Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00305.P1
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: 2566
ACGTcount: A:0.34, C:0.10, G:0.32, T:0.24
Found at i:446 original size:3 final size:3
Alignment explanation
Indices: 440--477 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
430 AGGAGGAGGA
* *
440 GGT GGT GGT GGT GGT AGT GGT GAT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
478 AAGTGGTAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.05, C:0.00, G:0.63, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:1552 original size:54 final size:54
Alignment explanation
Indices: 1494--1601 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
1484 CTGGTAGGGT
* * * *
1494 AAAAGGACAAGGTGGAGGAGATGGTAGTGGTGACACAGATGCAAGTGGTAAAGA
1 AAAAGGACAAGGTCGAGGAGATAGTAGTGGTAACACAAATGCAAGTGGTAAAGA
*
1548 AAAAGGACAAGGTCGAGGAGATAGTAGTGGTAATACAAATGCAAGTGGTAAAGA
1 AAAAGGACAAGGTCGAGGAGATAGTAGTGGTAACACAAATGCAAGTGGTAAAGA
1602 TGAAGCTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.42, C:0.07, G:0.35, T:0.16
Consensus pattern (54 bp):
AAAAGGACAAGGTCGAGGAGATAGTAGTGGTAACACAAATGCAAGTGGTAAAGA
Found at i:1706 original size:210 final size:204
Alignment explanation
Indices: 1344--1757 Score: 623
Period size: 210 Copynumber: 2.0 Consensus size: 204
1334 CTAGTGGGGT
* * * * *
1344 AAAAGAACAAGGTGGAGGAGATGGTAGTGGTAATATAGATGCAAGTGGTAAAGATGAAACTAAAG
1 AAAAGAACAAGGTCGAGGAGATAGTAGTGGTAATACAAATGCAAGTGGTAAAGATGAAAATAAAG
*
1409 CTAAAGTTGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTAGAAGTGATAGC
66 CTAAAGTTGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTAGAAGTGACAGC
* * * *
1474 TCTAGTTATTCTGGTAGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTGACAC-AGATGCAA
131 TCTAATGATTCCGGTAGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAACACAAG-TGCAA
1538 GTGGTAAAGA
195 GTGGTAAAGA
*
1548 AAAAGGACAAGGTCGAGGAGATAGTAGTGGTAATACAAATGCAAGTGGTAAAGATGAAGCTAAAG
1 AAAAGAACAAGGTCGAGGAGATAGTAGTGGTAATACAAATGCAAGTGGTAAAGAT---G--AAA-
* *
1613 ATAAAGCTGAAGTTGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTGGAAGT
60 ATAAAGCTAAAGTTGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTAGAAGT
* *
1678 GACGGCTCTAATGATTCCGGTAGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAAG
125 GACAGCTCTAATGATTCCGGTAGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAACACAAG
1743 TGCAAGTGGTAAAGA
190 TGCAAGTGGTAAAGA
1758 TGAAGCTAAA
Statistics
Matches: 188, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
204 50 0.27
207 1 0.01
209 3 0.02
210 132 0.70
211 2 0.01
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (204 bp):
AAAAGAACAAGGTCGAGGAGATAGTAGTGGTAATACAAATGCAAGTGGTAAAGATGAAAATAAAG
CTAAAGTTGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTAGAAGTGACAGC
TCTAATGATTCCGGTAGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAACACAAGTGCAAG
TGGTAAAGA
Found at i:1769 original size:6 final size:6
Alignment explanation
Indices: 1760--1956 Score: 119
Period size: 6 Copynumber: 32.8 Consensus size: 6
1750 GGTAAAGATG
* * * ** * *
1760 AAGCTA AAGCTG AAGCTG AAGCTC AAGCTA AAGCTA AAAATG AAGTTA
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA
* * * * * * * *
1808 AAGCTG AAGATG AAGCTC AAGCTA AAGTTA AAGATG AAGCTA AAGCTG
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA
* * * * * *
1856 AATCTG AAGCTA AAGCTA AATCTA AAG-AA GAAGCTA AAGTTG AAGCTA
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA -AAGCTA AAGCTA AAGCTA
* * ** * *
1904 AAGCTA AAGCTG AAGCTAA AAG-TG AAGCCG AAGATG AAGCTA AAGCTA
1 AAGCTA AAGCTA AAGCT-A AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA
1952 AAGCT
1 AAGCT
1957 GAAGGAAAGG
Statistics
Matches: 147, Mismatches: 40, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
5 4 0.03
6 139 0.95
7 4 0.03
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (6 bp):
AAGCTA
Found at i:1773 original size:12 final size:12
Alignment explanation
Indices: 1752--2033 Score: 146
Period size: 12 Copynumber: 23.5 Consensus size: 12
1742 GTGCAAGTGG
*
1752 TAAAGATGAAGC
1 TAAAGCTGAAGC
1764 TAAAGCTGAAGC
1 TAAAGCTGAAGC
* *
1776 TGAAGCTCAAGC
1 TAAAGCTGAAGC
* **
1788 TAAAGCTAAAAA
1 TAAAGCTGAAGC
* * *
1800 TGAAGTTAAAGC
1 TAAAGCTGAAGC
* *
1812 TGAAGATGAAGC
1 TAAAGCTGAAGC
* * *
1824 TCAAGCTAAAGT
1 TAAAGCTGAAGC
*
1836 TAAAGATGAAGC
1 TAAAGCTGAAGC
*
1848 TAAAGCTGAATC
1 TAAAGCTGAAGC
* *
1860 TGAAGCTAAAGC
1 TAAAGCTGAAGC
* *
1872 TAAATCTAAAG-
1 TAAAGCTGAAGC
* * *
1883 AAGAAGCTAAAGT
1 TA-AAGCTGAAGC
* *
1896 TGAAGCTAAAGC
1 TAAAGCTGAAGC
1908 TAAAGCTGAAGC
1 TAAAGCTGAAGC
1920 TAAAAG-TGAAGC
1 T-AAAGCTGAAGC
** *
1932 CGAAGATGAAGC
1 TAAAGCTGAAGC
*
1944 TAAAGCTAAAGC
1 TAAAGCTGAAGC
*
1956 TGAAG--GAAAGGC
1 TAAAGCTG-AA-GC
*
1968 TGAAGCTGAAGC
1 TAAAGCTGAAGC
1980 TGAAA-CTGAAGC
1 T-AAAGCTGAAGC
*
1992 AAAAGCTGAAGC
1 TAAAGCTGAAGC
2004 -AAAGGCTGAAGC
1 TAAA-GCTGAAGC
*
2016 -AAACACTGAAGC
1 TAAA-GCTGAAGC
*
2028 AAAAGC
1 TAAAGC
2034 AAAAGCTGAA
Statistics
Matches: 210, Mismatches: 48, Indels: 24
0.74 0.17 0.09
Matches are distributed among these distances:
11 12 0.06
12 186 0.89
13 11 0.05
14 1 0.00
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (12 bp):
TAAAGCTGAAGC
Found at i:1781 original size:18 final size:18
Alignment explanation
Indices: 1758--1991 Score: 150
Period size: 18 Copynumber: 13.0 Consensus size: 18
1748 GTGGTAAAGA
1758 TGAAGCTAAAGCTGAAGC
1 TGAAGCTAAAGCTGAAGC
* *
1776 TGAAGCTCAAGCTAAAGC
1 TGAAGCTAAAGCTGAAGC
* ** * * *
1794 TAAAAATGAAGTTAAAGC
1 TGAAGCTAAAGCTGAAGC
* * *
1812 TGAAGATGAAGCTCAAGC
1 TGAAGCTAAAGCTGAAGC
* * *
1830 TAAAGTTAAAGATGAAGC
1 TGAAGCTAAAGCTGAAGC
* * *
1848 TAAAGCTGAATCTGAAGC
1 TGAAGCTAAAGCTGAAGC
* * * *
1866 TAAAGCTAAATCTAAAGA
1 TGAAGCTAAAGCTGAAGC
* *
1884 AGAAGCTAAAGTTGAAGC
1 TGAAGCTAAAGCTGAAGC
*
1902 TAAAGCTAAAGCTGAAGC
1 TGAAGCTAAAGCTGAAGC
* * * *
1920 TAAAAG-TGAAGCCGAAGA
1 T-GAAGCTAAAGCTGAAGC
*
1938 TGAAGCTAAAGCTAAAGC
1 TGAAGCTAAAGCTGAAGC
*
1956 TGAAG-GAAAGGCTGAAGC
1 TGAAGCTAAA-GCTGAAGC
1974 TGAAGCTGAAA-CTGAAGC
1 TGAAGCT-AAAGCTGAAGC
1992 AAAAGCTGAA
Statistics
Matches: 168, Mismatches: 43, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
17 6 0.04
18 155 0.92
19 4 0.02
20 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (18 bp):
TGAAGCTAAAGCTGAAGC
Found at i:1816 original size:42 final size:42
Alignment explanation
Indices: 1752--2003 Score: 247
Period size: 42 Copynumber: 6.0 Consensus size: 42
1742 GTGCAAGTGG
* *
1752 TAAAGATGAAGCTAAAGCTGAAGCTGAAGCTCAAGCTAAAGC
1 TAAAAATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
* * * *
1794 TAAAAATGAAGTTAAAGCTGAAGATGAAGCTCAAGCTAAAGT
1 TAAAAATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
* * *
1836 TAAAGATGAAGCTAAAGCTGAATCTGAAGCTAAAGCTAAATC
1 TAAAAATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
* * *
1878 TAAAGAA-GAAGCTAAAGTTGAAGCTAAAGCTAAAGCTGAAGC
1 TAAA-AATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
* ** * * *
1920 TAAAAGTGAAGCCGAAGATGAAGCTAAAGCTAAAGCTGAAG-
1 TAAAAATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
* ** * * * *
1961 GAAAGGCTGAAGCTGAAGCTGAAACTGAAGCAAAAGCTGAAGC
1 TAAA-AATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
2004 AAAGGCTGAA
Statistics
Matches: 177, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
41 4 0.02
42 172 0.97
43 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.17
Consensus pattern (42 bp):
TAAAAATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
Found at i:2008 original size:42 final size:43
Alignment explanation
Indices: 1758--2043 Score: 235
Period size: 42 Copynumber: 6.8 Consensus size: 43
1748 GTGGTAAAGA
* * * **
1758 TGAAGCTAAAGCTGAAGCTGAAGCTCAAGCTAAAGCTAAA-AA
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
* * * * * * *
1800 TGAAGTTAAAGCTGAAGATGAAGCTCAAGCTAAAGTTAAA-GA
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
* * * * *
1842 TGAAGCTAAAGCTGAATCTGAAGCTAAAGCTAAATCTAAA-GA
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
* * *
1884 AGAAGCTAAAGTTGAAGCTAAAGCTAAAGCTGAAGCTAAAAG-
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
** * *
1926 TGAAGCCGAAGATGAAGCTAAAGCTAAAGCTGAAG-GAAAGGC
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
* * * *
1968 TGAAGCTGAAGCTGAAACTGAAGCAAAAGCTGAAGC-AAAGGC
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
* * *
2010 TGAAGC-AAACACTGAAGCAAAAGCAAAAGCTGAA
1 TGAAGCTAAA-GCTGAAGCTAAAGCTAAAGCTGAA
2044 ATAGGAGGAC
Statistics
Matches: 208, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
41 6 0.03
42 201 0.97
43 1 0.00
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (43 bp):
TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
Found at i:2039 original size:24 final size:24
Alignment explanation
Indices: 1988--2039 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1978 GCTGAAACTG
* **
1988 AAGCAAAAGCTGAAGCAAAGGCTG
1 AAGCAAAAGCTGAAGCAAAAGCAA
2012 AAGCAAACA-CTGAAGCAAAAGCAA
1 AAGCAAA-AGCTGAAGCAAAAGCAA
2036 AAGC
1 AAGC
2040 TGAAATAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.19, G:0.23, T:0.06
Consensus pattern (24 bp):
AAGCAAAAGCTGAAGCAAAAGCAA
Found at i:2103 original size:6 final size:6
Alignment explanation
Indices: 2085--2210 Score: 94
Period size: 6 Copynumber: 21.0 Consensus size: 6
2075 GTGGTGGTGG
* * * *
2085 TGAAGC CGAAGC TGAAGC TAAAGC TAAAGC TGAAG- -GAAAGGC TAAAGC
1 TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC TG-AA-GC TGAAGC
** * ** *
2133 TGAAGC TGAAGC CAAAGC TGAAGC GGAAGC AAAAGC CGAAGC TGAAGC
1 TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC
** * *
2181 TGAAGC AAAAGC CGAAGC TGAAGC CGAAGC
1 TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC
2211 AAACACCGAA
Statistics
Matches: 94, Mismatches: 22, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
4 1 0.01
5 2 0.02
6 89 0.95
7 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.30, T:0.10
Consensus pattern (6 bp):
TGAAGC
Found at i:2114 original size:18 final size:18
Alignment explanation
Indices: 2093--2210 Score: 105
Period size: 18 Copynumber: 6.6 Consensus size: 18
2083 GGTGAAGCCG
*
2093 AAGCTGAAGCTAAAGCTA
1 AAGCTGAAGCTGAAGCTA
2111 AAGCTGAAG--GAAAGGCTA
1 AAGCTGAAGCTG-AA-GCTA
*
2129 AAGCTGAAGCTGAAGCCA
1 AAGCTGAAGCTGAAGCTA
* *
2147 AAGCTGAAGCGGAAGCAA
1 AAGCTGAAGCTGAAGCTA
* *
2165 AAGCCGAAGCTGAAGCTG
1 AAGCTGAAGCTGAAGCTA
** * *
2183 AAGCAAAAGCCGAAGCTG
1 AAGCTGAAGCTGAAGCTA
*
2201 AAGCCGAAGC
1 AAGCTGAAGC
2211 AAACACCGAA
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.02
18 78 0.94
19 2 0.02
20 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.30, T:0.09
Consensus pattern (18 bp):
AAGCTGAAGCTGAAGCTA
Found at i:2198 original size:36 final size:36
Alignment explanation
Indices: 2087--2268 Score: 128
Period size: 36 Copynumber: 5.2 Consensus size: 36
2077 GGTGGTGGTG
* * *
2087 AAGCCGAAGCTGAAGCTAAAGCTAAAGCTGAAGGAA
1 AAGCCGAAGCTGAAGCTGAAGCAAAAGCTGAAGCAA
* ** *
2123 AGGCTAAAGCTGAAGCTGAAGCCAAAGCTGAAGC--
1 AAGCCGAAGCTGAAGCTGAAGCAAAAGCTGAAGCAA
** * **
2157 --G--GAAGCAAAAGCCGAAGCTGAAGCTGAAGCAA
1 AAGCCGAAGCTGAAGCTGAAGCAAAAGCTGAAGCAA
* *
2189 AAGCCGAAGCTGAAGCCGAAGCAAACA-CCGAAGCAA
1 AAGCCGAAGCTGAAGCTGAAGCAAA-AGCTGAAGCAA
* * * *
2225 AAGCCAAAGC-AAAGGCTGAAGCAAAGGCCGAAGCAA
1 AAGCCGAAGCTGAA-GCTGAAGCAAAAGCTGAAGCAA
2261 AAGCCGAA
1 AAGCCGAA
2269 ATAGGAGGAC
Statistics
Matches: 115, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
30 23 0.20
32 1 0.01
34 1 0.01
35 2 0.02
36 87 0.76
37 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.28, T:0.07
Consensus pattern (36 bp):
AAGCCGAAGCTGAAGCTGAAGCAAAAGCTGAAGCAA
Found at i:2211 original size:24 final size:24
Alignment explanation
Indices: 2141--2268 Score: 143
Period size: 24 Copynumber: 5.3 Consensus size: 24
2131 GCTGAAGCTG
* *
2141 AAGCCAAAGCTGAAGCGGAAGCAA
1 AAGCCGAAGCTGAAGCCGAAGCAA
*
2165 AAGCCGAAGCTGAAGCTGAAGCAA
1 AAGCCGAAGCTGAAGCCGAAGCAA
2189 AAGCCGAAGCTGAAGCCGAAGCAA
1 AAGCCGAAGCTGAAGCCGAAGCAA
** *
2213 ACA-CCGAAGCAAAAGCCAAAGCAA
1 A-AGCCGAAGCTGAAGCCGAAGCAA
* * *
2237 AGGCTGAAGC-AAAGGCCGAAGCAA
1 AAGCCGAAGCTGAA-GCCGAAGCAA
2261 AAGCCGAA
1 AAGCCGAA
2269 ATAGGAGGAC
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.03
24 86 0.96
25 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.27, T:0.04
Consensus pattern (24 bp):
AAGCCGAAGCTGAAGCCGAAGCAA
Found at i:2266 original size:12 final size:12
Alignment explanation
Indices: 2153--2268 Score: 126
Period size: 12 Copynumber: 9.7 Consensus size: 12
2143 GCCAAAGCTG
*
2153 AAGCGGAAGCAA
1 AAGCCGAAGCAA
**
2165 AAGCCGAAGCTG
1 AAGCCGAAGCAA
*
2177 AAGCTGAAGCAA
1 AAGCCGAAGCAA
**
2189 AAGCCGAAGCTG
1 AAGCCGAAGCAA
2201 AAGCCGAAGCAA
1 AAGCCGAAGCAA
2213 ACA-CCGAAGCAA
1 A-AGCCGAAGCAA
*
2225 AAGCCAAAGCAA
1 AAGCCGAAGCAA
* *
2237 AGGCTGAAGCAA
1 AAGCCGAAGCAA
*
2249 AGGCCGAAGCAA
1 AAGCCGAAGCAA
2261 AAGCCGAA
1 AAGCCGAA
2269 ATAGGAGGAC
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
11 1 0.01
12 83 0.98
13 1 0.01
ACGTcount: A:0.46, C:0.23, G:0.28, T:0.03
Consensus pattern (12 bp):
AAGCCGAAGCAA
Done.