Example pairwise alignment generated with PanGEA-BlastN

Comments are shown in green

A pairwise alignment as produced by PanGEA-BlastN starts with '>>' and ends with '<<'. Pairwise alignments consist of the main header, which contains some general info about the alignment and a summary of the form a b c d e f g. After the header, all partial alignments are listed with a summary for each, again in the form a b c d e f g. The summary for the whole alignment (cumulative alignment) is shown after 'summary:' whereas the summary for each partial alignment is shown after the symbol '>'.

If the intron-exon mode was not used, each alignment should contain only one partial alginment. All partial alignments, of course, have to map to the same database sequence.

Summaries are shown in the form a b c d e f g:

a start of alignment (partial alignment) with respect to the database sequence
b end of alignment (partial alignment) with respect to the database sequence
c start of alignment (partial alignment) with respect to the query squence
d end of alignment (partial alignment) with respect to the query sequence
e bit score of alignment (partial alignment)
f similarity in percent (not considering indels)
g number of indels