Exceptions to this were both sequences of BRK1 for one P. pyriforme accession (Nordhausen, Europe), and one sequence representing one locus of P. collenchymatum (Shaw Nature Reserve, Franklin County, MO, USA) which were each obtained only once.
The main exception to this collinearity is represented by two major gaps in the alignment, due to LTR retrotransposon insertions in the locus on chromosome 5. Notably, the region containing the Gmpgip copies shows the most exceptions to the sequence collinearity, as no clear diagonal is visible in this region and alignments are limited to the coding regions of different pgip members.
BESs 2, 4, 7 and 15 are exceptions to this rule, showing additional sequences (ingi element, VSG or ESAG3 pseudogene).
Interestingly, exceptions to this observation were found in two sequences that have an alanine in this position, which we called CAM1 and CAM2.
Sequences were required to match the human genome sequence perfectly to be carried further for additional computational analysis, with the only exception to this being sequences that demonstrated addition of 1 3 non-templated nucleotides at the 3' terminus.
The only exception to this was a sequence originating from Selaginella moellendorffii (Phytozome-Id: 418746) that serves as an outgroup, which contains only one of the two regions that are conserved in all FAF and FAF-like proteins.
Recovery rates remain relatively constant over different sequence lengths with the only exception to this being at short sequence lengths when the difference in likelihood values can result in an overly-simplistic model being selected (+G instead of +I+G).
One exception to this was the caltrain sequence.
There was only one exception to this: 7 TS subtelomeric sequences in group III were distributed into groups VII (1 TESA gene) and VIII (6 complement regulatory proteins genes).
A few exceptions to the consensus sequence were found among Tritryps.
