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.
FormatOutput 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
Alignment accurancy  Alignment accurancy:
Weak (fast)
Normal (slow)
Mapping accurancy  Mapping accurancy:
Weak (fast)
Normal (slow)
Score methodScoring 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).
Restrictions  Target:
By length - Alignment region on target sequence does not exceed given length.
By multiplier - Alignment region on target sequence does not exceed length of query sequence multiplied to N (N - is floting poin number).
By range - Alignment region on target sequence does not exceed length of query sequence plus N.

Query:
By length - Alignment region on query sequence does not exceed given length.
By multiplier - Alignment region on query sequence does not exceed length of query sequence multiplied to N (N - is floting poin number).
By range - Alignment region on query sequence does not exceed length of query sequence plus N.
Maximal allowed intron length   Maximal allowed intron length