Hi ovo, if i understood your question correctly, here is one way to do it.

use strict;

local $/;

my $seqs = <DATA>;

my @match = $seqs =~ /(\>(?:(?:(?!>).)*))/gs;

print join "\n", @match;

__DATA__
>gi|77641047|gb|ABB00395.1| I2 [Lycopersicon esculentum]
TRTPSTSLVVDSGIFGRQNEIEDLVGRLLSMDTKGKNLAVVPIVGMGGLGKTTLAKAVYNDERVKKHFGL
TAWFCVSEAYDAFRITKGILQEIGSTDLKADHNLNQLQVKVKESLKGKKFLIVLDDVWNDNYNEWDDLRN
IFVQGDIGSKIIVTTRKNSVALMMGNEQISMNNLSTEASWSLFKRHAFENMNPMGYPELEEVGKQIAAKC
KGLPLALKTLAGMLCSKSEIDEWKRILRSEIW

>gi|77641045|gb|ABB00394.1| I2 [Lycopersicon esculentum]
TRTPSTSLVVDSGIFGRQNEIEDLVGRLLSMDTKGKNLAVVPIVGMGGLGKTTLAKAVYNDERVKKHFGL
TAWFCVSEAYDAFRITKGILQEIGSTDLKADHNLNQLQVKVKESLKGKKFLIVLDDVWNDNYNEWDDLRN
(many more lines repeated like this)

output:

>gi|77641047|gb|ABB00395.1| I2 [Lycopersicon esculentum]
TRTPSTSLVVDSGIFGRQNEIEDLVGRLLSMDTKGKNLAVVPIVGMGGLGKTTLAKAVYNDERVKKHFGL
TAWFCVSEAYDAFRITKGILQEIGSTDLKADHNLNQLQVKVKESLKGKKFLIVLDDVWNDNYNEWDDLRN
IFVQGDIGSKIIVTTRKNSVALMMGNEQISMNNLSTEASWSLFKRHAFENMNPMGYPELEEVGKQIAAKC
KGLPLALKTLAGMLCSKSEIDEWKRILRSEIW


>gi|77641045|gb|ABB00394.1| I2 [Lycopersicon esculentum]
TRTPSTSLVVDSGIFGRQNEIEDLVGRLLSMDTKGKNLAVVPIVGMGGLGKTTLAKAVYNDERVKKHFGL
TAWFCVSEAYDAFRITKGILQEIGSTDLKADHNLNQLQVKVKESLKGKKFLIVLDDVWNDNYNEWDDLRN
(many more lines repeated like this)
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