--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small.fasta.align	Wed May 02 20:18:11 2018 -0400
@@ -0,0 +1,104 @@
+18 0.00 0.00 0.00 scaffold_1 613 632 (13519) (GT)n#Simple_repeat 1 20 (0) m_b1s252i0 1
+
+  scaffold_1           613 GTGTGTGTGTGTGTGTGTGT 632
+                                               
+  (GT)n#Simple_          1 GTGTGTGTGTGTGTGTGTGT 20
+
+Matrix = Unknown
+Transitions / transversions = 1.00 (0/0)
+Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0)
+
+
+16 18.30 2.22 2.22 scaffold_1 780 824 (13327) (ATAATA)n#Simple_repeat 1 45 (0) m_b1s252i1 2
+
+  scaffold_1           780 ATATTAAT-ATACTAAATAATGATAATATTAATTCTAATAATGATA 824
+                              v    -   v -      i      v    vv       i   
+  (ATAATA)n#Sim          1 ATAATAATAATAAT-AATAATAATAATAATAATAATAATAATAATA 45
+
+Matrix = Unknown
+Transitions / transversions = 0.40 (2/5)
+Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2)
+
+
+12 23.88 4.55 0.00 scaffold_1 2231 2274 (11877) (CAGA)n#Simple_repeat 1 46 (0) m_b1s252i2 3
+
+  scaffold_1          2231 CAGA-AAACAGTCAGCCAATCAGA-GGACAGACTCAGAGACAGACA 2274
+                               - i    v   v  iv    -i       vv v         
+  (CAGA)n#Simpl          1 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 46
+
+Matrix = Unknown
+Transitions / transversions = 0.50 (3/6)
+Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2)
+
+
+15 18.42 10.20 0.00 scaffold_1 4853 4901 (9250) (TC)n#Simple_repeat 1 54 (0) m_b1s252i3 4
+
+  scaffold_1          4853 TCTATTTTTCTCTCTCTCTCT-TCGGTCAGTTTCTCT-TCT-TCTC-CTC 4898
+                              v i i             -  vv  vv i     -   -    -   
+  (TC)n#Simple_          1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50
+
+  scaffold_1          4899 -CTC 4901
+                           -   
+  (TC)n#Simple_         51 TCTC 54
+
+Matrix = Unknown
+Transitions / transversions = 0.60 (3/5)
+Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5)
+
+
+13 19.07 1.82 7.69 scaffold_1 6230 6284 (7867) (TAATTAA)n#Simple_repeat 1 52 (0) m_b1s252i4 5
+
+  scaffold_1          6230 TAATGAGT-ATTACTAATTAATAATTGGATGAGTTTATGAATTCATCATT 6278
+                               v i -    v            -i  - i  v  -    v  v   
+  (TAATTAA)n#Si          1 TAATTAATAATTAATAATTAATAATT-AAT-AATTAAT-AATTAATAATT 47
+
+  scaffold_1          6279 AAATAA 6284
+                           -     
+  (TAATTAA)n#Si         48 -AATAA 52
+
+Matrix = Unknown
+Transitions / transversions = 0.60 (3/5)
+Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5)
+
+
+15 28.31 0.00 3.51 scaffold_1 6548 6606 (7545) (GACA)n#Simple_repeat 1 57 (0) m_b1s252i5 6
+
+  scaffold_1          6548 GACAGAGAGATAAACAGACAGACATGGAAACAGAGGGACATAGAAAACAA 6597
+                                 v   i i           viv i     vi    v -v i  - 
+  (GACA)n#Simpl          1 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA-CAGAC-A 48
+
+  scaffold_1          6598 GACAGAGAG 6606
+                                 v  
+  (GACA)n#Simpl         49 GACAGACAG 57
+
+Matrix = Unknown
+Transitions / transversions = 0.86 (6/7)
+Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2)
+
+
+67 2.94 1.43 0.00 scaffold_1 11981 12050 (2170) (CT)n#Simple_repeat 1 71 (0) c_b1s251i0 7
+
+  scaffold_1         11981 CTCTCTCTCTCTCCCTCTCCCTCTC-CTCTCTCTCTCTCTCTCTCTCTCT 12029
+                                        i     i     -                        
+  (CT)n#Simple_          1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50
+
+  scaffold_1         12030 CTCTCTCTCTCTCTCTCTCTC 12050
+                                                
+  (CT)n#Simple_         51 CTCTCTCTCTCTCTCTCTCTC 71
+
+Matrix = Unknown
+Transitions / transversions = 1.00 (2/0)
+Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1)
+
+
+19 15.37 2.78 0.00 scaffold_1 12078 12113 (2107) (CT)n#Simple_repeat 1 37 (0) m_b1s252i6 8
+
+  scaffold_1         12078 CTCGCTCTCTCACTCTCTCCCTCTCTC-CCCACTCTC 12113
+                              v       v       i       - i v     
+  (CT)n#Simple_          1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 37
+
+Matrix = Unknown
+Transitions / transversions = 0.67 (2/3)
+Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1)
+
+