primer3 in msatcommander not producing any primers

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What steps will reproduce the problem?
1. uploaded my scaffold file in fasta format
2. all the options was chosen in msatcommander 
3. no custom tag

What is the expected output? What do you see instead
i saw a primer3 folder created, but noprimertag excel file contains nothing and 
i have a string of .txt that states INPUT PROBLEM: TARGET beyond end of sequence

What version of the product are you using? On what operating system?
version of software used: msatcommander-0.8.2-WINXP , os:windows 7 pro 64-bit  

Please provide any additional information below.

Original issue reported on code.google.com by sueasmy1...@gmail.com on 8 Aug 2014 at 9:49

Attachments:

• scaffold00535_primer.txt
• scaffold01330_primer.txt
• primer3_temp.txt
• primerCombined.csv