diff --git a/alignment/align.py b/alignment/align.py
index 7a35de0..ef6dd73 100644
--- a/alignment/align.py
+++ b/alignment/align.py
@@ -1,3 +1,4 @@
+
 MATCH_SCORE = 1
 MISMATCH_SCORE = 0
 DELETION_SCORE = 0
@@ -5,29 +6,29 @@ INSERTION_SCORE = 0
 
 def align(left, right):
 
-    matrix = {}
+    matrix = [[0] * (len(right) + 1) for i in range(len(left) + 1)]
 
     # Initialise
-    matrix[0, 0] = 0
-    traceback = {}
+    matrix[0][0] = 0
+    traceback = [[None] * (len(right) + 1) for i in range(len(left) + 1)]
     for i in xrange(len(left)):
-        matrix[i+1, 0] = (i+1) * DELETION_SCORE
-        traceback[i+1, 0] = i, 0
+        matrix[i+1][0] = (i+1) * DELETION_SCORE
+        traceback[i+1][0] = i, 0
 
     for i in xrange(len(right)):
-        matrix[0, i+1] = (i+1) * INSERTION_SCORE
-        traceback[0, i+1] = 0, i
+        matrix[0][i+1] = (i+1) * INSERTION_SCORE
+        traceback[0][i+1] = 0, i
 
 
 
     for i, symbol_left in enumerate(left):
         for j, symbol_right in enumerate(right):
-            match_score = matrix[i, j] + MATCH_SCORE if symbol_left == symbol_right else MISMATCH_SCORE
-            deletion = matrix[i, j+1] + DELETION_SCORE
-            insertion = matrix[i+1, j] + INSERTION_SCORE
-            matrix[i+1, j+1], traceback[i+1, j+1] = max((match_score, (i, j)),
+            match_score = matrix[i][j] + MATCH_SCORE if symbol_left == symbol_right else MISMATCH_SCORE
+            deletion = matrix[i][j+1] + DELETION_SCORE
+            insertion = matrix[i+1][j] + INSERTION_SCORE
+            matrix[i+1][j+1], traceback[i+1][j+1] = max((match_score, (i, j)),
                                                         (deletion, (i, j+1)),
                                                         (insertion, (i+1, j)),
                                                         key=lambda x: x[0])
 
-    return matrix[len(left), len(right)], traceback
\ No newline at end of file
+    return matrix[len(left)][len(right)], traceback
diff --git a/alignment/alignment.py b/alignment/alignment.py
index f10c00e..0a085e7 100644
--- a/alignment/alignment.py
+++ b/alignment/alignment.py
@@ -9,7 +9,7 @@ def construct_alignment(left, right, traceback):
 
     # While we're not at the border
     while l > 0 or r > 0:
-        new_l, new_r = traceback[l, r]
+        new_l, new_r = traceback[l][r]
 
         if new_l == l:  # insertion
             sequence_l.append('-')
@@ -47,7 +47,12 @@ def main(left, right):
 
 if __name__ == '__main__':
     from sequences import P53_MOUSE, P53_HUMAN
-    main(P53_HUMAN, P53_MOUSE)
-
+    import time
+    t = []
+    for i in range(4):
+        t0 = time.time()
+        main(P53_HUMAN, P53_MOUSE)
+        t.append(time.time() - t0)
+    print t