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if( $self->{'_seq'}->{$name} ) { $self->warn("Replacing one sequence [
+$name]\n") unless $self->verbose < 0; }

hit1_AM161438.1_1-497/20-516             gAGAAACCCUGGAA
hit1_AM161438.1_1-497/1-1:497-993        gGAAAAUCCGUCGA
...
hit1_EF374296.1_509-949/509-509:949-1389 GGAAAAUCCGUCGA
hit1_EF374296.1_509-949/938-1382         AUAGUAAGAGGAAA
hit1_EF374297.1_30-470/30-30:470-910     GGAAAAUCCGUCGA

-------------------- WARNING ---------------------
MSG: Replacing one sequence [hit1_EF374296.1_1-432/1-432]

---------------------------------------------------

use strict;
use warnings;
...
open ( ALIGN, "<inputAlignmentFile" ) or die "failed to open inputAlig
+nmentFile";
$aln -> read_alignment ( \*ALIGN );
close ALIGN;

use Bio::SimpleAlign;

...
    }
    return $count; 
}