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#!/usr/bin/perl                                                       
+              
use strict;
...
        print "<font color=\"red\">$frag</font>\n";
    }
}

 Data file:
>gi|292658763|ref|NM_014143.3| Homo sapiens CD274 molecule (CD274), tr
+anscript variant 1, mRNA
GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCTTCCCGAGGCTCCGCACC
...
TGAACTGACATGTCAGGCTGAGGGCTACCCCAAGGCCGAAGTCATCTGGACAAGCAGTGACCATCAAGTC
CTGAGTGGTAAGACCACCACCACCAATTCCAAGAGAGAGGAGAAGCTTTTCAATGTGACCAGCACACTGA
GAATCAACACAACAACTAATGAGATTTTCTACTGCACTTTTAGGAGATTAGATCCTGAGGAAAACCATAC

 Desired output:
<font color="red">GGCGCAACGCTGAGC</font>AGCTGGCGCGTCCCG<font color="re
+d">CGCGGCCCCA</font>GTTCTGCGCA<font color="red">GCTTCCCGAG</font>GCTC
+CGCACC
AGCCGCGCTTCTGTCCGCCTGCAGGGCATTCCAGAAAGATGAGGATATTTGCTGTCTTTATATTCATGAC
...
CTGAGTGGTAAGACCACCACCACCAATTCCAAGAGAGAGGAGAAGCTTTTCAATGTGACCAGCACACTGA
GAATCAACACAACAACTAATGAGATTTTCTACTGCACTTTTAGGAGATTAGATCCTGAGGAAAACCATAC