The alnout file contains alignments in human-readable format. One alignment is shown for each hit. With local alignments, there may be more than one alignment for a given query-target pair. Below is an example showing a query sequence with one hit to the database.
The -rowlen option sets the length of an alignment row. Default is 60.
For each query sequence, there is a summary report with one line for each hit. In this report, query and target segments are summarized in the format Lo-Hi(Un), giving start-end coordinates (1-based) and number of unaligned letters following the end of the aligned segment. Other information such as percent identity and E-value may also be given, depending on the type of alignment.
Query and target labels and sequence lengths in nucleotides (nt) or amino acids (aa) are given immediately before each alignment.
Summary statistics including number of identities, percent identity, number of gaps etc. are given immediately following each alignment.
Between the query and target sequence is a row of symbols indicating sequence similarity. Identities are given by a vertical bar (|). For protein alignments, these symbols are also used: colon (:) is a match with BLOSUM62 score >= 2.0, period (.) is a positive score < 2.0.
Query >CF1A_DROME Score Evalue %Id Frame QueryLo-Hi(Un) TargetLo-Hi(Un) Target 343 1e-037 88% +1 58-279(69) 23-96(44) POU1_DUGJA Query 348nt >CF1A_DROME Target 140aa >POU1_DUGJA Qry 58 QTDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQ 249 : |||| ||| |||||||||:||||||||||||||||||||||||||||||||||||||:|||| Tgt 23 EVDDLEQFAKMFKQRRIKLGYTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLRPLLQ 86 Qry 250 KWLEEADSTT 279 ||| ||||.. Tgt 87 KWLHEADSSS 96 Frame +1, 74 cols, 65 ids (88%), 0 gaps (0%), score 343 (137 bits), Evalue 1.1e-037