Dear All, I have done multiple sequence alignment using mafft and got the alignment. But I could not get the alignment score for the MSA results. Where do I find alignment score for this?. I also tried t-coffee with the mafft-method. I got the same alignment as in Mafft website. I have attached the results of my msa. http://tcoffee.crg.cat/apps/tcoffee/result?rid=4c2b758a But the score are weird.
* BAD AVG GOOD * V13_V34_overlap : 100 V1_V3-03e56d38c : 100 V3-V4-08e0cead1 : 100 cons : 100
I got consensus score as 100 even though they are not perfectly align. Could anyone please guide me this?