#!/usr/bin/perl -w
undef $/; use strict;

$_ = <DATA>;

while (m/\G(>IDnumber\d+ length=)350\n([^\n]+)\n([^\n]+)\n/g) {

        print $1.length($2.$3)."\n$2$3\n";

}







__DATA__
>IDnumber1 length=350
AGCTG
AAGTCGCT
>IDnumber2 length=350
AGAACGT
ACC
>IDnumber3 length=350
AGC
ACTTCGCTAACT
[download]

Hope that's helpful to you.

Best wishes, andye