layed using a different colour, i.e., a light colour indicating its

ency with other four sequences at this residue. However, the

G which was conserved in other four sequences was displayed

same colour, i.e., in red. Using this function, the main input is an

ct generated by the XStringSet function (either the

ingSet function, the AAStringSet function or the

ingSet function). It is also possible to specify which interval of

equences of interest by assigning values to the start parameter

nd parameter of the ggmsa function, shown below,

sa(mySeq,start=1,end=20,colour=‘clustal’)

he visualised msa alignment of the five sequences with the same length using

function.

ose another five sequences with different lengths were used for an

t,

GAATGGACCCG

GATGTATGGACCCG

TGTATCCACCCG

CATGTATGGCCCG

ATATCGCTTCT

sa alignment result is shown below:

names

ATCAGA-ATG--GACCCG 1

ATCACATGTAT-GGCCCG 4

ATTTGATGTATGGACCCG 2

ACAGATGTATCCACCCG 3

TCCAATATCGCTTCT-- 5

ATCAGATGTAT?GACCCG Consensus