#! perl -slw
use strict;
use Data::Dumper;

local $/ = '>'; # Set record delimiter

my @sequences; # AoA

(undef) = scalar <DATA>; # Discard first (blank) record.

while( my $record = <DATA> ) { # Read each paragraph

	# Split to lines
	my @lines = split "\n", $record;

	# Discard the last line if necessary
	pop @lines if $lines[-1] eq '>';

	# Build the array
	push @sequences, [ split( '\|', shift @lines), join( '', @lines ) ];
}

print Dumper \@sequences;

__DATA__
>gi|2695846|emb|Y13255.1|ABY13255 Acipenser baeri mRNA for immunoglobulin heavychain, clone ScH 3.3
TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAACAGCTCTCTGTATAATAATGA
CAGCTCTATCAAGTGTCCGGTCTGATGTAGTGTTGACTGAGTCCGGACCAGCAGTTATAAAGCCTGGAGAGTCCCATAAA
CTGTCCTGTAAAGCCTCTGGATTCACATTCAGCAGCGCCTACATGAGCTGGGTTCGACAAGCTCCTGGAAAGGGTCTGGA
ATGGGTGGCTTATATTTACTCAGGTGGTAGTAGTACATACTATGCCCAGTCTGTCCAGGGAAGATTCGCCATCTCCAGAG
ACGATTCCAACAGCATGCTGTATTTACAAATGAACAGCCTGAAGACTGAAGACACTGCCGTGTATTACTGTGCTCGGGGC
GGGCTGGGGTGGTCCCTTGACTACTGGGGGAAAGGCACAATGATCACCGTAACTTCTGCTACGCCATCACCACCGACAGT
GTTTCCGCTTATGGAGTCATGTTGTTTGAGCGATATCTCGGGTCCTGTTGCTACGGGCTGCTTAGCAACCGGATTCTGCC
TACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAAGCTTTT
>gi|2695846|emb|Y13255.1|ABY13255 Acipenser baeri mRNA for immunoglobulin heavychain, clone ScH 3.3
TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAACAGCTCTCTGTATAATAATGA
CAGCTCTATCAAGTGTCCGGTCTGATGTAGTGTTGACTGAGTCCGGACCAGCAGTTATAAAGCCTGGAGAGTCCCATAAA
CTGTCCTGTAAAGCCTCTGGATTCACATTCAGCAGCGCCTACATGAGCTGGGTTCGACAAGCTCCTGGAAAGGGTCTGGA
ATGGGTGGCTTATATTTACTCAGGTGGTAGTAGTACATACTATGCCCAGTCTGTCCAGGGAAGATTCGCCATCTCCAGAG
ACGATTCCAACAGCATGCTGTATTTACAAATGAACAGCCTGAAGACTGAAGACACTGCCGTGTATTACTGTGCTCGGGGC
GGGCTGGGGTGGTCCCTTGACTACTGGGGGAAAGGCACAATGATCACCGTAACTTCTGCTACGCCATCACCACCGACAGT
GTTTCCGCTTATGGAGTCATGTTGTTTGAGCGATATCTCGGGTCCTGTTGCTACGGGCTGCTTAGCAACCGGATTCTGCC
TACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAAGCTTTT
>gi|2695846|emb|Y13255.1|ABY13255 Acipenser baeri mRNA for immunoglobulin heavychain, clone ScH 3.3
TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAACAGCTCTCTGTATAATAATGA
CAGCTCTATCAAGTGTCCGGTCTGATGTAGTGTTGACTGAGTCCGGACCAGCAGTTATAAAGCCTGGAGAGTCCCATAAA
CTGTCCTGTAAAGCCTCTGGATTCACATTCAGCAGCGCCTACATGAGCTGGGTTCGACAAGCTCCTGGAAAGGGTCTGGA
ATGGGTGGCTTATATTTACTCAGGTGGTAGTAGTACATACTATGCCCAGTCTGTCCAGGGAAGATTCGCCATCTCCAGAG
ACGATTCCAACAGCATGCTGTATTTACAAATGAACAGCCTGAAGACTGAAGACACTGCCGTGTATTACTGTGCTCGGGGC
GGGCTGGGGTGGTCCCTTGACTACTGGGGGAAAGGCACAATGATCACCGTAACTTCTGCTACGCCATCACCACCGACAGT
GTTTCCGCTTATGGAGTCATGTTGTTTGAGCGATATCTCGGGTCCTGTTGCTACGGGCTGCTTAGCAACCGGATTCTGCC
TACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAAGCTTTT
>gi|2695846|emb|Y13255.1|ABY13255 Acipenser baeri mRNA for immunoglobulin heavychain, clone ScH 3.3
TGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGATTTTAACAGCTCTCTGTATAATAATGA
CAGCTCTATCAAGTGTCCGGTCTGATGTAGTGTTGACTGAGTCCGGACCAGCAGTTATAAAGCCTGGAGAGTCCCATAAA
CTGTCCTGTAAAGCCTCTGGATTCACATTCAGCAGCGCCTACATGAGCTGGGTTCGACAAGCTCCTGGAAAGGGTCTGGA
ATGGGTGGCTTATATTTACTCAGGTGGTAGTAGTACATACTATGCCCAGTCTGTCCAGGGAAGATTCGCCATCTCCAGAG
ACGATTCCAACAGCATGCTGTATTTACAAATGAACAGCCTGAAGACTGAAGACACTGCCGTGTATTACTGTGCTCGGGGC
GGGCTGGGGTGGTCCCTTGACTACTGGGGGAAAGGCACAATGATCACCGTAACTTCTGCTACGCCATCACCACCGACAGT
GTTTCCGCTTATGGAGTCATGTTGTTTGAGCGATATCTCGGGTCCTGTTGCTACGGGCTGCTTAGCAACCGGATTCTGCC
TACCCCCGCGACCTTCTCGTGGACTGATCAATCTGGAAAAGCTTTT