If your data truely looks that way, why don't you avoid all that aggravation and just slurp in the file in paragraph mode?

use warnings;
use strict;

my @sequences;
{
  local $/ = '';
  @sequences = <DATA>;
}

print @sequences;

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

>gi|77641045|gb|ABB00394.1| I2 [Lycopersicon esculentum]
TRTPSTSLVVDSGIFGRQNEIEDLVGRLLSMDTKGKNLAVVPIVGMGGLGKTTLAKAVYNDERVKKHFGL
TAWFCVSEAYDAFRITKGILQEIGSTDLKADHNLNQLQVKVKESLKGKKFLIVLDDVWNDNYNEWDDLRN

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

>gi|77641045|gb|ABB00394.1| I2 [Lycopersicon esculentum]
TRTPSTSLVVDSGIFGRQNEIEDLVGRLLSMDTKGKNLAVVPIVGMGGLGKTTLAKAVYNDERVKKHFGL
TAWFCVSEAYDAFRITKGILQEIGSTDLKADHNLNQLQVKVKESLKGKKFLIVLDDVWNDNYNEWDDLRN
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