查找文本中中间彼此靠近的重复字符串

Question

我需要在文本文件中找到一个 13 个字符长度的字符串，该字符串附近有一个重复项。
它指的是基因组的突变13。

例如：

ACGAATTGCAGCCACAGTACGAATCGCAGCC。

它以 ACGAATTGCAGCC 开头并以它结尾，但中间是长度未知的随机字符。

到目前为止我想到的是：

grep -Eo '((.){13}).{1,100}\1'

我必须在这个里面找到它

GTACCATAACTAACAACCTGAAAAGTCACAAAAACATATACAATAAAAGAACTAGATTTCGCATAGGATATATATTAATAAAGTGAACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAAAACTTACTCATACGAGGACTAATAAAAGATTCAAAACAATACAATTGACGAAAACTCAACGAGGAAAGCTAGAAAACCACCAGAGAAACTCAAAACACAAATAGAGATAAAAAAAAAAACCATAAAGAAAAATTCTTACATCGTCACAGCCAAGGAAAAAAAGAAATCGTTAAAATGGAACGCAGTCGAACACAAAAAGACAACACAGAACAAAAAAGGCAAACAGCGTAGAAACAAATACACTCGCGTAGCAAAGGGGCGGCGTCACGCTTGAAACATAAAAATAACCACTGTATATCACGACAATCAACAAAGTCTACATCAAGAAAATCAAAAAAATAC

Answer 1

你已经很接近了，问题是 100，太窄了！您可能需要考虑使用 Perl PCRE 而不是 Posix Extended。性能差异非常明显。

grep -Po '((.){13}).{1,1000}?\1' genom
AACAAAAAAAAAATAACAACAACAACAACGAATGAAGAAAGGAAAAGGAATGATAAAAAAACGAGTAATAATTGAAAACAATTATAAAGTAAGAAAACCGCAACGGCCCAAGTAAGCAAAGCAAGGATAGGAAATTGATCGACACAACTCCATAAAATTTACAACTAGTACTCAGAAAAAATAACTAAGCTATATCCATATCTACTCTAAAAAAGAAAAGGAATAACGGAACACCCACAAAGAAACTCAATTAGCAAAAACCACAGATAATACAAACCAGAGAAGACCACATAAAAAAATGAACGAGTTACCCTTCAAATTAAAATAAATCTACCAGTAAGCATAAAAACAACAAAGTTACAAAACCAAAGACCAAAAGTAGAAATCAGAACAAGGGACATAAACGTTCACCAAATGAATGAAACAACACAATTTAGAAACAAAAAAGAGGAATAAAAAGCCAGAACAGGAGTACGAACATAATTAATTATGAAAGTGACCTACAAATAAGAAGGAAACACAAACAGAAAACAACTAACCACAAAAAAGACATAATAGTAAACAAAAAAAAAA

我的机器上的时间比较：

Posix: (-E)  0m4.816s
Perl:  (-P)  0m0.011s