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#!/user/bin/perl -w                                                   
+                                                        
# Use your own path                                                   
+                                                        
...
    my $sample = splice @file, $rand, 1; # Cut out the $rand-th line, 
+offset 1 means just one line                            
    print OUT $sample;
} # end of for loop

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CTTTTCTTCGGACTACTTACAAGGTGTTGCATGGTCGTC
>FW4WBAJ01DVAX5.ICM_PML_Bv6.PML_43_2003_06_09
...
TGGTGCCTTCGGGAATCTAGTGACAGGTGATGCATGGCTGTCG
CACACCAACGCGAAAAACCTTACCAACACTTGACATGTTCGTCGCGACTCTAAGAGATTA
TTCGGTTCGGCCGGACGAAACACAGGTGTTGCATGGCTGTC

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FW4WBAJ01DVAX5.ICM_PML_Bv6.PML_43_2003_06_09
FMS0R7002J2YH1.ICM_CAM_Bv6.CAM_0011_2000_03_26
E6SXMJY02I00IR.ICM_BMO_Bv6.BMO_0005_2007_09_22

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>FRZPY5Q02F00L9.ICM_AWP_Bv6.AWP_0001_2007_08_23
ACTGCCAACGCGCAGAACCTTACCAGGTCCTGACTTCCTGACTATGGTTATTAGAAATAA
...
>FRZPY5Q02F023C.ICM_AWP_Bv6.AWP_0001_2007_08_23
ACTGCCAACGCGCAGAACCTTACCAACCCTTGACATCCAGAGAATTTTCTAGAGATAGAT
TTGTGCCTTCGGGAACTCTGTGACAGGTGATGCATGGCTGTC