Well, you must be careful when you use match variables, especially when you work with big strings. But they aren't slow per se:

Update: Thank you all for your comments and suggestions (here and in the CB)! See How do I get what is to the left of my match? for an updated benchmark and better explanations. 

use Benchmark qw(:all);
use Regexp::MatchContext;

my $count = 300000;

my $seq
    = 'GGGTTGAAGTTTAGACCGCTCACAGTAGTTCTACCTATAGAAAAGATCATGAAAGAGGCGATC
+AGAATGGTACTCGAATCCATTTACGATCCCGAGTTTCCAGACACATCGCATTTCCGCTCGGGTCAAGGC
+TGCCACTCGGTCCTAAGACGGATCAAAGAAGAGTGGGGAATCTCTCGCTGGTTTTTAGAATTCGACATC
+AGGAAGTGTTTTCACACCATCGACCGACATCGACTCATCCAAATTTTGAAGGAAGAGATCGACGATCCC
+AAGTTCTTTTACTCCATTCAGAAAGTATTTTCCGCCGGACGACTCGTAGGAGTTGAGAGGGGCCCTTAC
+TCCGTCCCACACAGTGTACTACTATCGGCCCTACCAGGCAACATCTACCTACACAAGCTCGATCAGGAG
+ATAGGGAGGATCCGACAGAAGTACGAAATTCCGATTGTTCAGAGAGTCAGATCGGTTCTATTAAGGACA
+GGTCGTCGTATTGATGACCAAGAAAACCCTGGAGAAGAAGCAAGCTTCAACGCTCCCCAAGACAACAGA
+GCCATCATTGTGGGGAGCGTTAAGAGCATGCAACGCAAAGCGGCCTTTCATTCCCTTGTTTCGTCGTGG
+CACACCCCCCCCACAAGCACCCTCCGGCTCAGGGGGGACCAGAAAAGGCCTTTCGTTTTCCCCCCTTCG
+TCGGCCCTTGCCGTCTTCCTTAACAAGCCCTCGAGCCTTCTTTGCGCCGCCTTCCTCATAGAAGCCGCC
+GGGTTGACCCCGAAGGCTGAATTCTATGGTGGAGAACGCTGTAATAATAATTGGGCCATGAGAGACCTT
+CTTAAGTATTGCAAAAGAAAGGGCCTGCTGATAGAGCTGGGCGGGGAGGCGATACTAGTTATCAGGTCA
+GAGAGAGGCCTGGCCCGTAAGCAGGCCCCCTTAAAAACCCATTACTTAATAAGGATTTGTTACGCGCGA
+TATGCCGACGACTTACTACTGGGAATCGTGGGTGCCGTAGAGCTTCTCATAGAAATACAAAAACGTATC
+GCCCATTTCCTACAATCTGGCCTGAACCTTTGGGTAGGCTCCGCAGGATCAACAACAATAGCTGCACGG
+AGTACGGTAGAATTCCTTGGTACGGTCATTCGGGAAGTCCCTCCGAGGACGACTCCCATACAATTTTTG
+CGAGAGCTGGAAAAGCGTCTACGGGTAAAGCACCGTATCCATATAACTGCTTGCCACCTACGCTCCGCC
+ATCCATTCAAAGTTTAGGAACCTAGGTGATAGTATCCCGATCAAACAGCTGACGAAGGGGATGAGCAAA
+ACAGGGAGTCTACAGGACGGGGTTCAACTAGCGGAGACTCTTGGAACAGCTGGAGTCAGAAGTCCCCAA
+GTTAGCGTATTATGGGGGACCGTCAAGCACATCCGGCAAGGATCAAGGGGGATCTCGTTCTTGCATAGC
+TCAGGTCGGAGCAACGCGTCATCGGACGTTCAACAGGTAGTCTCACGATCGGGCACTCATGCCCGTAAG
+TTGTCATTGTATACTCCCCCGGGTCGGAAGGCGGCGGGGGAGGGAGGAGGACACTGGGCGGGATCTATC
+AGCAGCGAATTCCCCATAAAGATAGAGGCACCTATAAAAAAGATACTCCGAAGGCTTCGGGATCGAGGT
+ATCATTAGCCGAAGAAGACCCTGGCCAATCCACGTGGCCTGTTTGACGAACGTCAGCGACGAAGACATC
+GTAAATTGGTCCGCGGGCATCGCGATAAGTCCTCTGTCCTACTACAGGTGCCGCGACAACCTTTATCAA
+GTCCGAACGATTGTCGACCACCAGATTCGCTGGTCTGCAATATTCACCCTAGCCCACAAGCACAAATCC
+TCGGCGCCGAATATAATCCTCAAGTACTCCAAAGACTCAAATATTGTAAATCAAGAAGGTGGCAAGATC
+CTTGCAGAGTTCCCCAACAGCATAGAGCTTGGGAAGCTCGGACCCGGTCAAGACCTGAACAAGAAGGAA
+CACTCAACTACTAGTCTAGTCTAG';

cmpthese(
    $count,
    {   'regex' => sub {
            my ( $prematch, $match, $postmatch )
                = $seq =~ m{(\A .*?) (CTGGCCCGTAA) (.*\z) }xms;       
+   
        },
        'matchvars' => sub {
            $seq =~ m{CTGGCCCGTAA}xms;
            my ($prematch, $match, $postmatch) = ($`, $&, $'); 
        },
        'matchcontext' => sub {
            $seq =~ m{(?p)CTGGCCCGTAA}xms;
            my ( $prematch, $match, $postmatch )
                = ( PREMATCH(), MATCH(), POSTMATCH() );
        },
    }
);

[download]
                 Rate        regex matchcontext    matchvars
regex         17065/s           --         -24%         -84%
matchcontext  22590/s          32%           --         -78%
matchvars    103806/s         508%         360%           --

[download]

In reply to Re^3: Style question: regex versus string builtin function by lima1
in thread Style question: regex versus string builtin function by eyepopslikeamosquito

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