Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012032.1 Corchorus olitorius cultivar O-4 contig12065, 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: 24762
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1742 original size:13 final size:14
Alignment explanation
Indices: 1726--1755 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1716 TTTTCTTTAA
1726 TTTTCTTGATT-AT
1 TTTTCTTGATTGAT
1739 TTTTCTTGATTGAT
1 TTTTCTTGATTGAT
1753 TTT
1 TTT
1756 AATTGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.13, C:0.07, G:0.10, T:0.70
Consensus pattern (14 bp):
TTTTCTTGATTGAT
Found at i:8663 original size:19 final size:19
Alignment explanation
Indices: 8627--8666 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8617 ATTGGCTGCA
**
8627 ATTGGATCTTGTTTGTTTG
1 ATTGGATCTTGTAGGTTTG
8646 ATTGGATCTTGTAGGTTTG
1 ATTGGATCTTGTAGGTTTG
8665 AT
1 AT
8667 AGATCCTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.05, G:0.28, T:0.53
Consensus pattern (19 bp):
ATTGGATCTTGTAGGTTTG
Found at i:10227 original size:24 final size:24
Alignment explanation
Indices: 10195--10240 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
10185 ATTGATCTTT
10195 TCTCACGACCACCATGTGGCCGAA
1 TCTCACGACCACCATGTGGCCGAA
*
10219 TCTCACGACCACTATGTGGCCG
1 TCTCACGACCACCATGTGGCCG
10241 TTTTTCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.20
Consensus pattern (24 bp):
TCTCACGACCACCATGTGGCCGAA
Found at i:10248 original size:24 final size:24
Alignment explanation
Indices: 10192--10248 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
10182 ATCATTGATC
10192 TTTTCTCACGACCACCATGTGGCCG
1 TTTT-TCACGACCACCATGTGGCCG
** * *
10217 AATCTCACGACCACTATGTGGCCG
1 TTTTTCACGACCACCATGTGGCCG
10241 TTTTTCAC
1 TTTTTCAC
10249 TTTTCTCCAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.19, C:0.33, G:0.18, T:0.30
Consensus pattern (24 bp):
TTTTTCACGACCACCATGTGGCCG
Found at i:10722 original size:2 final size:2
Alignment explanation
Indices: 10715--10746 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10705 TTGGAGTGCA
10715 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
10747 GGCCTATTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16529 original size:24 final size:24
Alignment explanation
Indices: 16380--16521 Score: 221
Period size: 24 Copynumber: 5.9 Consensus size: 24
16370 ATTGGTCTTT
*
16380 TCTCACGACCACCATGTGGTCGAA
1 TCTCACGACCACCATGTGGCCGAA
16404 TCTCACGACCACCATGTGGCCGAA
1 TCTCACGACCACCATGTGGCCGAA
*
16428 TCTCTCGACCACCATGTGGCCGAA
1 TCTCACGACCACCATGTGGCCGAA
* *
16452 TCTCTCGACCACCATGTGGGCGAA
1 TCTCACGACCACCATGTGGCCGAA
*
16476 TCTCACGACCACCATGTGGCCAAA
1 TCTCACGACCACCATGTGGCCGAA
* *
16500 TCTCACGAGCACTATGTGGCCG
1 TCTCACGACCACCATGTGGCCG
16522 TTTCTCACTT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 109 1.00
ACGTcount: A:0.23, C:0.35, G:0.22, T:0.20
Consensus pattern (24 bp):
TCTCACGACCACCATGTGGCCGAA
Found at i:17620 original size:39 final size:39
Alignment explanation
Indices: 17576--17741 Score: 217
Period size: 39 Copynumber: 4.3 Consensus size: 39
17566 ATTAACTGAT
* * *
17576 AAGCAATGATTCTAAATCAGGATTGAAATAAAACTAACA
1 AAGCAATAATCCTAAATCAGGATTGAAATAAAACTGACA
* * *
17615 AAGCAATAATCCTAAGTCAGGATTG-AATAAGACTGATA
1 AAGCAATAATCCTAAATCAGGATTGAAATAAAACTGACA
* * * *
17653 AAGCAATAATTCTAAACCAGGATTGGAATAAAACTGATA
1 AAGCAATAATCCTAAATCAGGATTGAAATAAAACTGACA
* *
17692 AAGCAATAATCCTAACTCAGGATTGAAATGAAACTGACA
1 AAGCAATAATCCTAAATCAGGATTGAAATAAAACTGACA
17731 AAGCAATAATC
1 AAGCAATAATC
17742 AAAAATCATG
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 32 0.29
39 78 0.71
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.22
Consensus pattern (39 bp):
AAGCAATAATCCTAAATCAGGATTGAAATAAAACTGACA
Found at i:17674 original size:77 final size:78
Alignment explanation
Indices: 17569--17740 Score: 251
Period size: 77 Copynumber: 2.2 Consensus size: 78
17559 TTATGAAATT
* * *
17569 AACTGAT-AAGCAATGATTCTAAATCAGGATTGAAATAAAACTAACAAAGCAATAATCCTAAGTC
1 AACTGATAAAGCAATAATTCTAAACCAGGATTGAAATAAAACTAACAAAGCAATAATCCTAACTC
17633 AGGATTG-AAT-A
66 AGGATTGAAATGA
* * *
17644 AGACTGATAAAGCAATAATTCTAAACCAGGATTGGAATAAAACTGATAAAGCAATAATCCTAACT
1 A-ACTGATAAAGCAATAATTCTAAACCAGGATTGAAATAAAACTAACAAAGCAATAATCCTAACT
17709 CAGGATTGAAATGA
65 CAGGATTGAAATGA
*
17723 AACTGACAAAGCAATAAT
1 AACTGATAAAGCAATAAT
17741 CAAAAATCAT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
75 1 0.01
76 6 0.07
77 58 0.67
78 19 0.22
79 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (78 bp):
AACTGATAAAGCAATAATTCTAAACCAGGATTGAAATAAAACTAACAAAGCAATAATCCTAACTC
AGGATTGAAATGA
Found at i:17770 original size:77 final size:77
Alignment explanation
Indices: 17576--17775 Score: 192
Period size: 77 Copynumber: 2.6 Consensus size: 77
17566 ATTAACTGAT
* * * * * * *
17576 AAGCAATGATTCTAAATCAGGAT-TGAAATAAAACTAACAAAGCAATAATCCTAAGTCAGGATTG
1 AAGCAATAATTCAAAACCAGGATCAG-AATAAAACTCATAAAGCAATAATCCTAACTCAGGATTG
*
17640 AATAAGACTGATA
65 AATAAGACTGACA
* ** *
17653 AAGCAATAATTCTAAACCAGGATTGGAATAAAACTGATAAAGCAATAATCCTAACTCAGGATTGA
1 AAGCAATAATTCAAAACCAGGATCAGAATAAAACTCATAAAGCAATAATCCTAACTCAGGATTG-
17718 AATGAA-ACTGACA
65 AAT-AAGACTGACA
* * **
17731 AAGCAATAA-TCAAAAATCATGATCAGAATTGAA-TCATAAAGCAAT
1 AAGCAATAATTC-AAAACCAGGATCAGAATAAAACTCATAAAGCAAT
17776 GATAAAATAA
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
77 69 0.66
78 33 0.32
79 2 0.02
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (77 bp):
AAGCAATAATTCAAAACCAGGATCAGAATAAAACTCATAAAGCAATAATCCTAACTCAGGATTGA
ATAAGACTGACA
Found at i:17965 original size:36 final size:36
Alignment explanation
Indices: 17916--17988 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
17906 TACCCGGGAG
17916 TTTTAATCAATTGCCCGGAGGACTTATCAGAATTAA
1 TTTTAATCAATTGCCCGGAGGACTTATCAGAATTAA
*
17952 TTTTAATCCATTGCCCGGAGGACTTATCAGAATTAA
1 TTTTAATCAATTGCCCGGAGGACTTATCAGAATTAA
17988 T
1 T
17989 ACCCGGAGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (36 bp):
TTTTAATCAATTGCCCGGAGGACTTATCAGAATTAA
Found at i:18401 original size:169 final size:169
Alignment explanation
Indices: 17961--18455 Score: 753
Period size: 170 Copynumber: 2.9 Consensus size: 169
17951 ATTTTAATCC
* * *
17961 ATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGACTTT-TGAAATTGTGCCAGGAGGACTTA
1 ATTGCCCGGAGGACTTATCAGAATTAATACCCGGAG-GTTTCTGAATTTGTGCCCGGAGGACTTA
*
18025 CCAATGTAAATTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTAAACATGAATCTTTGATG-
65 CCAATGTAAACTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTAAACATGAATCTTTGATGA
*
18089 AAAACTTGATAAAATGAAATGGTACCCGGAAGCTTTACCG
130 AAAACTTGATGAAATGAAATGGTACCCGGAAGCTTTACCG
* **
18129 ATTGCCCGGAGGACTTATCAGCATTAATACCCGGAGGTTTCTGAATTTGTGCCCACAGGACTTAC
1 ATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTAC
* * * * *
18194 CAATGCAAACTCTGAA-AAAGGAACCTTAAACAAGGATTTTAAACTTAAACATGAATCTTTAATG
66 CAATGTAAACTCTGAATAGA-G-ACCTTGACCAAGGATTTTAAACTTAAACATGAATCTTTGATG
* * * *
18258 AAAAACTTAATGAAATGAAATGGTACCCGGAGGTTTTACTG
129 AAAAACTTGATGAAATGAAATGGTACCCGGAAGCTTTACCG
*
18299 ATTGCCCGGAGGACTTATCAGAATTAATTCCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTAC
1 ATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTAC
* *
18364 CAATGTAAACTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTAATCATGAATTTTTGATGAA
66 CAATGTAAACTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTAAACATGAATCTTTGATGAA
*
18429 AAACTTGATGAAATGAAATGATACCCG
131 AAACTTGATGAAATGAAATGGTACCCG
18456 TATTGAAACT
Statistics
Matches: 292, Mismatches: 30, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
167 5 0.02
168 70 0.24
169 103 0.35
170 112 0.38
171 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (169 bp):
ATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTAC
CAATGTAAACTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTAAACATGAATCTTTGATGAA
AAACTTGATGAAATGAAATGGTACCCGGAAGCTTTACCG
Found at i:18953 original size:35 final size:35
Alignment explanation
Indices: 18906--18981 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
18896 CTCGATCATT
* *
18906 CTGACATAAACTGGAGAAAAACCACCCCGGG-TCAA
1 CTGAAATAAACTGAAGAAAAACCACCCCGGGTTC-A
* * *
18941 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTTCA
1 CTGAAATAAACTGAAGAAAAACCACCCCGGGTTCA
18976 CTGAAA
1 CTGAAA
18982 GTCAAAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 33 0.94
36 2 0.06
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.14
Consensus pattern (35 bp):
CTGAAATAAACTGAAGAAAAACCACCCCGGGTTCA
Found at i:20712 original size:13 final size:13
Alignment explanation
Indices: 20684--20725 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
20674 TGCCTTTATT
20684 TTCA-TTTTTTCA
1 TTCATTTTTTTCA
20696 -TCATTTTTTTCA
1 TTCATTTTTTTCA
*
20708 TTCATTCTTTTC-
1 TTCATTTTTTTCA
20720 TTCATT
1 TTCATT
20726 GTTTCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 3 0.11
12 14 0.52
13 10 0.37
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (13 bp):
TTCATTTTTTTCA
Done.