In order to align partition with parted you can use --align option. Valid alignment types are:
none - Use the minimum alignment allowed by the disk type.
cylinder - Align partitions to cylinders.
minimal - Use minimum alignment as given by the disk topology information. This and the opt value will use layout information provided by the disk to align the logical partition table addresses to actual physical blocks on the disks. The min value is the minimum alignment needed to align the partition properly to physical blocks, which avoids performance degradation.
optimal Use optimum alignment as given by the disk topology information. This aligns to a multiple of the physical block size in a way that guarantees optimal performance.
Other useful tip is that you can set the size with percentages to get it aligned. Start at 0% and end at 100%. For example:
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parted -a optimal /dev/sda mkpart primary 0% 4096MB