Input
Target sequence	Place your query file with nucleotide sequences.
Query sequence(s)	Place file with one ore more nucleotide sequences.
Output
Result	Name of the output file.
Format	Output format: List of alignment blocks coordinates List of alignment blocks coordinates and blocks sequences Output alignment (default) General alignment information General alignment information, blocks list and alignment
Sort blocks	Sort regions of homology for "List of alignment blocks coordinates" value of "Output format" option : Don't sort (default) Incremental on Target Incremental on Query Decremental by score Decremental by weight Decremental by length
Flank type	Flank type: Length - Output for given amount of symbols in flank of alignment block. All - unlimited flank
Position number	Print additional strings with position number for target and query strings.
Numeration Offset	Numeration Offset: Target - Given value will be added to taget sequence numeration on output Query - Given value will be added to query sequence numeration on output
Special symbols:	Special symbols: Homology - Output symbol as separator lines between target and query, each line separator position shows similarity between target and query positions Gap - Use given simbol to print output gaps Tailing Gap - Use given simbol to print output flanking gaps in profile output, default: '-' Line Tearing - String used for displaying of big gaps in alignment.
Output string	Output for given amount of symbols in each line.
Unalignment info	Produce output information for sequences where no similarity found.
Perfect only	Output perfect and near-perfect alignment.
Preprocessing
Remove	Remove: PolyA - Remove polyA tail from taget sequence. It is may be useful if target sequence is mRNA or EST. PolyT - Remove polyT head from taget sequence. It is may be useful if target sequence is complemented mRNA or EST. Trailing N - Remove trailing N symbols from both ends of target sequence.
Cut Sequence	Cut Sequence: Start - Search in target sequence from given position End - Search in target sequence to given position. "0" - get to end
Apply to chain	Search in target sequence is applied to reverse chain.
Options
Base	Base: Large genomes/contigs Typical genomes/contigs Small genomes/contigs
Score method	Scoring methods for whole alignment: No scoring the alignment (default) By probability of the best block in alignment By probability of the summary of all blocks Blast-like (in SD units) Blast-like (in probability units)
Threshold	If alignment has score less then given value then alignment is not printed.
Target chain(s)	Search in chain(s) in target: In direct chain only In reverse chain only In both chains
Fine adjustment	Fine adjustment of alignment blocks ends.
Multiply variants:	Alternate variants - Produce given best alternate variants of alignments. "All" - Produce all alternate variants of alignments. "Number" - Produce given best alternate variants of alignments. Non-overlapped variants - Produce given non-overlapped variants of alignments. "All" - Produce all alternate variants of alignments. "Number" - Produce given best non-overlapped alignments. Different variants - Produce given different variants of alignments. "All" - Produce all alternate variants of alignments. "Number" - Produce different variants of alignments.
Local alignment	Produce local alignment. Split alignment to several local alignments.
Split diagonal recursively	Split diagonal recursively (if possible).
Minimal required homology	Minimal required homology of the whole alignment.
Minimal required alignment length	Minimal required sum of alignment blocks length