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This unusual property of green plant tRNase ZSs is likely due to multiple sequence determinants including the TM-type-specific flexible arm comprising the KL motif, Motif I and lack of the PxKxRN motif.
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Due to multiple internal sequence repetitions within the TAS fragment, all of the PCR reactions resulted in multiple bands.
This could be due to multiple binding sites per sequence both with and without the extra base.
Some motifs were recognized more than once due to multiple cysteine residues; the sequence closest to a conventional motif was used for further analysis.
In order to determine whether these results are due to a major recombination event involving many genes, or due to multiple small events, conserved sequences that shown evidence of recombination were mapped on strain ATCC BAA-1116 chromosupplementarymentary fig. S3, Supplementary Material online).
In several cases no clear sequence reads were obtained, even after repeated PCR and sequencing attempts, due to multiple copies of the ITS2 which varied in primary sequences (see Results).
For a little more than half of the nuclear sequences, due to multiple polymorphic sites in heterozygous individuals, PCR products were cloned into a pGEM vector (pGEM™-T EasyVector System I, Promega), averaging three clones per polymorphic sequence.
All phylogenetic analyses were performed with protein sequences, to avoid errors due to multiple substitutions and homoplasic characters present in nucleotide sequences.
It is possible that there is more than one recombination partner of a single ST60 gene due to multiple recombination events involving the same sequence.
Three core glycolytic enzymes were not characterised, due to multiple expressed copies (hexokinase) or insufficient sequence information in the original transcriptomes (phosphofructokinase and aldose).
The rearrangements between CO92 and KIM were primarily due to multiple inversions of genome segments at insertion sequences [12].
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