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Imperfect Simple Sequence Repeat (SSR) Finder

The Imperfect SSR Finder is an online tool to help geneticists find Simple Sequence Repeats (SSR), aka microsatellites or Short Tandem Repeats (STR), in uploaded FASTA sequences.

  1. General Options Completed
  2. Perfect SSR Minimums Not completed
  3. Imperfect SSR Minimums Not completed
  4. Sequences Not completed

Step 1 of 4 General Options

Quick Reference

  • A red asterisk * indicates a required field.
  • Default values: Fields are pre-filled; adjust as needed or leave defaults.
  • Output linewrap width: Set columns for output wrapping (70–80 typical, 0 for no wrap)
  • Output case: Choose UPPER or lower for output sequences
  • Invert SSR case: Highlight found SSRs by inverting case (e.g., ataaaTGTGTGTGcgatg)
  • Ignore initial/trailing pairs: Skip unreliable base pairs at sequence ends
  • Aggressive join: Join SSRs when only one side "wants" to connect
(0 = no wrap)
Example: ataaaTGTGTGTGcgatg
Number of initial base pairs in each sequence to ignore.
Number of trailing base pairs in each sequence to ignore.
Yes: join NRR-separated SSRs if only one "wants" to join. No: join only if both "want" to join.