Question 4. Write down the names of the contigs which came up.

1 NW_003316123.1
3 NW_003316155.1
1 NW_003316243.1
1 NW_003316251.1
3 NW_003316303.1
4 NW_003316924.1
18 NW_003317490.1
2 NW_003318243.1
7 NW_003318978.1
15 NW_003319141.1
11 NW_003319270.1
8 NW_003319334.1
10 NW_003319378.1
10 NW_003319432.1
7 NW_003319444.1
1 NW_003319464.1
5 NW_003319465.1
4 NW_003319469.1
22 NW_003319476.1
7 NW_003319505.1
11 NW_003319508.1
11 NW_003319528.1
18 NW_003319548.1
15 NW_003319590.1
16 NW_003319636.1
1 NW_003319662.1
13 NW_003319666.1
12 NW_003319670.1
10 NW_003319677.1
15 NW_003319679.1
14 NW_003319693.1
2 NW_003319695.1

Question 6. Go back to the main page. Left of the search field, you have a drop-down menu
listing the different databases. Again, which ones do you think will be relevant to us? And
where did the input files you received in this lab come from?

The relevant ones are the assembly database, protein database, nucleotide database and
genome database. The input files are probably from the assembly database and the protein
database.
Question 7. Does the fragment belong to a mitochondria? Does it belong to the species you
are interested in?

I looked at the 6 most common contigs: None was found in the Phodopus sungorus, but they
were found in the Caenorhabditis remanei.

The following belong to the mitochondria:

22 NW_003319476.1 Yes
18 NW_003319548.1 Yes
18 NW_003317490.1 Yes
15 NW_003319590.1 Yes

The following don't:

15 NW_003319679.1 No
16 NW_003319636.1 No

Question 8. Search for your species of interest. How many results do you get?

I got 330 results for Phodopus sungorus.

Question 12. What is the size of the mitochondrial genome? What is the identifier of the
sequence? (there might be several identifiers)

Species: Mus musculus C57BL/6J

identifier:: NC_005089.1
size: 16299 bp

Question 14. What is the position (in base pairs) of the first nucleotide of the start codon in
your study species? (before you oriented it) You can validate your answer by finding it on
NCBI on the page of the mitochondria of your study species.

The position was 5311 bp. This number was found in the alignment and also on the NCBI
page on the mitochondria for Phodopus sungorus.