Table 1.
Amino acid/Pseudo genes | Numbers of tRNAscan-SE predictions | Numbers of RepMask3 tRNAs | RepMask % of removed tRNAs | Numbers of tRNAs without RE4 | Numbers of tRNAs with 95% similarity | |||||
Chr1-X1 | ChrUn2 | Chr 1-X | ChrUn | Chr 1-X | ChrUn | Chr 1-X | ChrUn | Chr 1-X | ChrUn | |
Ala | 293 | 41 | 216 | 30 | 73.7 | 73.2 | 77 | 11 | 18 | 2 |
Arg | 811 | 120 | 755 | 109 | 93.1 | 90.8 | 56 | 11 | 18 | 5 |
Asn | 57 | 24 | 25 | 4 | 43.9 | 16.7 | 32 | 20 | 20 | 11 |
Asp | 316 | 44 | 238 | 29 | 75.3 | 65.9 | 78 | 15 | 12 | 5 |
Cys | 12062 | 2061 | 12033 | 2059 | 99.8 | 99.9 | 29 | 2 | 25 | 0 |
Gln | 142 | 30 | 79 | 15 | 55.6 | 50.0 | 63 | 15 | 14 | 9 |
Glu | 2163 | 330 | 817 | 113 | 37.8 | 34.2 | 1346 | 217 | 14 | 10 |
Gly | 7449 | 927 | 7141 | 881 | 95.9 | 95.0 | 308 | 46 | 22 | 10 |
His | 193 | 44 | 178 | 36 | 92.2 | 81.8 | 15 | 8 | 10 | 8 |
Ile | 59 | 9 | 29 | 5 | 49.2 | 55.6 | 30 | 4 | 17 | 3 |
Leu | 144 | 30 | 92 | 11 | 63.9 | 36.7 | 52 | 19 | 12 | 4 |
Lys | 300 | 57 | 93 | 20 | 31.0 | 35.1 | 207 | 37 | 14 | 7 |
Met | 39 | 7 | 10 | 2 | 25.6 | 28.6 | 29 | 5 | 12 | 2 |
Phe | 352 | 61 | 324 | 58 | 92.1 | 95.1 | 28 | 3 | 11 | 3 |
Pro | 27 | 10 | 8 | 1 | 29.6 | 10.0 | 19 | 9 | 15 | 9 |
Ser | 539 | 98 | 491 | 88 | 91.1 | 89.8 | 48 | 10 | 14 | 2 |
Thr | 48 | 7 | 14 | 5 | 29.2 | 71.4 | 34 | 2 | 8 | 0 |
Trp | 1558 | 191 | 1519 | 191 | 97.5 | 100.0 | 39 | 0 | 5 | 0 |
Tyr | 822 | 145 | 799 | 144 | 97.2 | 99.3 | 23 | 1 | 15 | 0 |
Val | 209 | 49 | 148 | 20 | 70.8 | 40.8 | 61 | 29 | 22 | 17 |
Pseudogenes | 163490 | 25693 | 158551 | 25038 | 97.0 | 97.5 | - | - | ||
Total | 191073 | 29978 | 183560 | 28859 | 96.1 | 96.3 | 2574 | 464 | 298 | 107 |
1Chr1-X refers to assembled cow chromosomes
2ChrUn refers to the unordered cow contigs
3RepMask refers to the RepeatMasker program
4RE refers to repetitive elements.