This produces the desired output: 
use warnings;
use strict;

my %data;
while (<DATA>) {
    my @cols = split;
    push @{ $data{$cols[0]} }, $cols[1] if $cols[3] > 4;
}

for my $k (sort keys %data) {
    my $i = 1;
    my @ns = @{ $data{$k} };
    my $n0 = shift @ns;
    my @ns2 = $n0;
    for my $n (@ns) {
        if ($n == $n0+1) {
            push @ns2, $n;
            $i++;
        }
        else {
            print "$k,$ns2[0],$ns2[-1],$i\n";
            @ns2 = $n;
            $i = 1;
        }
        $n0 = $n;
    }
    print "$k,$ns2[0],$ns2[-1],$i\n";
}

__DATA__
C10000035    12    C    4    ....^>.    HHFCC
C10000035    13    C    6    .....^>.    HHFFCC
C10000035    14    C    6    ......    JHFFCC
C10000035    15    C    6    ......    IHFFFC
C10000035    16    A    4    .GG...^>G    JGHFFFC
C10000035    17    C    7    .......    JGHFFFC
C10000035    18    C    8    .......^].    JIHHFFC@
C10000035    19    A    8    ........    IJHHFFFC
C10000035    20    C    9    ..T...T.^].    JIHGHFF@C
C10000035    21    G    10    A........^].    AJJHHHFDCC
C10000040    30    C    5    ....^>.    HHFCC
C10000040    31    C    6    .....^>.    HHFFCC
C10000040    32    C    6    ......    JHFFCC
C10000040    33    C    6    ......    IHFFFC
C10000040    34    C    4    ......    IHFFFC
C10000040    35    C    4    ......    IHFFFC
C10000040    36    C    4    ......    IHFFFC
C10000040    37    C    6    ......    IHFFFC
C10000040    38    C    6    ......    IHFFFC

[download]

See also:

In reply to Re: Looking for series in consecutive lines of a file by toolic
in thread Looking for series in consecutive lines of a file by mbp

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