Index: modlib/modeller/alignment.py
===================================================================
--- modlib/modeller/alignment.py	(revision 7152)
+++ modlib/modeller/alignment.py	(revision 7153)
@@ -426,15 +426,35 @@
                 raise modeller.FileFormatError("expecting SEQ2: line " + \
                                          "in suboptimal alignment output file")
             seq2 = [int(x) for x in seq2]
+            if len(seq1) != len(seq2):
+                raise modeller.FileFormatError("SEQ1 and SEQ2 lines should "
+                                               "be the same length")
 
             _set_seq_gaps_subopt(self[0], seq1)
             _set_seq_gaps_subopt(self[1], seq2)
-            if seq1[0] > 1 and seq2[0] > 1:
-                raise NotImplementedError("Neither sequence starts at 1")
-            elif seq1[0] > 1:
-                self[1].residues[0].add_leading_gaps(seq1[0] - seq2[0])
-            elif seq2[0] > 1:
-                self[0].residues[0].add_leading_gaps(seq2[0] - seq1[0])
+            # If the first alignment position is not the first residue in
+            # either sequence, deliberately misalign the first stretch of
+            # residues
+            misalign = min(seq1[0], seq2[0]) - 1
+            if misalign > 0:
+                seq1[0] -= misalign + 1
+                seq2[0] -= misalign + 1
+                self[0].residues[misalign+seq1[0]
+                                 -1].add_trailing_gaps(misalign+seq2[0])
+                self[1].residues[0].add_leading_gaps(misalign+seq1[0])
+            else:
+                self[0].residues[0].add_leading_gaps(seq2[0] - 1)
+                self[1].residues[0].add_leading_gaps(seq1[0] - 1)
+            # If both sequences extend past the end of the alignment, add
+            # the shortest number of gaps necessary to deliberately misalign
+            # these termini
+            extra1 = len(self[0].residues) - seq1[-1]
+            extra2 = len(self[1].residues) - seq2[-1]
+            if extra1 > 0 and extra2 > 0:
+                if extra1 > extra2:
+                    self[0].residues[-extra1].add_leading_gaps(extra2)
+                else:
+                    self[1].residues[-extra2].add_leading_gaps(extra1)
             yield self
 
     def __contains__(self, code):
@@ -557,6 +577,6 @@
                 elif gaps_to_add < gaps:
                     res.remove_leading_gaps(gaps - gaps_to_add)
                 if subopt_pos[pos_n] != n + 1:
-                    raise Modeller.FileFormatError("suboptimal alignment " + \
+                    raise modeller.FileFormatError("suboptimal alignment " + \
                               "file SEQ1 and SEQ2 indices should be sequential")
                 pos_n += 1