The relative position of a given nucleotide in a multiple sequence alignement


I am a molecular biologist and my question may seem (very!) trivial.

In a multiple sequence alignment (nucleic acid), I would like to be able to obtain the relative position of any nucleotide along its sequence. In other words, if I am interested in a particular nucleotide of a reference sequence (say, A at position 28 relative to the 5’-end), I would like to obtain the relative position of this conserved nucleotide in the other sequences in the alignment.

Could I use Jalview in a simple way to obtain such information? Do you know any other tricks to get these positions? Do you know other softwares capable of performing such a task, perhaps simply by positioning the mouse cursor on the nucleotide of interest?

Thank you in advance for your attention and apologies for the inconvenience.

Have a nice day,


Hi JC,

If I think I’ve understood correctly, you can inspect an alignment of nucleic acid sequences and hover the mouse arrow over the aligned column to see the position of the aligned bases in the other sequences. The position of the base in its sequence can be seen in parentheses in the information area at the bottom of the alignment frame.

I’ve made a short video to demonstrate. The example in the video is the example Fetched sequence from ENSEMBL, and I’ve highlighted (reference) position 227 and then moved down the alignment to show the positions of the other aligned bases. I’ve circled where that information is shown with a red circle.

Hope this helps.


Hi Ben,

Thank you very much for your quick and clear answer.
I had actually positioned the mouse cursor but didn’t look down, and so I thought it wasn’t active…
I feel so stupid !!! On the other hand, this is my first time using Jalview… :+)
Have a nice day,

No problem!

There’s a lot of information to be gleaned, it’s very easy to miss something. Hope you get a lot more use out of Jalview, and don’t hesitate to ask if you come across other problems (there are no stupid questions!).