$re = '/(?<=E-\d\d)(?=-\d+.)/m';
$str = '0.4066145E-07-0.3677403
0.4066145E-07-0.345465E-07';
$subst = ",";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php