I found out it is pretty easy to do with python's difflib:
import difflib
def seq_equivs(s1, s2):
equiv = []
s = difflib.SequenceMatcher(a=s1, b=s2)
for m in s.get_matching_blocks():
if m[2] == 0:
break
for n in range(1, 1+m[2]):
equiv.append((m[0]+n, m[1]+n))
return equiv
Example usage:
f1 = open('file1.txt').read().split('\n')
f2 = open('file2.txt').read().split('\n')
for equivs in seq_equivs(f1, f2):
print('%d %d' % equivs)