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while (<FILE1>) {
    my ($ID1, undef, undef, undef, $Seq1) = split;
    $bow1{$ID1} = $ID1; # your id is the key and can be got again
}

while (<FILE1>) {
    my ($ID1, undef, undef, undef, $Seq1) = split;
    $bow1{$ID1} = $Seq1;   # ID is hash key, Seq is hash value
}