I have changed code for blinking the min and sec digits alone
Try this code:
DEMO
if( hrs <= 0 && mins <= 4)
{
document.getElementById('list').style.color="red";
}
else
{
document.getElementById('list').style.color="black";
styleFlag = 1;
}
if(styleFlag == 0) {
styleFlag = 1;
document.getElementById('hr').innerHTML = hours;
document.getElementById('mins').innerHTML = "";
document.getElementById('sec').innerHTML = "";
}
else
{
styleFlag = 0;
document.getElementById('hr').innerHTML = hours;
document.getElementById('mins').innerHTML = minutes;
document.getElementById('sec').innerHTML = seconds;
}