overlap.py

#!/usr/bin/python

import sys

try:
    f=open(sys.argv[1],'rU')
except:
    f=sys.stdin

value,key,s="","",{}

# load the dictionary s with the FASTA names and strings

for x in f:
    if x[0]!=">":
        value=value+x.strip()
    else:
        if key!="": s[key]=value
        value=''
        key=x[1:].strip()
s[key]=value

# compute the links
adj=[]
for x ./in s:
    for y in s:
        if x!=y and s[x][:3]==s[y][-3:]:
            adj.append(y+' '+x)

for x in adj:
    print x