Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga08g00003.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: 4089
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Found at i:1671 original size:23 final size:23
Alignment explanation
Indices: 1641--1687 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1631 GTTGAAGTAT
1641 GCCTTGAAGGCTGTGTCTAAGAA
1 GCCTTGAAGGCTGTGTCTAAGAA
1664 GCCTTGAAGGCTGTGTCTAAGAA
1 GCCTTGAAGGCTGTGTCTAAGAA
1687 G
1 G
1688 ACGAAGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (23 bp):
GCCTTGAAGGCTGTGTCTAAGAA
Found at i:1712 original size:18 final size:18
Alignment explanation
Indices: 1691--1749 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
1681 TAAGAAGACG
1691 AAGTATGCCTTGAAGGCT
1 AAGTATGCCTTGAAGGCT
* * * * *
1709 AAGTGT-CATAGAAGACG
1 AAGTATGCCTTGAAGGCT
*
1726 AAGCATGCCTTGAAGGCT
1 AAGTATGCCTTGAAGGCT
1744 AAGTAT
1 AAGTAT
1750 TTGAGAAGAC
Statistics
Matches: 28, Mismatches: 12, Indels: 2
0.67 0.29 0.05
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (18 bp):
AAGTATGCCTTGAAGGCT
Found at i:1722 original size:35 final size:36
Alignment explanation
Indices: 1664--1824 Score: 178
Period size: 35 Copynumber: 4.7 Consensus size: 36
1654 TGTCTAAGAA
1664 GCCTTGAAGGCT--GTGTC-TAAGAAGACGAAGTAT
1 GCCTTGAAGGCTAAGTGTCATAAGAAGACGAAGTAT
*
1697 GCCTTGAAGGCTAAGTGTCAT-AGAAGACGAAGCAT
1 GCCTTGAAGGCTAAGTGTCATAAGAAGACGAAGTAT
* * * *
1732 GCCTTGAAGGCTAAGTAT-TTGAGAAGACGAAGTTT
1 GCCTTGAAGGCTAAGTGTCATAAGAAGACGAAGTAT
* ** *
1767 GCCTTAAAGGCTAAGTG-CCGAAGAAGATGAAGTAT
1 GCCTTGAAGGCTAAGTGTCATAAGAAGACGAAGTAT
1802 GCCTTGAAGGCT--GTGTC-TAAGAA
1 GCCTTGAAGGCTAAGTGTCATAAGAA
1825 TAGAAAGTAT
Statistics
Matches: 108, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
33 20 0.19
34 2 0.02
35 85 0.79
36 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (36 bp):
GCCTTGAAGGCTAAGTGTCATAAGAAGACGAAGTAT
Found at i:1771 original size:70 final size:70
Alignment explanation
Indices: 1683--1813 Score: 201
Period size: 70 Copynumber: 1.9 Consensus size: 70
1673 GCTGTGTCTA
* *
1683 AGAAGACGAAGTATGCCTTGAAGGCTAAGTGTC-ATAGAAGACGAAGCATGCCTTGAAGGCTAAG
1 AGAAGACGAAGTATGCCTTAAAGGCTAAGTGCCGA-AGAAGACGAAGCATGCCTTGAAGGCTAAG
1747 TATTTG
65 TATTTG
* * *
1753 AGAAGACGAAGTTTGCCTTAAAGGCTAAGTGCCGAAGAAGATGAAGTATGCCTTGAAGGCT
1 AGAAGACGAAGTATGCCTTAAAGGCTAAGTGCCGAAGAAGACGAAGCATGCCTTGAAGGCT
1814 GTGTCTAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 54 0.98
71 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (70 bp):
AGAAGACGAAGTATGCCTTAAAGGCTAAGTGCCGAAGAAGACGAAGCATGCCTTGAAGGCTAAGT
ATTTG
Found at i:1856 original size:103 final size:104
Alignment explanation
Indices: 1682--1884 Score: 243
Period size: 103 Copynumber: 2.0 Consensus size: 104
1672 GGCTGTGTCT
*
1682 AAGAAGACGAAGTATGCCTTGAAGGCTAAGTGTCATAGAAGACGAAGCATGCCTTGAAGGCTAAG
1 AAGAAGACGAAGTATGCCTTGAAGGCT-AGTGTCATAGAAGACGAAGCATGCCTCGAAGGCTAAG
* * *
1747 TATTTGAGAAG-ACGAAGTTTGCCTTAAAGGCTAAGTGCCG
65 TATTTGAGAAGTA-GAAGTATGCATTAAAAGCTAAGTGCCG
* * * * * *
1787 AAGAAGATGAAGTATGCCTTGAAGGCT-GTGTC-TAAGAATA-GAAAGTATGTCTCGTAGGTTAA
1 AAGAAGACGAAGTATGCCTTGAAGGCTAGTGTCAT-AGAAGACG-AAGCATGCCTCGAAGGCTAA
*
1849 GTGTTTGAGAAGTAGAAGTATGCATTAAAAGCTAAG
64 GTATTTGAGAAGTAGAAGTATGCATTAAAAGCTAAG
1885 CTCCTGGAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
102 2 0.02
103 55 0.65
104 1 0.01
105 26 0.31
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (104 bp):
AAGAAGACGAAGTATGCCTTGAAGGCTAGTGTCATAGAAGACGAAGCATGCCTCGAAGGCTAAGT
ATTTGAGAAGTAGAAGTATGCATTAAAAGCTAAGTGCCG
Found at i:3972 original size:18 final size:18
Alignment explanation
Indices: 3909--3969 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
3899 CAAGGTCACG
3909 ATCAATAGCGTCACTATC
1 ATCAATAGCGTCACTATC
*
3927 ATCAATAGCGTCACTAGC
1 ATCAATAGCGTCACTATC
*
3945 ATCAATATCGTCACTATC
1 ATCAATAGCGTCACTATC
3963 ATCAATA
1 ATCAATA
3970 TCGATATCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (18 bp):
ATCAATAGCGTCACTATC
Found at i:3977 original size:15 final size:17
Alignment explanation
Indices: 3909--3984 Score: 84
Period size: 18 Copynumber: 4.4 Consensus size: 17
3899 CAAGGTCACG
*
3909 ATCAATAGCGTCACTATC
1 ATCAATATCG-CACTATC
* *
3927 ATCAATAGCGTCACTAGC
1 ATCAATATCG-CACTATC
3945 ATCAATATCGTCACTATC
1 ATCAATATCG-CACTATC
3963 ATCAATATCG-A-TATC
1 ATCAATATCGCACTATC
3978 ATCAATA
1 ATCAATA
3985 AGAAAACCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.20
16 1 0.02
18 43 0.78
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.29
Consensus pattern (17 bp):
ATCAATATCGCACTATC
Done.