Exercise 2

Using the online tool 'Tinoco Plot' try building a dot-plot for one each of the 'A', 'B' and 'C' type sequences. Can you infer a good structure for your sequences from this?:

>A1

AAAAAAGGCGACAGAGUAAUCUGUCGCCUUUUUUCUUUGCUUGC

>A2

AAGAAAAACGGGUCGCCAGAAGGUGACCCGUUUUUUUUAUUCUUUUA

>A3

AAAAAAGCCCGCACCUGACAGUGCGGGCUUUUUUUUUC

>A4

AAAGCCCGUGAGUAUUCACGGGCUUUUUUAUUAUUUAAU

>B1

UGGGAGGGACGGCCCUCCUAUCCACCAGCAUAUCAGCCGCGGGGACGACCCUG

>B2

GCCCGGGGACGGCCCCGGGCCGUUCGCUUCAACGGGGACGACCCC

>B3

CCUCGGGGACGACCUCGAGGCCUCCUGAUACGCAGGGACGACCCUG

>B4

GAAGCGGGACGACCCGUUUUCCUUCUUUCAUUGCGCGGGGACGACCCUG

>C1

CCAGCCGCUGACGACGGGGCUGGACUUGCUGGGAGCGCCGCCUUUCGGCGCUUCCGUACCCAUGUUGCUUCAAGGAGGAUAUGGCUAUGGCAA

>C2

GCCGAUGCCAAUUGGGUCGGCAUGGUCAGGGAGCGCCACGCUUCUUGGCGCUUCCUCGUAUCUAUGUUGCUCUACGGAGGAUGUAGCUAUGAGAA

>C3

AGAGCCGCCUGUAAGGGGCUCGCAGUCGAGGAGCUCCGUUCUCUUCGGCGCUCCUCAUCGUCCAUGUUGCUCAAGGAGGAUAUGGCUAUGAGAA

>C4

UCGGUCGCCGCAUAAGGGGCCGAUGUGUCAGGGAGCGCCAUGCUUCUUGGCGUUCCCUCGUAUCUAUGUUGCUCCAAGGAGGAUGUAGUUAUGAGAA