How about this?
#!/usr/bin/perl
use strict;
use Data::Dumper;
local $/ = ">";
my %hash;
while (<DATA>) {
s/>//;
s/(^SEQ\d)//;
$hash{">". $1} = $_ if ( defined( $1 ));
}
print Dumper(\%hash);
__DATA__
>SEQ1
-----I--RL--AAIDVDG-NLT----------D--R--D-RL-ISTKA-IESIRS--A-
-E-K--------K-GLT-VSL----LS------GN-V----I-PVV---YA-L------K
IF---------------L-----GINGPVF------------------------------
>SEQ2
-MKI----KA--ISIDIDG-TIT------YPN-R-------MIHEK--A-LEAIRR--A-
-E-S--------L-GIP-IML----VT------GN-T----V-QFA---EA-A------S
IL---------------I-----G----TS-----------------GP-VV--------
>SEQ3
--KI----KA--ISIDIDG-TIT------YPN-R-------MIHEK--A-LEAIRR--A-
-E-S--------L-GIP-IML----VT------GN-T----V-QFA---EA-A------S
IL---------------I-----G----TS-----------------GP-VV--------
---AE--D------GG---A---------------------------------------I
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