.443 6120.3
GNNAGAGWANNNGND m6A 43.3 104 − 3.330 515.1
GCGGNAATNNNGNG mod_base 100.0 6 − 2.462 363.0
DGNNNNACCTVAY m6A 19.2 99 − 2.413 325.6
40 RAATTY m6A 98.9 30,196 RAATTY 5.840 11278810.0
CCYGA m6A 99.0 2,085 − 5.603 750188.0
GKAAYG m6A 98.8 1,555 − 5.957 612288.7
ACNNNNNCTC m6A 99.5 1,226 GAGNNNNNGT 5.449 446525.9
GAGNNNNNGT m6A 99.3 1,226 ACNNNNNCTC 5.996 439218.7
TAAYNNNNNTGC m6A 99.5 618 GCANNNNNRTTA 5.405 225145.7
GCANNNNNRTTA m6A 98.9 618 TAAYNNNNNTGC 5.727 215850.6
CAGNTAANCANNNNNNA mod_base 77.8 9 − 1.914 366.1
50 RAATTY m6A 98.8 30,196 RAATTY 5.841 11266493.0
CCYGA m6A 99.0 2,085 − 5.603 750188.0
GKAAYG m6A 98.6 1,555 − 5.958 611083.9
ACNNNNNCTC m6A 99.3 1,226 GAGNNNNNGT 5.451 445776.1
GAGNNNNNGT m6A 99.2 1,226 ACNNNNNCTC 6.000 438851.8
TAAYNNNNNTGC m6A 99.0 618 GCANNNNNRTTA 5.403 224003.4
GCANNNNNRTTA m6A 98.7 618 TAAYNNNNNTGC 5.726 215486.2
GAGADNNNGMTR m6A 52.7 186 − 2.468 5510.5
DNNBNACCTGAY m6A 43.3 90 − 2.448 1770.6
HNNNNACGCGANANNNA m6A 92.9 14 − 2.722 1673.6
70 RAATTY m6A 98.6 30,196 RAATTY 5.842 11236039.0
CCYGA m6A 98.6 2,085 − 5.605 746719.4
GKAAYG m6A 98.0 1,555 − 5.966 606910.3
ACNNNNNCTC m6A 98.9 1,226 GAGNNNNNGT 5.455 443441.6
GAGNNNNNGT m6A 98.8 1,226 ACNNNNNCTC 6.007 436927.9
TAAYNNNNNTGC m6A 98.7 618 GCANNNNNRTTA 5.405 223224.5
GCANNNNNRTTA m6A 98.2 618 TAAYNNNNNTGC 5.734 214349.2
WNNNNCRSGAATNT m4C 36.2 149 − 3.571 4449.8
GAGWDNNNGMTR m6A 30.5 325 − 2.611 4048.9
100 RAATTY m6A 97.8 30,196 RAATTY 5.848 11142688.0
CCYGA m6A 97.4 2,085 − 5.608 736426.2
GKAAYG m6A 97.0 1,555 − 5.969 599839.9
ACNNNNNCTC m6A 97.7 1,226 GAGNNNNNGT 5.457 437677.1
GAGNNNNNGT m6A 97.5 1,226 ACNNNNNCTC 6.012 430320.7
TAAYNNNNNTGC m6A 97.7 618 GCANNNNNRTTA 5.409 220690.8
GCANNNNNRTTA m6A 96.4 618 TAAYNNNNNTGC 5.753 209890.8
ARGTAATGNNNNND m6A 48.0 150 − 3.691 5429.8
WNNNNCRSGAATNT m4C 33.6 149 − 3.646 4023.6
HHNNNNNACGCGANNNB m6A 43.8 80 − 3.375 2962.1
CCCTGANNNRNANT m4C 88.9 9 − 3.508 1441.8
140 RAATTY m6A 96.7 30,196 RAATTY 5.852 10980916.0
CCYGA m6A 95.7 2,085 − 5.620 720469.8
GKAAYG m6A 95.3 1,555 − 5.977 587514.6
ACNNNNNCTC m6A 96.4 1,226 GAGNNNNNGT 5.456 430640.8
GAGNNNNNGT m6A 95.9 1,226 ACNNNNNCTC 6.013 421956.2
TAAYNNNNNTGC m6A 95.3 618 GCANNNNNRTTA 5.408 214009.7
GCANNNNNRTTA m6A 94.7 618 TAAYNNNNNTGC 5.757 205157.1
DNNNNCRSGAATNT m4C 28.3 159 − 3.809 3330.1
HNNNNNARGTAATG m6A 29.3 150 − 4.008 2475.4
CGCGASTNNANNNNND m6A 100.0 8 − 4.424 2365.0
DNNDCCCTGAY m4C 25.9 85 − 3.430 1375.3
ACGCGANNNNNNTNANW m6A 100.0 6 − 3.118 1085.0
170 RAATTY m6A 96.0 30,196 RAATTY 5.855 10886096.0
CCYGA m6A 94.4 2,085 − 5.630 708218.3
GKAAYG m6A 94.1 1,555 − 5.979 578480.0
ACNNNNNCTC m6A 95.8 1,226 GAGNNNNNGT 5.456 426831.5
GAGNNNNNGT m6A 94.8 1,226 ACNNNNNCTC 6.036 415825.4
TAAYNNNNNTGC m6A 94.3 618 GCANNNNNRTTA 5.409 211109.1
GCANNNNNRTTA m6A 92.9 618 TAAYNNNNNTGC 5.773 200120.3
DNNNNCRSGAATNT m4C 23.9 159 − 3.997 2560.3
CGCGASTNNANNNNND m6A 100.0 8 − 4.424 2365.0
200 RAATTY m6A 95.3 30,196 RAATTY 5.863 10775063.0
CCYGA m6A 92.9 2,085 − 5.646 691808.3
GKAAYG m6A 93.2 1,555 − 5.983 571029.3
ACNNNNNCTC m6A 95.5 1,226 GAGNNNNNGT 5.457 425312.0
GAGNNNNNGT m6A 93.9 1,226 ACNNNNNCTC 6.049 410360.9
TAAYNNNNNTGC m6A 92.2 618 GCANNNNNRTTA 5.424 204586.9
GCANNNNNRTTA m6A 90.8 618 TAAYNNNNNTGC 5.784 193836.7
DNNNNCRSGAATNT m4C 28.2 103 − 4.008 2328.9
CGCGAGTWNA m6A 100.0 5 − 4.488 1530.0

aModified bases are boldfaced. bmod_base: undetermined modification. cIPD: Inter-pulse duration.