JASAT 
J
A
Sequence Alignment Tool
Start by choosing a pair of sequences to align from the menu below.
For a given pair of sequences, JASAT displays the alignment graph
 a graph showing the possible ways the sequences might be aligned.
In this graph:

a horizontal line indicates base Y was inserted (I)
into the first sequence (or that Y was deleted from the second sequence);

a vertical line indicates base X was deleted (D) from the
first sequence (or that X was inserted into the second sequence);

a diagonal arc indicates a substitution (S):
base X in the first sequence was replaced with
base Y in the second sequence;

a diagonal line indicates that the two bases are the
same (S) in the two sequences.
Clicking the Compute Least Cost Alignment button
computes and displays:

the least cost path through the graph
(for the given cost settings),

BLASTlike alignment strings corresponding to this path,
showing how the sequences were aligned,

the edit string,
showing the sequence operations (I, D, or S) for
transforming
the first sequence into the second, and

the total cost of that alignment.
Have fun!