Raw plot data for 'Six-frame' plot:


Likelihood ratios:

1. Frame.
2. Alignment coordinate of window centre.
3. Likelihood ratio: 'Window is coding in addition to the input Known CDS(s)' versus 'Only the input Known CDS(s) are coding'.
4. Alignment coordinate of window start.
5. Alignment coordinate of window end.
6. Sum over sequence pairs of (number of nt used in window) x (pairwise sequence divergence), where here the sequence divergence of each pair is the mean number of mutations per nucleotide for the whole sequence (rather than just in the window), and the number of nt used is generally equal to the window length, but may be reduced for gaps, ambiguous nt codes or stop to non-stop transitions. This is basically a measure of how much data is available in each window to calculate the likelihood ratio statistic; lower values correspond to lower signal-to-noise.

Stop codon positions:

1. Frame.
2. Sequence ID.
3. Alignment coordinate.

Start codon positions:

1. Frame.
2. Sequence ID.
3. Alignment coordinate.

Gap (and ambiguous nt) positions:

1. Sequence ID.
2. Alignment coordinate.

Summed sequence divergences:

1. Alignment coordinate.
2. Divergence of contributing sequence pairs (i.e. not gapped etc), summed over phylogenetic tree.