Graphical summary of analysis of Trinity objects. The ‘frame’ for all data are the sequence of the Trinity object (numbers on x-axis of top graph). At top is the result of analysis of genomic reads aligned to the Trinity object. (A) The red/black bars are alignment islands, where red indicates identical sequence to Trinity and black non-identical sequence. The blue joining arrows indicate high-scoring splice junctions (if detected, junctions on the opposite strand are in yellow). Below is a quantitative trace of splice junction locations and scores (standardized to the maximum possible score of ∼15; the cutoff value for acceptance of 11 is illustrated by the red line). The blue lines are splices in our model; green lines below are splices from the reference transcript model aligned to the Trinity object. Red lines indicate splice junctions on the opposite strand in the Trinity sequence. The green bars indicate regions of alignment (HSPs) to the specified Phytozome reference transcript. The black triangle indicates that the gap in the Blastn alignment to the Phytozome transcript model is the approximate location of putatively spliced-out N-islands in the reference. The bottom graph indicates the positions of Blastx alignment to the Volvox proteome. (A) Typical cases for ‘bridging’ Trinity objects. In these four cases the entire set of consensus islands are joined into one ‘connected island’ by same-sense splices. (B) Rare aberrant cases where the Trinity object is due to ‘track-crossing’ in silico, and contains regions of two distinct reference transcripts (top two examples), or where splice detection fails even on the same reference transcript (bottom two examples). In these cases there are multiple connected islands (gray outlines).