### see the blog here:

### There are two different coordinate base systems in different files: 0-base and 1-base. Different files use different base systems, and sometimes it causes confusions (especially when one tries to calculate the length of the region). Here I show the differences in two systems, and summarize several file formats that use both sytems.Bases in sequence positions

**0-base system**: the first base is 0. You represent a region as [a, b). This is also called "

**half-close-half-open**", "

**0-base end exclusive**", or "

**1-base end inclusive**". When calculating the length of the region, subtract a from b directly:

*L=b-a*

**1-base system**: the first base is 1, and you represent a region as [a,b]. When calculating the length of the region, don't forget to add 1:

*L=b-a+1*

Here is an example. Suppose you want to represent a region of X in the following sequence:

000

**XXX**0000

In the 0-base system, this is represented as [3,6), and the length is 6-3=3. In the 1-base system, use [4, 6], and the length is 6-4+1=3.

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