Table 5.
The number and percentage of each repeat motif type found in the SSR search in each of the four test data sets for four sequencing platforms (MiSeq, HiSeq1, HiSeq2, PacBio).
| Software package | MiSeq (ERR365834)a | HiSeq1 (ERR368422)b | HiSeq2 (ERR965681)c | PacBio (SRR1284764)d |
| GMATo | ||||
| No. of dinucleotides (%) | 395,657 (82.1) | 123,902 (72.5) | 565,192 (78.2) | 95,584 (91.4) |
| No. of trinucleotides (%) | 82,874 (17.2) | 42,764 (25.0) | 151,596 (21.0) | 8366 (8.0) |
| No. of tetranucleotides (%) | 2333 (0.5) | 2290 (1.3) | 3390 (0.5) | 556 (0.5) |
| No. of pentanucleotides (%) | 525 (0.1) | 803 (0.5) | 895 (0.1) | 99 (0.1) |
| No. of hexanucleotides (%) | 695 (0.1) | 1257 (0.7) | 1563 (0.2) | 25 (0.0) |
| MISA | ||||
| No. of dinucleotides (%) | 395,740 (82.0) | 123,918 (72.4) | 565,328 (78.2) | 95,634 (91.3) |
| No. of trinucleotides (%) | 83,016 (17.2) | 42,817 (25.0) | 151,850 (21.0) | 8454 (8.1) |
| No. of tetranucleotides (%) | 2357 (0.5) | 2294 (1.3) | 3406 (0.5) | 564 (0.5) |
| No. of pentanucleotides (%) | 525 (0.1) | 806 (0.5) | 905 (0.1) | 99 (0.1) |
| No. of hexanucleotides (%) | 698 (0.1) | 1260 (0.7) | 1573 (0.2) | 27 (0.0) |
| MSATCOMMANDER | ||||
| No. of dinucleotides (%) | 325,676 (83.8) | 99,465 (73.6) | 432,335 (79.5) | 77,096 (93.4) |
| No. of trinucleotides (%) | 60,629 (15.6) | 32,118 (23.8) | 107,818 (19.8) | 5148 (6.2) |
| No. of tetranucleotides (%) | 1613 (0.4) | 1824 (1.3) | 1925 (0.4) | 286 (0.3) |
| No. of pentanucleotides (%) | 313 (0.1) | 650 (0.5) | 619 (0.1) | 45 (0.1) |
| No. of hexanucleotides (%) | 432 (0.1) | 1111 (0.8) | 913 (0.2) | 13 (0.0) |
| PAL_FINDER | ||||
| No. of dinucleotides (%) | 251,678 (81.1) | 114,219 (72.2) | 460,072 (77.8) | 41,581 (85.2) |
| No. of trinucleotides (%) | 56,389 (18.2) | 40,088 (25.3) | 126,509 (21.4) | 6595 (13.5) |
| No. of tetranucleotides (%) | 1570 (0.5) | 2042 (1.3) | 2909 (0.5) | 531 (1.1) |
| No. of pentanucleotides (%) | 359 (0.1) | 717 (0.5) | 774 (0.1) | 98 (0.2) |
| No. of hexanucleotides (%) | 499 (0.2) | 1097 (0.7) | 1353 (0.2) | 26 (0.1) |
| Phobos (Geneious, STAMP) | ||||
| No. of dinucleotides (%) | 396,367 (82.1) | 124,755 (72.4) | 566,081 (78.2) | 95,743 (91.3) |
| No. of trinucleotides (%) | 83,088 (17.2) | 43,156 (25.0) | 151,949 (21.0) | 8462 (8.1) |
| No. of tetranucleotides (%) | 2359 (0.5) | 2314 (1.3) | 3409 (0.5) | 565 (0.5) |
| No. of pentanucleotides (%) | 525 (0.1) | 810 (0.5) | 905 (0.1) | 99 (0.1) |
| No. of hexanucleotides (%) | 698 (0.1) | 1274 (0.7) | 1573 (0.2) | 27 (0.0) |
| SSR Locator | ||||
| No. of dinucleotides (%) | 395,436 (82.1) | 123,818 (72.4) | 565,033 (78.2) | 95,062 (91.3) |
| No. of trinucleotides (%) | 82,881 (17.2) | 42,773 (25.0) | 151,690 (21.0) | 8373 (8.0) |
| No. of tetranucleotides (%) | 2335 (0.5) | 2288 (1.3) | 3384 (0.5) | 561 (0.5) |
| No. of pentanucleotides (%) | 516 (0.1) | 800 (0.5) | 904 (0.1) | 97 (0.1) |
| No. of hexanucleotides (%) | 695 (0.1) | 1255 (0.7) | 1569 (0.2) | 27 (0.0) |
a
6.6 million paired-end reads (2 × 250; 13.2 million total reads); 3.3-Gbp sequence; FASTA file: 3.9 GB.
b
10.9 million single-end reads (1 × 100); 1.5-Gbp sequence; FASTA file: 2.2 GB.
c
48.5 million paired-end reads (2 × 100; 97 million total reads); 8.7-Gbp sequence; FASTA file: 5.7 GB.
d
163,500 reads; 476-Mbp sequence; FASTA file: 445 MB.