Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g00987.F1
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: 5356
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:1068 original size:11 final size:11
Alignment explanation
Indices: 1052--1092 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
1042 ATACAAGTTA
1052 AAAAAAATTCG
1 AAAAAAATTCG
1063 AAAAAAAATTCG
1 -AAAAAAATTCG
1075 AAAAAAA-TCTG
1 AAAAAAATTC-G
1086 AAAAAAA
1 AAAAAAA
1093 AAAGTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 2 0.07
11 15 0.54
12 11 0.39
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:1068 original size:12 final size:12
Alignment explanation
Indices: 1051--1093 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
1041 TATACAAGTT
1051 AAAAAAAATTCG
1 AAAAAAAATTCG
1063 AAAAAAAATTCG
1 AAAAAAAATTCG
1075 -AAAAAAA-TCTG
1 AAAAAAAATTC-G
1086 AAAAAAAA
1 AAAAAAAA
1094 AAGTGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.07
11 8 0.28
12 19 0.66
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:2033 original size:21 final size:20
Alignment explanation
Indices: 1999--2065 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
1989 ACATTCTTGT
1999 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
2020 AAAGAAAAAGCAAAAGAAGA
1 AAAGAAAAAGCAAAAAAAGA
*
2040 AAA-AAAAATGAAATAAAAAGA
1 AAAGAAAAA-GCAA-AAAAAGA
2061 AAAGA
1 AAAGA
2066 GGGACAAGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 5 0.13
20 15 0.38
21 18 0.46
22 1 0.03
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:2130 original size:12 final size:12
Alignment explanation
Indices: 2113--2142 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2103 TTGAGAGAAC
2113 TTGAAAAAGCCT
1 TTGAAAAAGCCT
2125 TTGAAAAAGCCT
1 TTGAAAAAGCCT
2137 TTGAAA
1 TTGAAA
2143 TGCAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:2167 original size:12 final size:12
Alignment explanation
Indices: 2140--2170 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
2130 AAAGCCTTTG
2140 AAATGCAAAAAGA
1 AAATG-AAAAAGA
2153 AAATGAAAAAGA
1 AAATGAAAAAGA
2165 AAATGA
1 AAATGA
2171 GATTGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.71, C:0.03, G:0.16, T:0.10
Consensus pattern (12 bp):
AAATGAAAAAGA
Found at i:2167 original size:18 final size:18
Alignment explanation
Indices: 2146--2195 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2136 TTTGAAATGC
*
2146 AAAAAGAAAATGAAAAAG
1 AAAATGAAAATGAAAAAG
* *
2164 AAAATGAGATTGAAAAAG
1 AAAATGAAAATGAAAAAG
*
2182 AGAATGAAAA-GAAA
1 AAAATGAAAATGAAA
2196 TTTGAGAGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (18 bp):
AAAATGAAAATGAAAAAG
Found at i:2180 original size:30 final size:31
Alignment explanation
Indices: 2146--2227 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
2136 TTTGAAATGC
*
2146 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* *
2176 AAAAAGAGAATG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
2206 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
2228 TGAAACAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.18
30 28 0.62
31 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:4320 original size:20 final size:21
Alignment explanation
Indices: 4278--4322 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
4268 AGCTCCGCCC
**
4278 AGCTCAAATCCAACTTATTTG
1 AGCTCAAATCCAACTTACCTG
*
4299 AGCTC-AATCCAACTTGCCTG
1 AGCTCAAATCCAACTTACCTG
4319 AGCT
1 AGCT
4323 AAACCGAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (21 bp):
AGCTCAAATCCAACTTACCTG
Found at i:4373 original size:30 final size:30
Alignment explanation
Indices: 4339--4435 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
4329 AGCTCACTCC
4339 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
4369 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * *
4399 CAACTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
4429 TAGCTCA
1 TAGCTCA
4436 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Done.