Probes with more than 20 contiguous identical bases to non-self transcript were excluded.
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Whether similar behavior of transcript self-aggregation is part of RNA foci formation by other repeats needs to be resolved.
This indicates that CUG repeat foci are formed not just by transcript self-aggregation but the process involves protein immobilization including MBNL1.
The answer might lie in a combination of three factors: scanning germline gene expression by the piRNA pathway (nonself RNA recognition), licensing of germline transcripts (self RNA recognition), and unpaired genomic DNA in meiosis.
However, dot matrix plots readily reveal self similarities within the transcript region spanned by exons 17 - 22 (Additional file 4, Figure S3).
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This clearly suggests an evolutionary constraint on the HH structure in the pDo500 satellite family, which has been hypothetized earlier on the basis of self cleavage of pDo500 transcripts from D. baccettii [ 15].
3) If the overlap between the merged plus and minus query coverages were less than 60 bp and less than 20% of the shorter one of the two, the sequence was labeled as trans-self chimera, and the transcript was cut leaving only the longer of the merged query coverages.
