Legend for Viewer

Exons are separated in distinct boxes, but connected with lines to indicate a single gene.

We indicate repetitive sequences identified in the genome as shaded boxes. These repeats were identified by RepeatMasker and the EMBOSS tools einverted and etandem and are generally unannotated. We used a low stringency to identify low homology repeats. The repeat data may be useful for interpreting the small RNA data.

For some genomes, typically those that are larger and more repetitive, we have calculated the average degree of repetitiveness, indicated by the "k-mer" line show in the viewer as the squared-off purple line graph. This can be compared to the scale at the left side of the image. Typically, a value >50 indicates that it is likely to be highly heterochromatic, and generate many siRNAs. In the most repetitive genomes (like maize), we may implement a filter on small RNAs and not show small RNAs matching above some arbitrary maximum value (like 50); this is indicated on the main page as the "maximum hits" value. In these cases, the k-mer line is a useful indicator that that genomic region may contain many filtered small RNAs.

We display these sequence images when the abundance view option is set to "Individual abundances".

In addition, sequence in 21 - 24 sizes can be displayed in different colors.

Each dot represents a "window" of ten cycles of small RNAs of length X nt (where X is set in the control panel under Select phasing analysis options), with the score for the degree of phasing indicated on the Y axis (scores calculated approximately as described by Howell et al., 2007). The red dot is the highest scoring window and has the best score in this region. Other colored dots are windows which are in phase with the highest scoring window -- exactly-in-phase windows appear as filled dots, and almost-in-phase (-1/+1) windows as hollow dots. Only those reads corresponding to the featured length (the default length is X nt) are considered.