Title: Characterization of Indels in Poxvirus Genomes

Title: Characterization of indels in poxvirus genomes

Journal: Virus Genes

Authors: Danielle Coulson and Chris Upton

Biochemistry and Microbiology, University of Victoria, Victoria, B.C., V8W 3P6 Canada

Corresponding author:

Online Resource-2 Table of VACV indels

Events in bold indicate events which do not match the phylogenetic tree of the orthopoxviruses.

Indels are listed for the VACVs, not all orthopoxviruses.

Indel number / Gapped position / REPEAT sequence / EVENT / score
1 / 37647 / TTTAAAA / Deletion in CVA + MVA / 6/7 (8)
2 / 37797 / ATATTA / Deletion / 6/6 (16)
3 / 37789 / TATC / Deletion in MVA / 4/4 (20)
4 / 37948 / AACT / Deletion in MVA / 4/4 (10)
5 / 38016 / GTTATTA / Deletion / 6/7 (12)
6 / 38100 / ATAC / Deletion / 4/4 (9)
7 / 38230 / AAAACGAT / Deletion / 8/8 (11)
8 / 38394 / AGTT / Deletion in MVA / 4/4 (13)
9 / 38479 / TTC / Insertion / 3/3 (14)
10 / 38849 / TATCCT / Deletion in CVA + MVA / 6/6 (18)
11 / 40033 / ATTCCA / Deletion / 6/6 (12)
12 / 40054 / GATATC / Deletion / 6/6 (6)
13 / 40222 / AAATCT / Deletion / 6/6 (6)
14 / 40509 / TACAGATG / Deletion in Acambis strains / 9/9 (18)
15 / 41131 / TGAAT / Deletion / 5/5 (10)
16 / 41194 / TAT / Deletion / 3/3 (23)
17 / 41319 / CCACT / Deletion in Acambis / 5/5 (9)
18 / 41437 / ACT / Deletion / 3/3 (3)
19 / 41479 / TTAAGAG / Insertion / 7/7 (7)
20 / 42334 / TGTTTAT / Deletion in MVA / 7/7 (13)
21 / 42683 / GGATATTA / Deletion in MVA + CVA / 8/8 (8)
22 / 44015 / TCAT / Deletion / 4/4 (22)
23 / 44723 / AACG / Insertion / 4/4 (4)
24 / 44974 / CGTCT / Deletion / 4/5 (12)
25 / 45450 / GTTG / Deletion / 4/4 (9)
26 / 45557 / CATAACTA / Deletion / 8/8 (10)
27 / 46470 / TTAT / Deletion in Acambis / 4/4 (8)
28 / 46780 / ATATAGA / Deletion / 7/7 (24)
29 / 47093 / GATA / Deletion in Acambis / 4/4 (10)
30 / 48007 / AGCATT / Deletion in Acambis / 6/6 (6)
31 / 48290 / GAGTT / Deletion / 5/5 (18)
32 / 49198 / ATT / Deletion in CVA + MVA / 3/3 (12)
33 / 49725 / ATAATTTCC / Deletion in MVA + CVA / 9/9 (21)
34 / 50536 / TATTTTATT / Deletion / 9/9 (15)
35 / 50913 / ATTAGT / Deletion / 6/6 (17)
36 / 51482 / TCCATG / Deletion in MVA / 6/6 (18)
37 / 52068 / AATC / Deletion / 4/4 (9)
38 / 52713 / TAT / Deletion / 3/3 (3)
39 / 52755 / CAT / Deletion / 3/3 (3)
40 / 54732 / ATTTTT / Deletion / 6/6 (16)
41 / 54992 / ATAT / Deletion / 4/4 (9)
42 / 56018 / CATCTT / Deletion / 6/6 (12)
43 / 56497 / TTAT / Deletion / 4/4 (9)
44 / 58324 / Not repeat / Deletion in WR branch
45 / 58380 / AATAAG / Deletion / 6/6 (24)
46 / 58407 / GTACCA / Deletion / 6/6 (21)
47 / 58592 / ATATGTAAT / Deletion / 9/9 (20)
48 / 58608 / CAATAT / Deletion / 6/6 (9)
49 / 62093 / AATC / Deletion in MVA / 4/4 (12)
50 / 64144 / ATCG / Deletion in MVA / 4/4 (24)
51 / 64174 / ATTATCAT / Deletion in CVA + MVA / 8/8 (9)
52 / 64354 / GTT / Insertion / 3/3 (3)
53 / 64418 / AAAC / Deletion in MVA / 4/4 (17)
54 / 65544 / TTCTTATTCTTA / Insertion / 12/12 (12)
55 / 65677 / Not repeat / Deletion in Acambis
56 / 68163 / GTTTTTAA / Deletion / 8/8 (18)
57 / 68315 / TCTTTT / Deletion in MVA / 6/6 (15)
58 / 68635 / ATCT / Deletion in MVA / 4/4 (17)
59 / 69179 / AAC / Insertion / 3/3 (3)
60 / 80080 / ATAACTA / Deletion / 7/7 (25)
61 / 82207 / TGGA / Deletion / 4/4 (13)
62 / 84659 / TCACA / Deletion / 5/5 (15)
63 / 85283 / ACATA / Deletion in MVA / 5/5 (15)
64 / 86375 / Not repeat / Deletion in Acambis
65 / 90483 / ACAGACA / Deletion in MVA / 7/7 (19)
66 / 90649 / ATCTTTG / Deletion in MVA / 7/7 (24)
67 / 91917 / ATTTT / Deletion / 5/5 (8)
68 / 93420 / ACCAA / Deletion / 5/5 (6)
69 / 93507 / TCTGTCA / Insertion / 7/7 (9)
70 / 110575 / GTTGGT / Deletion / 6/6 (6)
71 / 130470 / ATTA / Deletion / 4/4 (18)
72 / 133317 / AAAAGGA / Deletion in HSPX / 7/7 (12)
73 / 133401 / CATCTCC / Deletion in HSPX / 6/7 (12)
74 / 138467 / GAAGATAT / Deletion in MVA / 8/8 (12)
75 / 154787 / TGGATT / Deletion in Acambis / 6/6 (6)
76 / 155144 / AGGAGC / Deletion in MVA / 6/6 (27)
77 / 155231 / CGGAAC / Insertion / 6/6 (6)
78 / 160310 / CATT / Deletion in CVA + MVA / 4/4 (42)
79 / 161886 / AGA / Insertion in RBPX / 3/3 (3)
80 / 164541 / GTA / Insertion / 3/3 (3)
81 / 164649 / ATTTTGTA / Deletion in MVA / 8/8 (15)
82 / 166056 / GAT / Insertion / 3/3 (3)
83 / 176163 / AGTT / Deletion / 4/4 (6)
84 / 176206 / ATCAAG / Insertion / 6/6 (6)
85 / 176502 / ACT / Insertion / 3/3 (3)
86 / 176531 / GAC / Insertion / 3/3 (3)
87 / 176562 / GTTCT / Deletion / 5/5 (6)
88 / 176757 / TTCACGTT / Deletion in MVA / 8/8 (26)
89 / 176826 / TCACGTTC / Deletion (HSPX) / 8/8 (12)
90 / 177016 / CCGTTTCC / Deletion (HSPX) / 8/8 (12)
91 / 177068 / CAA / Deletion (HSPX) / 3/3 (10)
92 / 177197 / Not repeat / Deletion (HSPX)
93 / 177268 / TCTCTT / Deletion (HSPX) / 6/6 (13)
94 / 177492 / TTGGCAT / Deletion (HSPX) / 7/7 (9)
95 / 178219 / CGAG / Deletion / 4/4 (12)
96 / 181073 / ATAG / Insertion in MVA / 4/4 (4)
97 / 187381 / AGTA / Deletion in MVA / 4/4 (27)
98 / 187598 / CATGAA / Insertion in HSPX / 6/6 (6)
99 / 187640 / ATCAT / Deletion in MVA / 5/5 (11)
100 / 188574 / GAAAAAAA / Deletion (HSPX) / 8/8 (19)
101 / 199907 / ATGCGG / Deletion in MVA / 6/6 (21)
102 / 189911 / AGGATA / Insertion / 6/6 (6)
103 / 190040 / Not repeat / Deletion
104 / 190451 / AGTCC / Deletion / 5/5 (13)
105 / 191360 / GGAACTAAA / Deletion (HSPX) / 9/9 (18)
106 / 191378 / GGAA / Deletion / 4/4 (13)
107 / 191444 / ACT / Deletion in MVA / 3/3 (32)
108 / 192600 / TCC / Deletion in MVA / 3/3 (15)
109 / 192909 / ATG / Deletion / 3/3 (3)
110 / 193048 / ATA / Insertion / 3/3 (3)
111 / 193100 / Not repeat / Insertion
112 / 193401 / AATGACA / Deletion in MVA / 7/7 (12)
113 / 193646 / AAAAAAG / Deletion / 6/7 (7)
114 / 193806 / ATA / deletion / 3/3 (3)
115 / 193870 / TACT / Deletion / 4/4 (5)
116 / 195089 / AGTT / Deletion in MVA / 4/4 (12)
117 / 195605 / CGGTTA / Deletion in GLV / 6/6 (12)
118 / 196368 / CTGTAA / Deletion / 6/6 (16)
119 / 196633 / CAAGAG / Deletion in MVA / 6/6 (27)
120 / 197019 / GAT / Deletion in MVA / 3/3 (15)
121 / 197867 / ATAAAT / Deletion / 6/6 (24)
122 / 200101 / AAA / Deletion / 3/3 (7)
123 / 200235 / TTGTGAAA / Deletion / 8/8 (12)
124 / 201823 / AAAGTTA / Deletion / 7/7 (7)
125 / 202038 / ATATACAGCTATTAATTTCGAAAATATAT / Insertion / 28/28 (50)
126 / 207863 / GAA / Deletion / 3/3 (3)
127 / 207945 / ATGAT / Deletion / 5/5 (15)
128 / 207971 / AATGAT / Deletion in RBPX / 6/6 (6)
129 / 208256 / AAAAGACT / Deletion (HSPX) / 8/8 (11)
130 / 208420 / GAA / Deletion in MVA + CVA / 3/3 (11)
131 / 209878 / GTCGAT / Deletion / 6/6 (17)
132 / 210041 / TGTCAG / Deletion in MVA / 6/6 (20)
133 / 210214 / ATCA / Deletion in MVA / 4/4 (14)
134 / 210845 / No repeat / Deletion in MVA
135 / 211014 / No repeat / Deletion in MVA
136 / 211085 / TATAC / Deletion in MVA / 5/5 (21)
137 / 211126 / No repeat / Deletion
138 / 211400 / GGTAT / Deletion in MVA + CVA / 4/4 (17)
139 / 211487 / No repeat / Deletion
141 / 211590 / TAAC / Deletion in MVA+CVA / 4/4 (5)
142 / 212256 / ATTTTA / Deletion in MVA / 6/6 (17)
143 / 212340 / AATCAG / Insertion in MVA / 6/6 (6)
144 / 212809 / CTAT / Deletion in MVA / 4/4 (18)
145 / 213419 / TAA / Deletion in MVA / 3/3 (18)
146 / 213491 / ATAAAATC / Deletion in MVA / 8/8 (16)
147 / 215554 / Not repeat / Deletion in MVA
148 / 215889 / AACAAACAA / Insertion in HSPX / 9/9 (17)
149 / 216199 / GGAC / Deletion in MVA / 4/4 (24)
150 / 216259 / CAT / Deletion in MVA / 3/3 (21)
151 / 216632 / ATTTAA / Deletion in MVA / 6/6 (23)
152 / 222838 / GAAGG / Deletion in MVA / 5/5 (15)
153 / 224968 / Not repeat / Deletion in MVA
154 / 226572 / ATCTTC / Deletion / 6/6 (18)
155 / 226936 / TGTCTCCT / Deletion / 8/8 (14)
156 / 227058 / GATGT / Deletion in CVA / 5/5 (11)
157 / 228038 / CCATCA / Deletion in MVA / 6/6 (18)
158 / 230472 / No repeat / Deletion
159 / 231840* / No repeat / Deletion in Listers
160 / 232423 / TATCAT / Insertion / 6/6 (6)
161 / 233096 / ATCAAGA / Deletion in MVA / 7/7 (22)