Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012908.1 Corchorus olitorius cultivar O-4 contig12941, whole genome shotgun sequence
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: 26713
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:10685 original size:18 final size:18
Alignment explanation
Indices: 10662--10696 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10652 ACAAAAACTG
10662 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
10680 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
10697 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:13648 original size:110 final size:110
Alignment explanation
Indices: 13455--13658 Score: 381
Period size: 110 Copynumber: 1.9 Consensus size: 110
13445 ATAATAAAAC
* *
13455 AAGTTAATAAGCAAGTGAATTAATAAAACAATTACTATAATAATAATATTTAAATGACAAACTAT
1 AAGTTAATAAGCAAGTAAATTAATAAAACAATTACTATAATAATAATATTTAAATGACAAACTAA
13520 TTAATTCCTAAATCCAAAAGAGCAGTATTGATAGGTAACTTTGAT
66 TTAATTCCTAAATCCAAAAGAGCAGTATTGATAGGTAACTTTGAT
*
13565 AAGTTAATAAGCAAGTAAATTAATAAAACAATTAGTATAATAATAATATTTAAATGACAAACTAA
1 AAGTTAATAAGCAAGTAAATTAATAAAACAATTACTATAATAATAATATTTAAATGACAAACTAA
13630 TTAATTCCTAAATCCAAAAGAGCAGTATT
66 TTAATTCCTAAATCCAAAAGAGCAGTATT
13659 ATATTATAAC
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 91 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (110 bp):
AAGTTAATAAGCAAGTAAATTAATAAAACAATTACTATAATAATAATATTTAAATGACAAACTAA
TTAATTCCTAAATCCAAAAGAGCAGTATTGATAGGTAACTTTGAT
Found at i:14896 original size:27 final size:28
Alignment explanation
Indices: 14844--14898 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
14834 GCTTTAGGTG
* **
14844 TTATTATATATATATATAATGTTATATA
1 TTATTATATATATAAATAATAATATATA
14872 TTATTA-ATATATAAATAATAATATATA
1 TTATTATATATATAAATAATAATATATA
14899 ATAAACGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TTATTATATATATAAATAATAATATATA
Found at i:14974 original size:35 final size:35
Alignment explanation
Indices: 14928--15002 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
14918 TTATATAAAC
*
14928 GAACACTTAAATGAACAATAAACGAACTTGTTTGT
1 GAACACTTAAATGAACAATAAACGAACATGTTTGT
*
14963 GAACACTTAAATGAACAATAAACGAGCATGTTTGT
1 GAACACTTAAATGAACAATAAACGAACATGTTTGT
14998 GAACA
1 GAACA
15003 TAAACGAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAACATGTTTGT
Found at i:16546 original size:6 final size:6
Alignment explanation
Indices: 16535--16588 Score: 99
Period size: 6 Copynumber: 9.0 Consensus size: 6
16525 TAAATTTGTG
*
16535 TCTATA TCTATA TTTATA TCTATA TCTATA TCTATA TCTATA TCTATA
1 TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA
16583 TCTATA
1 TCTATA
16589 ATAATAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTATA
Found at i:17681 original size:27 final size:27
Alignment explanation
Indices: 17651--17715 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
17641 AAGTGTAATT
* *
17651 TTGGTCATTTTCCTCACC-AGGCGTATC
1 TTGGTCATTTTCCCCACCAAGG-GCATC
*
17678 TTGGTCATTTTCCCCACCAAGGGCATT
1 TTGGTCATTTTCCCCACCAAGGGCATC
17705 TTGGTCATTTT
1 TTGGTCATTTT
17716 ATACTAGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 31 0.91
28 3 0.09
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.40
Consensus pattern (27 bp):
TTGGTCATTTTCCCCACCAAGGGCATC
Found at i:21903 original size:2 final size:2
Alignment explanation
Indices: 21896--21928 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21886 ACATATACAT
21896 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
21929 TATATATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21933 original size:2 final size:2
Alignment explanation
Indices: 21928--21967 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
21918 ACACACACAC
* *
21928 AT AT AT AT AT GT GT AT AT AT AT AT -T AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21968 GGTTGACATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22411 original size:42 final size:42
Alignment explanation
Indices: 22324--22429 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
22314 AATTTTAAAG
*
22324 GATGTTGTTGCGGCCCCAATCTGTTCTACTTGACCTTCAACA
1 GATGTTGTTGCAGCCCCAATCTGTTCTACTTGACCTTCAACA
* * * *
22366 GATGCTGTTGCAGCCCCAAGT-TGTTCTACTTTATC-TCCACTA
1 GATGTTGTTGCAGCCCCAA-TCTGTTCTACTTGACCTTCAAC-A
*
22408 GATGTTATTGCAGCCCCAATCT
1 GATGTTGTTGCAGCCCCAATCT
22430 TTTCATCAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 5 0.09
42 48 0.89
43 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (42 bp):
GATGTTGTTGCAGCCCCAATCTGTTCTACTTGACCTTCAACA
Found at i:22702 original size:99 final size:99
Alignment explanation
Indices: 22531--22733 Score: 352
Period size: 99 Copynumber: 2.1 Consensus size: 99
22521 TATCTCCACT
22531 GGATGTTGTTGCAGCCCCAATCTTTTCATCAAGCTTCCCCTCGTGTTGCGCATCAAAGCTTTCTA
1 GGATGTTGTTGCAGCCCCAATCTTTTCATCAAGCTTCCCCTCGTGTTGCGCATCAAAGCTTTCTA
**
22596 TTGATTTGGAACCTTCTATTATGTATTTTTTTAG
66 TTGATTTGGAACCTTCTATTATGTATTTTTCGAG
* * *
22630 GGATGTTGTTGCAGCTCCAATCTTTTCATCAAGCTTCCCTTCGTGTTGCGCATCGAAGCTTTCTA
1 GGATGTTGTTGCAGCCCCAATCTTTTCATCAAGCTTCCCCTCGTGTTGCGCATCAAAGCTTTCTA
*
22695 TTGATTTGGAACCTTCTATTATTTATTTTTCGAG
66 TTGATTTGGAACCTTCTATTATGTATTTTTCGAG
22729 GGATG
1 GGATG
22734 AAAAAGATTT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (99 bp):
GGATGTTGTTGCAGCCCCAATCTTTTCATCAAGCTTCCCCTCGTGTTGCGCATCAAAGCTTTCTA
TTGATTTGGAACCTTCTATTATGTATTTTTCGAG
Found at i:23780 original size:10 final size:10
Alignment explanation
Indices: 23765--23803 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
23755 GCTCTAACAA
23765 AAAATAAATT
1 AAAATAAATT
23775 AAAATAAATT
1 AAAATAAATT
* * *
23785 ATAAGAATTT
1 AAAATAAATT
23795 AAAATAAAT
1 AAAATAAAT
23804 AAACAAATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (10 bp):
AAAATAAATT
Found at i:25769 original size:18 final size:18
Alignment explanation
Indices: 25748--25784 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
25738 ACTATCTCCA
25748 TTTTT-TTGAGTTTGCTC
1 TTTTTCTTGAGTTTGCTC
25765 TTTTTCTTGAGTTTGCTC
1 TTTTTCTTGAGTTTGCTC
25783 TT
1 TT
25785 CTTAAGAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.05, C:0.14, G:0.16, T:0.65
Consensus pattern (18 bp):
TTTTTCTTGAGTTTGCTC
Done.