TRLA: The Tandem Repeat Locator Algorithm

Help Files

example input:

Pattern To Search On: GCTA
Text Sequence: CTAGGCCTAGCTAG
Window Length: 14

Text Contains Ambiguity Characters (click above link for assistance with entering ambiguity characters.)

Pattern To Search On:

Text Sequence:

Processing Options:

E-mail Results To:<-- insert email address here

E-mail Results

Interactive (Non-Graphical) Results

use interactive only for smaller text sequences.

Scoring Options:

Use Default Scoring Matrix

Use Genetic Algoritm Approximations for Scoring Matrix

Custom Scoring Matrix (specify below):

for explanation of the scoring matrix, click here

Initial Gap:

Successive Gap

Match:

Substitution :

Use Convex Gap Function Ax-B
(x is the number of gapped bases, and A and B are defined below)

A: B:

For Information on Concept and Theory: Deborah Joseph - joseph@cs.wisc.edu
Amy Hauth - kryder@cs.wisc.edu

For Information on Implementation and Use: David Zimmerman - dzimm@cs.wisc.edu
Ben Geisler - bgeisler@cs.wisc.edu

Send bug reports to: bgeisler@cs.wisc.edu