how to calculate the sequence pattern from the alignment result?

[hylei]

Hi,

Can anyone recommed me the tools to find how many sequences pattern in the dataset? here is part of sequence alignment result. 1-16 sequences are similar to the reference, but not exactly same. I want to know how many kinds of sequence patterns and the frequecncy of each pattern in my dataset. Does any tools can show me this pattern? Thanks very much.

HY


Ref acggttaccccacagccttgcctcacctgaacccccctaaagcacggcctcccgcctgcc
1 acggtgaacccacagccttgcctcacctgaacccccctaaaacacggcctcccgcctgcc
2 acggtgaacccacagccttgcctcacctgaacccccctaaaacacggcctcccgcctgcc
3 acggtgaacccacagccttgcctcacctgaacccccctaaaacacggcctcccgcctgct
4 -cggtgaacccacagccttgcctcacctgaacccccctaaaacacggcctcccgcctgct
5 acggtgaacccacagccttgcctcacctgaacccccctaaaacacggcctcccgcctgct
6 acggtgaacccacagccttgcctcacctgaacccccctaaaacacggcctcccgcctgcc
7 acggtgaacccacagccttgcctcacctgaacccccctaaaacacggcctcccgcctgcc
8 acggtgaacccacagccttgcctcacctgaacccccctaaaacacggcctcccgcctgcc
9 acggtgaacccacagccttgcctcacctgaacccccctaaaacacggcctcccgcctgcc
10 acggttaccccacagccttgcctcacctgaacccccctaaagcacagcctcccgcctgcc
11 acggttaccccacagccttgcctcacctgaacccccctaaagcacagcctcccgcctgcc
12 acggttaccccacagccttgcctcacctgaacccccctaaagcacggcctcccgcctgcc
13 acggttaccccacagccttgcctcacctgaacccccctaaagcacagcctcccgcctgcc
14 acggttaccccacagccttgcctcacctgaacccccctaaagcacggcctcccgcctgcc
15 acggttaccccacagccttgcctcacctgaacccccctaaagcacagcctcccgcctgcc
16 acggttaccccacagccttgcctcacctgaacccccctaaagcacagcctcccgcctgcc
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