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#!/usr/bin/perl
use strict;
use warnings;
...
CLS_S3_Contig10031_st    CLS_S3_Contig10031    61    12    0.547
CLSS3627.b1_F19.ab1    CLS_S3_Contig10031    62    11    0.5129
CLSS3627.b1_F19.ab1    CLS_S3_Contig10031    64    11    0.5789

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CLS_S3_Contig100    1            0
CLS_S3_Contig100    2            0
CLS_S3_Contig100    3            0
...
CLS_S3_Contig10031    70            1
CLS_S3_Contig10031    71            1
CLS_S3_Contig10031    72            1