Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006999.1 Corchorus capsularis cultivar CVL-1 contig07020, 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: 33796
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1508 original size:2 final size:2
Alignment explanation
Indices: 1501--1530 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1491 AACAATTTTC
1501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1531 GCTACTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1752 original size:32 final size:32
Alignment explanation
Indices: 1716--1797 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
1706 GGATATAACG
1716 TTATATAGCGGCGTCTGAAG-AACA-AAACGCCC
1 TTATATAGCGGCGTCT-AAGCAA-ATAAACGCCC
1748 TTATATAGCGGCGTCTAAGCAAATAAACGCCC
1 TTATATAGCGGCGTCTAAGCAAATAAACGCCC
*
1780 TTATATAGAGGCGTCTAA
1 TTATATAGCGGCGTCTAA
1798 ATATCCAGAC
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
31 4 0.09
32 43 0.91
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (32 bp):
TTATATAGCGGCGTCTAAGCAAATAAACGCCC
Found at i:2136 original size:31 final size:34
Alignment explanation
Indices: 2095--2160 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 34
2085 ATTGGTTAGT
*
2095 TTAGTGAGGGATCATTA-TA-A-ACTAATATTGG
1 TTAGTAAGGGATCATTATTATAGACTAATATTGG
2126 TTAGTAAGGGATCATTATTATAGACTAATATTGG
1 TTAGTAAGGGATCATTATTATAGACTAATATTGG
2160 T
1 T
2161 AATTGGTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 16 0.52
32 2 0.06
33 1 0.03
34 12 0.39
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (34 bp):
TTAGTAAGGGATCATTATTATAGACTAATATTGG
Found at i:7116 original size:131 final size:131
Alignment explanation
Indices: 6882--7124 Score: 425
Period size: 131 Copynumber: 1.9 Consensus size: 131
6872 TAAACATCTG
*
6882 TTCTATAAGTAGAAAGTTTAGAGCTTTTGCAAATTTTTGTAGGAAGTTGTATGTAGAAATGGAGT
1 TTCTATAAGCAGAAAGTTTAGAGCTTTTGCAAATTTTTGTAGGAAGTTGTATGTAGAAATGGAGT
*
6947 TTTCAATTCATCATCTGCTTGGAGAACTGGTATGGGTTTTGCCCTTCATACAAGCTTTTGCAAAT
66 TTTCAATTCATCATCTACTTGGAGAACTGGTATGGGTTTTGCCCTTCATACAAGCTTTTGCAAAT
7012 T
131 T
*
7013 TTCTATAAGCAGAAAGTTTAGAGCTTTT-CGAAATTTTTGTGGGAAGTTGTATGTAGAAATGGAG
1 TTCTATAAGCAGAAAGTTTAGAGCTTTTGC-AAATTTTTGTAGGAAGTTGTATGTAGAAATGGAG
* *
7077 TTTTCAATTTATCATCTACTTGGATAACTGGTATGGGTTTTGCCCTTC
65 TTTTCAATTCATCATCTACTTGGAGAACTGGTATGGGTTTTGCCCTTC
7125 TTTATATGCC
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
130 1 0.01
131 105 0.99
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.40
Consensus pattern (131 bp):
TTCTATAAGCAGAAAGTTTAGAGCTTTTGCAAATTTTTGTAGGAAGTTGTATGTAGAAATGGAGT
TTTCAATTCATCATCTACTTGGAGAACTGGTATGGGTTTTGCCCTTCATACAAGCTTTTGCAAAT
T
Found at i:7885 original size:21 final size:21
Alignment explanation
Indices: 7845--7885 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7835 TATGTTTTTT
*
7845 TTTTTTTTGCTCTTTCTAATC
1 TTTTTTTTCCTCTTTCTAATC
7866 TTTTTTTTCCTTCTTT-TAAT
1 TTTTTTTTCC-TCTTTCTAAT
7886 GAGGTGTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTTTTCCTCTTTCTAATC
Found at i:19740 original size:7 final size:7
Alignment explanation
Indices: 19718--19774 Score: 80
Period size: 7 Copynumber: 8.3 Consensus size: 7
19708 AGGTGATGCG
19718 GAAGGAA
1 GAAGGAA
**
19725 GAATAAA
1 GAAGGAA
*
19732 GAAAGAA
1 GAAGGAA
19739 GAAGGAA
1 GAAGGAA
19746 GAAGGAA
1 GAAGGAA
19753 GAAGGAA
1 GAAGGAA
19760 GAAGGAA
1 GAAGGAA
19767 GAA-GAA
1 GAAGGAA
19773 GA
1 GA
19775 CGAGAAAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 5 0.11
7 40 0.89
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (7 bp):
GAAGGAA
Found at i:19802 original size:13 final size:13
Alignment explanation
Indices: 19786--19840 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 13
19776 GAGAAAAAGA
19786 AAAAAGCAAAAAT
1 AAAAAGCAAAAAT
* **
19799 AAAAAGGAAAAGG
1 AAAAAGCAAAAAT
*
19812 AAAAA-CAAAAAC
1 AAAAAGCAAAAAT
*
19824 AAAAAG-AAATAT
1 AAAAAGCAAAAAT
19836 AAAAA
1 AAAAA
19841 TTAATAAGCC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
12 18 0.55
13 15 0.45
ACGTcount: A:0.78, C:0.05, G:0.11, T:0.05
Consensus pattern (13 bp):
AAAAAGCAAAAAT
Found at i:19809 original size:19 final size:18
Alignment explanation
Indices: 19786--19840 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
19776 GAGAAAAAGA
*
19786 AAAAAGCAAAAATAAAAAGG
1 AAAAAG-AAAAATAAAAA-C
* *
19806 AAAAGGAAAAACAAAAAC
1 AAAAAGAAAAATAAAAAC
*
19824 AAAAAGAAATATAAAAA
1 AAAAAGAAAAATAAAAA
19841 TTAATAAGCC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 14 0.48
19 10 0.34
20 5 0.17
ACGTcount: A:0.78, C:0.05, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAATAAAAAC
Found at i:24765 original size:42 final size:42
Alignment explanation
Indices: 24681--24774 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
24671 ATGCCCAACT
* * *
24681 ACAGCC-CGGCCAACCGCGCCACTTGCTCGGTCATTCCAGGCC
1 ACAGCCGC-GCCAACCGCGCCACCTGCTCGGCCATACCAGGCC
*
24723 ACAGCCGCGCCAACCGCGCCACCTGC-CTGGCCATACCCGGCC
1 ACAGCCGCGCCAACCGCGCCACCTGCTC-GGCCATACCAGGCC
* *
24765 AAAGCAGCGC
1 ACAGCCGCGC
24775 AGTCGCCCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 42 0.95
43 1 0.02
ACGTcount: A:0.19, C:0.47, G:0.24, T:0.10
Consensus pattern (42 bp):
ACAGCCGCGCCAACCGCGCCACCTGCTCGGCCATACCAGGCC
Found at i:33758 original size:15 final size:15
Alignment explanation
Indices: 33738--33767 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33728 CGTCATCATG
33738 AGCAATATATATATA
1 AGCAATATATATATA
33753 AGCAATATATATATA
1 AGCAATATATATATA
33768 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
AGCAATATATATATA
Found at i:33762 original size:2 final size:2
Alignment explanation
Indices: 33757--33796 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
33747 TATATAAGCA
33757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.