This report was automatically generated by Krait v1.3.3, Krait is a robust and ultrafast tool with a user-friendly graphic interface for genome-wide investigation of microsatellites and primer design
Citation: Du L, Zhang C, Liu Q, Zhang X, Yue B (2018) Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. Bioinformatics. 34(4):681-683.
Input FASTA file: C:/Users/xavie/OneDrive/Documents/Murdoch/Honours/Read Isolations/viro-assem.fa
| Item | Description | Number |
|---|---|---|
| Total number of sequences | Counts | 4956 |
| Total length of sequences | A+T+C+G+N (bp) | 2195478 |
| Total valid length of sequences | A+T+C+G (bp) | 2195478 |
| Unkown bases (Ns) in sequences | Bp | 0 |
| Percentage of unkown bases | Percentage (%) | 0.0 |
| GC content | (G+C)/(A+T+C+G) not include Ns (%) | 47.29 |
The minimum repeats for each perfect SSR type were set to 12 for Mono-, 7 for Di-, 5 for Tri, 4 for Tetra-, 4 for Penta-, 4 for Hexa-, and motif standardization level was set to Level 3
| Item | Description | Number |
|---|---|---|
| Total number of perfect SSRs | Counts | 361 |
| Total length of perfect SSRs | Bp | 7059 |
| The average length of SSRs | total ssr length/total ssr counts (bp) | 19.56 |
| SSRs per sequence | total SSR counts/sequence counts | 0 |
| The percetage of sequence covered by SSRs | total ssr length/total sequence length (%) | 0.33 |
| Relative abundace | total SSRs/total valid length (loci/Mb) | 164.43 |
| Relative density | total SSR length/total valid length ( bp/Mb) | 3215.25 |
| Type | Counts | Length (bp) | Percent (%) | Average Length (bp) | Relative Abundance (loci/Mb) | Relative Density (bp/Mb) |
|---|---|---|---|---|---|---|
| Mono | 70 | 1073 | 19.39 | 15.33 | 31.88 | 488.73 |
| Di | 82 | 1712 | 22.71 | 20.88 | 37.35 | 779.78 |
| Tri | 80 | 1440 | 22.16 | 18.0 | 36.44 | 655.89 |
| Tetra | 117 | 2544 | 32.41 | 21.74 | 53.29 | 1158.75 |
| Penta | 11 | 260 | 3.05 | 23.64 | 5.01 | 118.43 |
| Hexa | 1 | 30 | 0.28 | 30.0 | 0.46 | 13.66 |
| Motif | Type | Counts | Length (bp) | Percent (%) | Average Length (bp) | Relative Abundance (loci/Mb) | Relative Density (bp/Mb) |
|---|---|---|---|---|---|---|---|
| A | 1 | 68 | 1038 | 18.84 | 15.26 | 30.97 | 472.79 |
| C | 1 | 2 | 35 | 0.55 | 17.5 | 0.91 | 15.94 |
| AC | 2 | 29 | 590 | 8.03 | 20.34 | 13.21 | 268.73 |
| AG | 2 | 22 | 376 | 6.09 | 17.09 | 10.02 | 171.26 |
| AT | 2 | 30 | 726 | 8.31 | 24.2 | 13.66 | 330.68 |
| CG | 2 | 1 | 20 | 0.28 | 20.0 | 0.46 | 9.11 |
| AAC | 3 | 7 | 135 | 1.94 | 19.29 | 3.19 | 61.49 |
| AAG | 3 | 3 | 51 | 0.83 | 17.0 | 1.37 | 23.23 |
| AAT | 3 | 13 | 285 | 3.6 | 21.92 | 5.92 | 129.81 |
| ACC | 3 | 3 | 54 | 0.83 | 18.0 | 1.37 | 24.6 |
| ACG | 3 | 8 | 129 | 2.22 | 16.12 | 3.64 | 58.76 |
| AGG | 3 | 6 | 96 | 1.66 | 16.0 | 2.73 | 43.73 |
| ATC | 3 | 35 | 591 | 9.7 | 16.89 | 15.94 | 269.19 |
| CCG | 3 | 5 | 99 | 1.39 | 19.8 | 2.28 | 45.09 |
| AAAC | 4 | 1 | 16 | 0.28 | 16.0 | 0.46 | 7.29 |
| AAAG | 4 | 36 | 604 | 9.97 | 16.78 | 16.4 | 275.11 |
| AAAT | 4 | 18 | 524 | 4.99 | 29.11 | 8.2 | 238.67 |
| AACC | 4 | 1 | 20 | 0.28 | 20.0 | 0.46 | 9.11 |
| AACG | 4 | 1 | 16 | 0.28 | 16.0 | 0.46 | 7.29 |
| AATC | 4 | 30 | 628 | 8.31 | 20.93 | 13.66 | 286.04 |
| ACAG | 4 | 13 | 288 | 3.6 | 22.15 | 5.92 | 131.18 |
| ACGC | 4 | 1 | 16 | 0.28 | 16.0 | 0.46 | 7.29 |
| ACTC | 4 | 2 | 36 | 0.55 | 18.0 | 0.91 | 16.4 |
| ATAC | 4 | 9 | 232 | 2.49 | 25.78 | 4.1 | 105.67 |
| ATAG | 4 | 4 | 128 | 1.11 | 32.0 | 1.82 | 58.3 |
| ATGC | 4 | 1 | 36 | 0.28 | 36.0 | 0.46 | 16.4 |
| AAAAC | 5 | 2 | 45 | 0.55 | 22.5 | 0.91 | 20.5 |
| AAAAG | 5 | 1 | 20 | 0.28 | 20.0 | 0.46 | 9.11 |
| AAACT | 5 | 1 | 20 | 0.28 | 20.0 | 0.46 | 9.11 |
| AACCT | 5 | 1 | 35 | 0.28 | 35.0 | 0.46 | 15.94 |
| AAGAG | 5 | 1 | 20 | 0.28 | 20.0 | 0.46 | 9.11 |
| AAGCC | 5 | 1 | 25 | 0.28 | 25.0 | 0.46 | 11.39 |
| AATCC | 5 | 3 | 60 | 0.83 | 20.0 | 1.37 | 27.33 |
| ACTGG | 5 | 1 | 35 | 0.28 | 35.0 | 0.46 | 15.94 |
| AAGTAT | 6 | 1 | 30 | 0.28 | 30.0 | 0.46 | 13.66 |
| Repeat | Counts | Length (bp) | Percent (%) | Average Length (bp) | Relative Abundance (loci/Mb) | Relative Density (bp/Mb) |
|---|---|---|---|---|---|---|
| 4 | 70 | 1148 | 19.39 | 16.4 | 31.88 | 522.89 |
| 5 | 60 | 1035 | 16.62 | 17.25 | 27.33 | 471.42 |
| 6 | 41 | 810 | 11.36 | 19.76 | 18.67 | 368.94 |
| 7 | 36 | 651 | 9.97 | 18.08 | 16.4 | 296.52 |
| 8 | 27 | 544 | 7.48 | 20.15 | 12.3 | 247.78 |
| 9 | 15 | 369 | 4.16 | 24.6 | 6.83 | 168.07 |
| 10 | 12 | 270 | 3.32 | 22.5 | 5.47 | 122.98 |
| 11 | 5 | 121 | 1.39 | 24.2 | 2.28 | 55.11 |
| 12 | 24 | 444 | 6.65 | 18.5 | 10.93 | 202.23 |
| 13 | 12 | 234 | 3.32 | 19.5 | 5.47 | 106.58 |
| 14 | 17 | 322 | 4.71 | 18.94 | 7.74 | 146.67 |
| 15 | 8 | 165 | 2.22 | 20.62 | 3.64 | 75.15 |
| 16 | 8 | 208 | 2.22 | 26.0 | 3.64 | 94.74 |
| 17 | 4 | 68 | 1.11 | 17.0 | 1.82 | 30.97 |
| 18 | 2 | 36 | 0.55 | 18.0 | 0.91 | 16.4 |
| 19 | 5 | 95 | 1.39 | 19.0 | 2.28 | 43.27 |
| 20 | 5 | 100 | 1.39 | 20.0 | 2.28 | 45.55 |
| 21 | 2 | 63 | 0.55 | 31.5 | 0.91 | 28.7 |
| 22 | 3 | 88 | 0.83 | 29.33 | 1.37 | 40.08 |
| 24 | 1 | 48 | 0.28 | 48.0 | 0.46 | 21.86 |
| 27 | 1 | 54 | 0.28 | 54.0 | 0.46 | 24.6 |
| 29 | 1 | 58 | 0.28 | 58.0 | 0.46 | 26.42 |
| 34 | 1 | 34 | 0.28 | 34.0 | 0.46 | 15.49 |
| 47 | 1 | 94 | 0.28 | 94.0 | 0.46 | 42.82 |
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