Figure 3.

Additional Output. The additional sections of the output page are shown. (A) The final merged sequence in FASTA format is displayed and can be downloaded. (B) The detailed output of each of the successive merges is provided in a table. The alignment of the two fragments for each merge, and their score (as generated by the merger program), are provided. Since the fragments are merged in order sequentially, the expectation is that the end of the first fragment in each merge will overlap with the start of the next fragment. If this is the case, a green table cell with the word “Correct” is shown under the “Orientation” column. If the merge has occurred in the other orientation, the cell is shaded red with the word “Check” displayed. The final column provides a hyperlink to the full, detailed output for each merge, as generated by the merger program. This output includes a table detailing any conflicts, which the merger program detected, between the two sequences, and the base, which was used in the output sequence. It is advisable to check this detailed output before continuing to use the final merged sequence in any downstream applications or analyses. (C) The alignment of the merged sequence against the reference sequence(s) is shown. Conserved loci across all sequences are indicated with a “|” character, mismatches are indicated with a space character, and the total number of matches and mismatches is shown. (D) An archive containing all input and output files (excluding chromatograms) can be downloaded. All the files in the archive are in a folder named with the date and time the merge was executed.