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