Re^5: Is it possible to make reference to substrings and sort them?

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C:\test>1120869 -BIG=5e6 -FUZZ=1 -MIN=10 -NSHORTS=10000 | wc -l
Indexed search took 1.509765148 secs
      2

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C:\test>1120869 -BIG=5e6 -FUZZ=2 -MIN=6 -NSHORTS=10000 | wc -l
Indexed search took 395.132736921 secs
...
CCAGTATATGATACGAACGC ~ CCAGTATCTGGTACGAACGC (CCAGTAT TG TACGAACGC) [18
+ of 20] at 2681307
CTCGCACGATTACGACCGAA ~ CTCGCAGAATTACGACCGAA (CTCGCA  ATTACGACCGAA) [18
+ of 20] at 4658451
...

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C:\test>1120869 -BIG=5e6 -FUZZ=3 -MIN=5 -NSHORTS=10000 | wc -l
Indexed search took 1763.693833113 secs
   1455

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