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How do I get the alignment score from multiple alignment in MAFFT

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?

t-coffee mafft multiple-alignment
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updated by Ram Ram • written by mail2steff mail2steff

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