If your task is to select those groups of lines in file 2 where the identifier in the first row of the group is in file 1, you should read file 1 into a hash for easier lookup and then loop over file 2. For example like this: 

use strict;
use warnings;

# read file 1 into hash, don't forget to chomp; 
# left as exercise
# result should look like this:
my %file1 = (
    '>SR1.2' => 1,
    '>SR1.3' => 1,
    );

# loop over file two
while(<DATA>){
    next unless /^(>.*?)\s/ and exists $file1{$1};
    print $_.<DATA>.<DATA>.<DATA>;
}

__DATA__
>SR1.1 HWI-ST
ATGCTGCT
TCGTCGAT
CTGATCAGCTAC
>SR1.2 HWI-ST0
TTTTGCTGCT
TCGTTGGG
CTTTATCAGCTAC
>SR1.3 HWI-ST0787
GGGGGCTGCT
AATCGTCGAT
AACTGATCAGCTAC
>SR1.4 HWI-ST0787
GGGGGCTGCT
AATCGTCGAT
AACTGATCAGCTAC

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In reply to Re: Two files, if the first line and the first column are the same, print this line, the second line, the third line,the fourth line. by hdb
in thread Two files, if the first line and the first column are the same, print this line, the second line, the third line,the fourth line. by yueli

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