Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: XM_021440380.1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2698
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Found at i:718 original size:99 final size:96
Alignment explanation
Indices: 603--780 Score: 257
Period size: 96 Copynumber: 1.8 Consensus size: 96
593 ATGGGTCAAG
* * *
603 CTTCACGGGAGACCTTCAACCAAGCGTGCCGGCAGTTCAGAATCCTGGAGGACAGGATTGGACGT
1 CTTCACGGAAGACCTTCAAACAAGCGTG-C--CAGGTCAGAATCCTGGAGGACAGGATTGGACGT
* *
668 GGCAGGGTAATTTGCAGCCGAATGCTGTACCAAT
63 GGCAGAGTAATTGGCAGCCGAATGCTGTACCAAT
* * *
702 CTTCACGGAAGGCCTTCAAAGAGGCGTGCCAGGTCAGAATCCTGGAGGACAGGATTGGACGTGGC
1 CTTCACGGAAGACCTTCAAACAAGCGTGCCAGGTCAGAATCCTGGAGGACAGGATTGGACGTGGC
767 AGAGTAATTGGCAG
66 AGAGTAATTGGCAG
781 TCAAATATCT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
96 47 0.66
98 1 0.01
99 23 0.32
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.19
Consensus pattern (96 bp):
CTTCACGGAAGACCTTCAAACAAGCGTGCCAGGTCAGAATCCTGGAGGACAGGATTGGACGTGGC
AGAGTAATTGGCAGCCGAATGCTGTACCAAT
Found at i:1086 original size:63 final size:64
Alignment explanation
Indices: 1013--1176 Score: 183
Period size: 63 Copynumber: 2.6 Consensus size: 64
1003 ACCAAGATGG
* * * * * * *
1013 AGATGGAGAGGCTTTATGAAGAAAATAATGCACATAGAAAACTCGAGGCAGAGAATAAGGTC-A
1 AGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAAAAACTCGAAGAAGAGAATAAGGTCGA
* *
1076 AGATTGAGAGGCTTTGTAAAG-AAATCGACGCAC-TCAAAAAACTCGAAGAAGAGAATAAGGTCG
1 AGATCGAGAGGCTTTGTAAAGAAAAT-GATGCACAT-AAAAAACTCGAAGAAGAGAATAAGGTCG
1139 A
64 A
* *
1140 A-ATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAA
1 AGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
1177 TTATTTCATC
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
62 5 0.06
63 72 0.86
64 7 0.08
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.18
Consensus pattern (64 bp):
AGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAAAAACTCGAAGAAGAGAATAAGGTCGA
Found at i:1286 original size:63 final size:63
Alignment explanation
Indices: 1213--1988 Score: 550
Period size: 63 Copynumber: 12.5 Consensus size: 63
1203 TTGTGTCCAG
* * * ** *
1213 AAACTAGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTTGCAAACTAAATGATGGACATAAA
1 AAACTCGAGGAAAAGAACAAGATCGAGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
* * * * *
1276 AAACTTGAGGAAGAGAACAATG-TC-ACGATTGAAAGGCTTCGTAAAGAAAATGATGCACATAAA
1 AAACTCGAGGAAAAGAACAA-GATCGA-GATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
* * * *
1339 AGACTCGAGGAAGAGAACAAGATTGAGATCAAGAGGCTTCT-TAAAGAAAATGATGCACATAAA
1 AAACTCGAGGAAAAGAACAAGATCGAGATCGAGAGGCTT-TGTAAAGAAAATGATGCACATAAA
* * * * * * * * *
1402 GAACTCGA--AAAAGAGACAAAGGTCAAGGTGGAGAGG-TTTCTTCAAGAAAGTAATGCACATAA
1 AAACTCGAGGAAAAGA-AC-AAGATCGAGATCGAGAGGCTTT-GTAAAGAAAATGATGCACATAA
1464 A
63 A
* * * * * * **
1465 GAACTTGAGGAAGAA-ACCAAGGTCAAGATCGAGAGGCTTCGTAAAGAAAATGATGCATTTAAA
1 AAACTCGAGGAA-AAGAACAAGATCGAGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
* * * * * ***
1528 AAACTTGAGGAAGAGAACAAGATCGAGATTGAGAGGCTTCGAAAAGAAAATGATGTGTATAAA
1 AAACTCGAGGAAAAGAACAAGATCGAGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
* ** * ** * *
1591 AAACTCGAGGAAGAGATTAAGATCGAGATCAAGAGGCTTCATGAAGAAAATGATGCATATAAA
1 AAACTCGAGGAAAAGAACAAGATCGAGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
* * * * * * * *
1654 AAACTGGAGGAAGAGAACAAGGTTGAGATTGAGAGGCTTCGTCAAGAAAATGATGCACATAAG
1 AAACTCGAGGAAAAGAACAAGATCGAGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
* * * * *
1717 GAACTTGA-G-AAAGAGACGAACATCGAGATCAAGAGGATTCT-TAAAGAAAATGATGCACATAA
1 AAACTCGAGGAAAAGA-AC-AAGATCGAGATCGAGAGGCTT-TGTAAAGAAAATGATGCACATAA
1779 A
63 A
* * *
1780 AAACTCGAGGAAGAA-AACAAGATCGAGATTGAGAGACTTCGTAAAGAAAATGATGCAC----A
1 AAACTCGAGGAA-AAGAACAAGATCGAGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
* * * ** * * * * *
1839 CAA----A-GAAAAGACCAAGGTTAAGATCAAAAGGCTTCGTAAAGAAAATGACGCACATCAA
1 AAACTCGAGGAAAAGAACAAGATCGAGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
* * * * * *
1897 AAACTCAAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAAAAAATGATGCACATGAA
1 AAACTCGAGGAAAAGAACAAGATCGAGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
* * *
1960 AAACTC-ATGGAAAATACCAAGATCAAGAT
1 AAACTCGA-GGAAAAGAACAAGATCGAGAT
1989 GAAAAGGCTT
Statistics
Matches: 565, Mismatches: 116, Indels: 64
0.76 0.16 0.09
Matches are distributed among these distances:
53 2 0.00
54 37 0.07
55 1 0.00
58 3 0.01
59 3 0.01
61 10 0.02
62 12 0.02
63 480 0.85
64 8 0.01
65 5 0.01
66 4 0.01
ACGTcount: A:0.46, C:0.12, G:0.24, T:0.17
Consensus pattern (63 bp):
AAACTCGAGGAAAAGAACAAGATCGAGATCGAGAGGCTTTGTAAAGAAAATGATGCACATAAA
Found at i:1396 original size:225 final size:225
Alignment explanation
Indices: 985--1401 Score: 534
Period size: 225 Copynumber: 1.9 Consensus size: 225
975 GGCAAAAAAA
* * * * ** * *
985 CAGAAACTCGAGGAAAATACCAAGATGGAGATGGAGAGGCTTTATGAAGAAAATAATGCACATAG
1 CAGAAACTAGAGGAAAAGAACAAGATGGAGATCGAGAGGCTTTACAAACAAAATAATGCACATAA
* * * *
1050 AAAACTCGAGGCAGAGAATAAGGTCAAGATTGAGAGGCTTTGTAAAGAAATCGACGCACTCAAAA
66 AAAACTCGAGGAAGAGAACAAGGTCAAGATTGAAAGGCTTCGTAAAGAAATCGACGCACTCAAAA
* *
1115 AACTCGAAGAAGAGAATAAGGTCGAAATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAATTA
131 AACTCGAAGAAGAGAACAAGATCGAAATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAATTA
1180 TTTCATCTTTTTGATCTGACTTTTTGTGTC
196 TTTCATCTTTTTGATCTGACTTTTTGTGTC
* * * * *
1210 CAGAAACTAGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTTGCAAACTAAATGATGGACATAA
1 CAGAAACTAGAGGAAAAGAACAAGATGGAGATCGAGAGGCTTTACAAACAAAATAATGCACATAA
* * * *
1275 AAAACTTGAGGAAGAGAACAATGTCACGATTGAAAGGCTTCGTAAAGAAAAT-GATGCACAT-AA
66 AAAACTCGAGGAAGAGAACAAGGTCAAGATTGAAAGGCTTCGTAAAG-AAATCGACGCAC-TCAA
* * * * *
1338 AAGACTCGAGGAAGAGAACAAGATTGAGATC-AAGAGGCTTCTTAAAGAAAATGATGCACATAAA
129 AAAACTCGAAGAAGAGAACAAGATCGAAATCGAA-AGGCTTCGTAAAGAAAATGATGCACATAAA
1402 GAACTCGAAA
Statistics
Matches: 161, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
224 2 0.01
225 154 0.96
226 5 0.03
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (225 bp):
CAGAAACTAGAGGAAAAGAACAAGATGGAGATCGAGAGGCTTTACAAACAAAATAATGCACATAA
AAAACTCGAGGAAGAGAACAAGGTCAAGATTGAAAGGCTTCGTAAAGAAATCGACGCACTCAAAA
AACTCGAAGAAGAGAACAAGATCGAAATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAATTA
TTTCATCTTTTTGATCTGACTTTTTGTGTC
Found at i:1449 original size:126 final size:126
Alignment explanation
Indices: 1214--1965 Score: 706
Period size: 126 Copynumber: 6.0 Consensus size: 126
1204 TGTGTCCAGA
* * * * * ** *
1214 AACTAGAGGAAAAGAACAAGATTGAGATCGAGAGGCTT-TGCAAACTAAATGATGGACATAAAAA
1 AACTCGAGGAAGAGAACAAGATCGAGATCAAGAGGCTTCT-TAAAGAAAATGATGCACATAAAAA
* * * *
1278 ACTTGAGGAAGAGAACAATGTCACGATTGAAAGGCTTCGTAAAGAAAATGATGCACATAAA-
65 ACTCGAGGAAGAGAACAAGGTCAAGATTGAGAGGCTTCGTAAAGAAAATGATGCACATAAAG
* *
1339 AGACTCGAGGAAGAGAACAAGATTGAGATCAAGAGGCTTCTTAAAGAAAATGATGCACATAAAGA
1 A-ACTCGAGGAAGAGAACAAGATCGAGATCAAGAGGCTTCTTAAAGAAAATGATGCACATAAAAA
** * * * * * * *
1404 ACTCGAAAAAGAG-ACAAAGGTCAAGGTGGAGAGGTTTCTTCAAGAAAGTAATGCACATAAAG
65 ACTCGAGGAAGAGAAC-AAGGTCAAGATTGAGAGGCTTCGTAAAGAAAATGATGCACATAAAG
* * * * * **
1466 AACTTGAGGAAGA-AACCAAGGTCAAGATCGAGAGGCTTCGTAAAGAAAATGATGCATTTAAAAA
1 AACTCGAGGAAGAGAA-CAAGATCGAGATCAAGAGGCTTCTTAAAGAAAATGATGCACATAAAAA
* * * * *** *
1530 ACTTGAGGAAGAGAACAAGATCGAGATTGAGAGGCTTCGAAAAGAAAATGATGTGTATAAAA
65 ACTCGAGGAAGAGAACAAGGTCAAGATTGAGAGGCTTCGTAAAGAAAATGATGCACATAAAG
** * * *
1592 AACTCGAGGAAGAGATTAAGATCGAGATCAAGAGGCTTCATGAAGAAAATGATGCATATAAAAAA
1 AACTCGAGGAAGAGAACAAGATCGAGATCAAGAGGCTTCTTAAAGAAAATGATGCACATAAAAAA
* ** * *
1657 CTGGAGGAAGAGAACAAGGTTGAGATTGAGAGGCTTCGTCAAGAAAATGATGCACATAAGG
66 CTCGAGGAAGAGAACAAGGTCAAGATTGAGAGGCTTCGTAAAGAAAATGATGCACATAAAG
* * * *
1718 AACTTGAGAAAGAG-ACGAACATCGAGATCAAGAGGATTCTTAAAGAAAATGATGCACATAAAAA
1 AACTCGAGGAAGAGAAC-AAGATCGAGATCAAGAGGCTTCTTAAAGAAAATGATGCACATAAAAA
* * * * *
1782 ACTCGAGGAAGAAAACAAGATCGAGATTGAGAGACTTCGTAAAGAAAATGATGCAC--ACA-
65 ACTCGAGGAAGAGAACAAGGTCAAGATTGAGAGGCTTCGTAAAGAAAATGATGCACATAAAG
* * ** * * * *
1841 AA---GA--AA-AGACCAAGGTTAAGATCAAAAGGCTTCGTAAAGAAAATGACGCACATCAAAAA
1 AACTCGAGGAAGAGAACAAGATCGAGATCAAGAGGCTTCTTAAAGAAAATGATGCACATAAAAAA
* * ** * *
1900 CTCAAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAAAAAATGATGCACATGAAA-
66 CTCGAGGAAGAGAACAAGGTCAAGATTGAGAGGCTTCGTAAAGAAAATGATGCACAT-AAAG
1961 AACTC
1 AACTC
1966 ATGGAAAATA
Statistics
Matches: 512, Mismatches: 100, Indels: 32
0.80 0.16 0.05
Matches are distributed among these distances:
117 90 0.18
118 3 0.01
120 6 0.01
123 2 0.00
124 1 0.00
125 5 0.01
126 400 0.78
127 5 0.01
ACGTcount: A:0.46, C:0.12, G:0.24, T:0.17
Consensus pattern (126 bp):
AACTCGAGGAAGAGAACAAGATCGAGATCAAGAGGCTTCTTAAAGAAAATGATGCACATAAAAAA
CTCGAGGAAGAGAACAAGGTCAAGATTGAGAGGCTTCGTAAAGAAAATGATGCACATAAAG
Found at i:1598 original size:189 final size:189
Alignment explanation
Indices: 1213--1965 Score: 731
Period size: 189 Copynumber: 4.0 Consensus size: 189
1203 TTGTGTCCAG
* * * * *** ** *
1213 AAACTAGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTTGCAAACTAAATGATGGACATAAAAA
1 AAACTCGAGGAAGAGAAAAAGATCGAGATCGAGAGGCTTCATAAAGAAAATGATGCACATAAAAA
* * * *
1278 ACTTGAGGAAGAGAACAATGTCACGATTGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAGAC
66 ACTTGAGGAAGAGAACAAGGTCAAGATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAAAC
* **
1343 TCGAGGAAGAGAACAAGATTGAGATCAAGAGGCTTCTTAAAGAAAATGATGCACATAAA
131 TCGAGGAAGAGAACAAGATCGAGATCAAGAGGCTTCGAAAAGAAAATGATGCACATAAA
* ** * * * * * * * * * * *
1402 GAACTCGAAAAAGAGACAAAGGTCAAGGTGGAGAGGTTTCTTCAAGAAAGTAATGCACATAAAGA
1 AAACTCGAGGAAGAGAAAAAGATCGAGATCGAGAGGCTTCATAAAGAAAATGATGCACATAAAAA
* **
1467 ACTTGAGGAAGA-AACCAAGGTCAAGATCGAGAGGCTTCGTAAAGAAAATGATGCATTTAAAAAA
66 ACTTGAGGAAGAGAA-CAAGGTCAAGATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAAA
* ** ***
1531 CTTGAGGAAGAGAACAAGATCGAGATTGAGAGGCTTCGAAAAGAAAATGATGTGTATAAA
130 CTCGAGGAAGAGAACAAGATCGAGATCAAGAGGCTTCGAAAAGAAAATGATGCACATAAA
** * * *
1591 AAACTCGAGGAAGAGATTAAGATCGAGATCAAGAGGCTTCATGAAGAAAATGATGCATATAAAAA
1 AAACTCGAGGAAGAGAAAAAGATCGAGATCGAGAGGCTTCATAAAGAAAATGATGCACATAAAAA
* ** * * * **
1656 ACTGGAGGAAGAGAACAAGGTTGAGATTGAGAGGCTTCGTCAAGAAAATGATGCACATAAGGAAC
66 ACTTGAGGAAGAGAACAAGGTCAAGATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAAAC
* * * * **
1721 TTGAGAAAGAG-ACGAACATCGAGATCAAGAGGATTCTTAAAGAAAATGATGCACATAAA
131 TCGAGGAAGAGAAC-AAGATCGAGATCAAGAGGCTTCGAAAAGAAAATGATGCACATAAA
* * * *
1780 AAACTCGAGGAAGA-AAACAAGATCGAGATTGAGAGACTTCGTAAAGAAAATGATGCAC---ACA
1 AAACTCGAGGAAGAGAAA-AAGATCGAGATCGAGAGGCTTCATAAAGAAAATGATGCACATAAAA
* * * * *
1841 AA---GA--AA-AGACCAAGGTTAAGATCAAAAGGCTTCGTAAAGAAAATGACGCACATCAAAAA
65 AACTTGAGGAAGAGAACAAGGTCAAGATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAAA
* * * *
1900 CTCAAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTAAAA-AAAATGATGCACATGAA
130 CTCGAGGAAGAGAACAAGATCGAGATCAAGAGGCTTCG-AAAAGAAAATGATGCACATAAA
1960 AAACTC
1 AAACTC
1966 ATGGAAAATA
Statistics
Matches: 454, Mismatches: 104, Indels: 21
0.78 0.18 0.04
Matches are distributed among these distances:
180 92 0.20
181 7 0.02
183 2 0.00
186 4 0.01
188 5 0.01
189 342 0.75
190 2 0.00
ACGTcount: A:0.46, C:0.12, G:0.24, T:0.17
Consensus pattern (189 bp):
AAACTCGAGGAAGAGAAAAAGATCGAGATCGAGAGGCTTCATAAAGAAAATGATGCACATAAAAA
ACTTGAGGAAGAGAACAAGGTCAAGATCGAAAGGCTTCGTAAAGAAAATGATGCACATAAAAAAC
TCGAGGAAGAGAACAAGATCGAGATCAAGAGGCTTCGAAAAGAAAATGATGCACATAAA
Found at i:1948 original size:117 final size:117
Alignment explanation
Indices: 1742--1955 Score: 329
Period size: 117 Copynumber: 1.8 Consensus size: 117
1732 ACGAACATCG
* * * *
1742 AGATCAAGAGGATTCTTAAAGAAAATGATGCACATAAAAAACTCGAGGAAGAAAACAAGATCGAG
1 AGATCAAAAGGATTCGTAAAGAAAATGACGCACATAAAAAACTCAAGGAAGAAAACAAGATCGAG
* *
1807 ATTGAGAGACTTCGTAAAGAAAATGATGCACACAAAGAAAAGACCAAGGTTA
66 ATCGAGAGACTTCGTAAAAAAAATGATGCACACAAAGAAAAGACCAAGGTTA
* * * *
1859 AGATCAAAAGGCTTCGTAAAGAAAATGACGCACATCAAAAACTCAAGGAAGAGAACAAGATTGAG
1 AGATCAAAAGGATTCGTAAAGAAAATGACGCACATAAAAAACTCAAGGAAGAAAACAAGATCGAG
*
1924 ATCGAGAGGCTTCGTAAAAAAAATGATGCACA
66 ATCGAGAGACTTCGTAAAAAAAATGATGCACA
1956 TGAAAAACTC
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 86 1.00
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.16
Consensus pattern (117 bp):
AGATCAAAAGGATTCGTAAAGAAAATGACGCACATAAAAAACTCAAGGAAGAAAACAAGATCGAG
ATCGAGAGACTTCGTAAAAAAAATGATGCACACAAAGAAAAGACCAAGGTTA
Found at i:2016 original size:63 final size:63
Alignment explanation
Indices: 1843--2008 Score: 199
Period size: 63 Copynumber: 2.6 Consensus size: 63
1833 TGCACACAAA
* * *
1843 GAAAAGACCAAGGTTAAGATCAAAAGGCTTCGTAAAGAAAATGACGCACATCAAAAACTCAAG
1 GAAAAGACCAAGATTAAGATGAAAAGGCTTCGTAAAGAAAATGATGCACATCAAAAACTCAAG
* * * * * * *
1906 GAAGAGAACAAGATTGAGATCG-AGAGGCTTCGTAAAAAAAATGATGCACATGAAAAACTCATG
1 GAAAAGACCAAGATTAAGAT-GAAAAGGCTTCGTAAAGAAAATGATGCACATCAAAAACTCAAG
* * *
1969 GAAAATACCAAGATCAAGATGAAAAGGCTTCGTGAAGAAA
1 GAAAAGACCAAGATTAAGATGAAAAGGCTTCGTAAAGAAA
2009 GGGATGCAAA
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
62 1 0.01
63 82 0.99
ACGTcount: A:0.48, C:0.14, G:0.22, T:0.16
Consensus pattern (63 bp):
GAAAAGACCAAGATTAAGATGAAAAGGCTTCGTAAAGAAAATGATGCACATCAAAAACTCAAG
Done.