I have a program which looks through a protein sequence (just a string of letters) to see if it has N's in it. The results look roughly like this:

BC001593 91 NPSL
BC001593 262 NASS
BC001593 293 NAST

I just need to match the numbers (91, 262, 293...) as these are the positions of the N's. I've tried this: 

if ($string =~/\w{1,12}\s+(\d{1,5})\s+[a-zA-Z]{4}/sm){
$sites = $1;
}

[download]

and it matches the first number 91, fine, but no more. I tried s and m modifiers but no luck. How can I search through every line and record the value of every match? In addition, there can be any number of such letters present, so I need to search until there are no more lines left. Any ideas?

In reply to matching every occurrence of a regex by Becky

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