Sequence Alignment Tool

Sequence One in FASTA Format: Use reverse complement

 

Sequence Two in FASTA Format: Use reverse complement

Alignment Type and Parameters:

Global Sequence To Global Sequence Alignment Parameters:
match score
cost of mismatch
cost of gap start
cost of gap extend

N matches:

N
All
None
Local Sequence To Local Sequence
Global Pattern to Local Sequence Which is Pattern:

Sequence One

Sequence Two
(WDP) Global Pattern To Sequence
(WDP) Local Pattern To Sequence
Compositional Global Pattern To Local Sequence
Compositional Local Sequence To Local Sequence Alignment Type:

Nucleotides

Dinucleotides

limit 
Compositional Global Sequence To Global Sequence
Cyclic
CPG Islands    start:     end:    (finds CG pairs and their ratio to the expected value, uses first sequence only)
Seed Search (ex: 1111x1111)  
use FASTA file with pairs
reverse complement second seq of each pair



Other Tools

Sequence Fraction Tool

2nd Order Markov Chain Tool

Random Sequence Generator

Simulation Control Tool