Off topic:Blast Short Sequences Containing Repeats

Question

[grafabian]

I try to detect repeats using blastn. I use the same sequence as query and subject. The sequence contains a 21bp tandem duplication. I expect three hits:

1. The whole sequence aligns itself.
2. First occurance of duplication in query aligns second occurance in subject.
3. Second occurance of duplication in query aligns first occurance in subject.

This works very well for Sequence1 in the web version and in my standalone version. But for Sequence2 this is not working. I tried this for many sequences and it is working very well, but for that case it fails. Any suggestions?

Sequence1:

>gtacgtgcattttaaagattttccaatggaaaagaaatgctgcagaaacatttggcacattccattcttaccttggcacattccattcttaccaaactctaaattttctcttggaaa

Sequence2:

>gagtacgtgcattttaaagattttccaatggaaaagaaatgctgcagaaacatttggcacattccattcttaccttggcacattccattcttaccaaactctaaattttctcttggaaa

Blastn command: blastn -query seq.fa -subject seq.fa -word_size 21