Try like this,
TIMTOWDI
use strict;
use warnings;
my @content = <DATA>;
@content = grep!/^\;/, @content;
print @content[6..$#content];
__DATA__
<h3>Warning</h3><blockquote><FONT SIZE=+1 color=#aa0000><B>
Circular contig NC_001224.1 leftmost feature 0 Q0050 le
+ft neighbour Q0275
</B></FONT></blockquote><BR><HR SIZE=3>
<h3>Warning</h3><blockquote><FONT SIZE=+1 color=#aa0000><B>
Circular contig NC_001224.1 rightmost feature 18 Q0275
+right neighbour Q0045
</B></FONT></blockquote><BR><HR SIZE=3>
>YJR152W|DAL5
TGATTTTGGATATTCATCAAAGGAAACCCTATTAATGGGTTTACCTACAGGTGCTGTTGA
ATTGGTAGGTTGTCCACTTTTTGGTATTCTAGCAGTTTATGCAGCCAATAAGAAGATACC
ATTTTGGAAATATAAGTTGAGTTGGGCTATTTTTGCAGCTGTCTTAGCATTGATTGCTAG
CTGCATGTTAGGGTTTGCAACAAACTCCAAAAAAGCAAGACTGGCTGGTGCTTACCTGTG
GTACATCTCGCCCGTCTCATTTATTTGCGTACTTTCCAATATCAGTGCGAATTCCTCGGG
ATATAGTAAAAAATGGACTGTATCTTCAATAAACTTAGTAGCATATGCTGCAGCTAACTT
GGCAGGACCACAAACCTTTATTGCTAAGCAGGCTCCTAAATATCATGGCGCTAAGGTCGC
TATGGTCGTATGTTATGCTGTTATGATCGTGCTTCTATCTATACTGCTCATCGTCAATTT
AAGGGAAAACAAGAGACGTGATAAGATAGCTGCCGAGAGAGGGTTCCCTGAAGAAACAGA
GAATTTAGAGTTTTCTGATTTGACTGATTTTGAAAATCCAAATTTCAGATACACTTTATG
>YKR039W|GAP1
CCTAGCTGAACAGAGATTTCTGCCAGAAATCTTTTCCTACGTTGACCGTAAGGGTAGACC
ATTGGTGGGAATTGCTGTCACATCTGCATTCGGTCTTATTGCGTTTGTTGCCGCCTCCAA
AAAGGAAGGTGAAGTTTTCAACTGGTTACTAGCCTTGTCTGGGTTGTCATCTCTATTCAC
ATGGGGTGGTATCTGTATTTGTCACATTCGTTTCAGAAAGGCATTGGCCGCCCAAGGAAG
AGGCTTGGATGAATTGTCTTTCAAGTCTCCTACCGGTGTTTGGGGTTCCTACTGGGGGTT
ATTTATGGTTATTATTATGTTCATTGCCCAATTCTACGTTGCTGTATTCCCCGTGGGAGA
TTCTCCAAGTGCGGAAGGTTTCTTCGAAGCTTATCTATCCTTCCCACTTGTTATGGTTAT
GTACATCGGACACAAGATCTATAAGAGGAATTGGAAGCTTTTCATCCCAGCAGAAAAGAT
GGACATTGATACGGGTAGAAGAGAAGTCGATTTAGATTTGTTGAAACAAGAAATTGCAGA
AGAAAAGGCAATTATGGCCACAAAGCCAAGATGGTATAGAATCTGGAATTTCTGGTGTTA
;WARNING invalid query foo
;WARNING invalid query bar
;WARNING invalid query qux
Regards,
Velusamy R.
eval"print uc\"\\c$_\""for split'','j)@,/6%@0%2,`e@3!-9v2)/@|6%,53!-9@2~j';
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