The Consensus properties window (Figure 4‑4) simply displays a FASTA version of the Consensus sequence displayed in the alignment, minus any gaps. Since the Consensus is formed from the alignment of many trimmed reads, there is no flanking sequence to report. The definition line of the sequence is annotated to provide the number and orientation of the reads that went into constructing the Consensus, and the length of the sequence.
The properties window of a forward read (Figure 4‑5) contains up to 4 FASTA sequences. The window first displays a block of sequences based on the alignment data: The aligned portion of the Read, the unused 5’-flanking sequence, and the unused 3’-flanking sequence are provided as three separate FASTA sequences. Following this, the FASTA sequence of the entire read is shown, as obtained from the Read Data sff file. Note that the sequences can have mixed case characters: the lower case characters are used to represent the sequencing key and low quality read regions.
The properties window for a reverse read (Figure 4‑6) has the same types of information and utility outlined for the forward read properties window, above (section
4.3.2.2) except that, as a convenience, the alignment data is presented in two blocks: in the first block, the sequences are presented as the reverse complements of the actual read data (thus the “_rc_” portion of the FASTA identifiers), so they can be easily related to the sequences you will see in the alignments, on the Global Align or Consensus Align tabs. The second alignment data block shows the same data (the aligned read and the flanking unused sequences) in the orientation of the read as it was sequenced (in the same orientation as the raw sequence from the Read Data file).
