The reason for the "substr outside of string" warning is that you assign the $seqarray variable to the empty string and you never assign it any other value. You are likely getting confused because you use the same name for two variables (an array and a scalar): $seqarray is a different variable from @seqarray. If you can specify what you want for output, you will get more specific help.

See also:

• Basic debugging checklist
• List::MoreUtils natatime