Note on threshold for including windows in Six-frame plot:

In the 'Six-frame' plot, the score for a particular window may be omitted from the plot if it is partially or total gapped in some or all of the sequence pairs. Specifically, for each window, the sum, S, over sequence pairs of (number of nt used in window) x (pairwise sequence divergence) is calculated. 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.

If the sum S is at least (threshold) x S_max then the likelihood ratio statistic for this window is included in the six-frame plot. Otherwise the window is omitted. The default threshold is 0.75. On the 'Redraw plots' page, you have the option to change this threshold value (minimum 0.01, maximum 0.99). S_max, the maximum possible value of S, is basically the window length (in nt) times the total pairwise divergence summed over all sequence pairs.

Before plotting, each window's likelihood score is scaled by S_max / S. This scaling is applied so that you don't get dips in the six-frame plot just due to some sequences being gapped in some regions. Be aware, however, that in partially gapped regions the signal-to-noise ratio will be lower compared with neighbouring ungapped regions.

The original unscaled likelihood scores can be found by following the link to 'raw plot data' -> 'Likelihood ratios' -> column 3. These scores represent the actual likelihood ratio statistics for each window, based on the information present in that window - i.e. if some sequences are partially gapped (or have ambiguous nt codes) then there is less information so, all other things being equal, the likelihood ratios are lower.