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This is likely to be due to the extremely high AT richness of the introns.
Analysis of complete mitochondrial genomes of Insecta and Nematoda also indicated the AT richness in their genomes (Figure 3c).
Here we have given the primary data on the effect of AT richness on palindrome occurrence and plausible reasons for origin of longer palindromes from short inverted repeats.
It is well known that AT richness and repeat structure of var genes poses large difficulties in the assembly of short sequence reads.
Sequencing downstream of the DBL1alpha domain poses difficulties because of the high AT richness, long homopolymeric sequence stretches, repeat units of various sizes and the fact that var genes evolve by frequent recombination.
To find out the correlation of AT richness with the frequency of occurrence of palindromes in CRs we estimated AT content of all CRs using a C program written in-house.
Similar(33)
The coding region is 74% AT-rich (Table 2), reflecting the AT-richness of the mitochondrial genome as a whole [ 45].
No common, general motif was conserved across all groups, barring AT-rich stretches, which were not statistically significant given the AT-richness of the genome.
Therefore we cannot ascribe our findings to random AT-richness of the sequences.
Third, although total intron length correlates best with AT-richness, intron number relates more directly to PCI positivity (Fig 4A).
The AT-richness of the var genes may explain why low sequence quality was obtained in some instances.
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