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try:
awk '
NR==FNR {a[$1]=$2; next;}
{c=0; for (i=1; i<=NF; i++) {for (s in a) if ($0 ~ s && c==0) {sub(s, a[s]); c=1}}}
1
' species-names.txt sequence-names.txt

awk -f thie.awk myFile
where thie.awk is:

BEGIN {
if (!chars) chars="A T G C"
nchars=split(chars, charsA, FS)
}
{
width=length($2)
for(i=1;i<=width;i++)
arr[substr($2,i,1),i]++...