TESS web tool

http://cbil.upenn.edu/cgi-bin/tess/tess/

TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest.

RepeatMasker

 

RepeatMasker

 RepeatMasker http://www.repeatmasker.org/ is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by the program cross_match, an efficient implementation of the Smith-Waterman-Gotoh algorithm developed by Phil Green.  

Tandem Repeats Database (TRDB)

Tandem Repeats Database (TRDB) is a public repository of information on tandem repeats in genomic DNA and contains a variety of tools for their analysis. These currently include, the Tandem Repeats Finder algorithm, query and filtering capabilities for finding particular repeats of interest, repeat clustering algorithms based on sequence similarity, polymorphism prediction based on common patterns of mutation, PCR primer selection, and data download in a variety of formats. In addition, TRDB serves as a centralized research workbench. It provides storage space for results of analysis and permits collaborators to privately share their data and analysis.

You can upload up to 100MB FASTA sequence to be analyzed online for tandem repeats!