Практикум 1, задание 5

Organism: SARS-CoV-2
Gene: S
First nucleotide: 21563
Last nucleotide: 25384 (TAA)
RefSeq (from a presentation): YP_009724390.1

Explanation: First, I selected the [21500: 21600] slice to find the ATG pattern. Two options appeared: 21536 and 21563. Both were equal to 2 mod 3. The scale of the picture allowed to conclude that the gene starts from 21563. Also there was a tandem repeat (AAAACACACAAAA) that could be found between positions 21536 and 21563 with fuzznuc -pattern N '/P/y20/SARS-CoV-2.fasta[21539:21562]' -stdout. In a similar way, I searched for stop codons TAA (ochre), TGA (opal), TAG (amber) at the slice [25300: 25400]. I found three variants of the beginning of the TGA codon: 25330, 25333, 25345 and one variant of TAA: 25382. Of these, only 25382 was equal to 2 mod 3. So, 25384 is the end of the gene.