According to Microsoft Disk performance may be slower than expected when you use multiple disks in Windows Server 2003, in Windows XP, and in Windows 2000, Read more here, the article also says the resolution for the issue. (It does not apply to Windows 7).
So if you are using any of the operating system stated above, here is another software from Paragon Software group, Paragon Alignment Tool which can do this and which is very user friendly.
The problem of inevitable degradation of the disk subsystem performance caused by misaligned partitions dates back to the nineties. From being a headache for IT administrators who wanted to get the most out of disk arrays, it's become crucial for all of us with appearance of SSD (solid state drive) and ultra high-capacity hard drives. Moreover, the growing popularity of virtualized systems has aggravated the situation even more.
Read more Here
The full version Paragon Alignment Tool worth 29.95$ while you can get a special edition absolutely Free, To get it
1. Open the promotional page here
2. Enter the required fields
4. Check mail for the download link and Serial number
[Via Techno 360]