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SilkSatDb: The First Comprehensive Database on Insect Microsatellites

Silkworm Biology



We analysed Total-Genomic and EST sequences for imperfection in di-, tri-, tetra- and pentanucleotide repeats longer than 10 bases.  The important observations we made in our data are listed below:

  1. Interruption of  the perfect repeat by the means of mutations is predominantly seen in the center of the repeat track.
  2. Mutations at 3′ end of the repeat motif are few but not uncommon, whereas, 5′ mutations are rarely found although they do exist.
  3. Shortest imperfect repeats were identified in di-, tri- and tetranucleotide repeats of 15 bases in length.
  4. The longest imperfect repeat was a tetranucleotide repeat of 611 bases.
  5. Transition (29/74) was found to be abundant in EST sequences compared to other type of mutations, whereas insertion was least  abundant (7/74).
  6. Transition/transversion accounted for 74% of the interruptions of perfect repeats, whereas insertion/deletions were observed in only 26% of the interruptions in ESTS.
  7. Gunanine to Adenine was the most common mutations disrupting repeat continuity in EST sequences.
  8. In total-Genomic sequences, repeats were interrupted most often by deletions (153/417), and least by insertions (19/417).
  9. Ratio of transition/transversion to insertion/deletion was found to be around 3:2 in total-Genomic sequences.
  10. Adenine to Guanine and Thymine to Adenine were the most common mutation disrupting the repeat continuity in total-Genomic sequences. 
  11. Double mutations, in which two types of mutations co-exist, were observed in 53 repeats (4 in ESTs and 49 in Genomic). Among these, double transitions and double transversions occured together in 10 and repeat motifs respectively; transition and transversions were associated together in 11/53: indels were together in 4/53; and indels and substitutions were associated in 23/53 imperfect repeats.
  12. Triple mutations occurred together in 9 repeat motifs while one (AC)n motif showed all the possible four mutations.

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