Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015887.1 Corchorus olitorius cultivar O-4 contig15920, 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: 15179
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Found at i:61 original size:27 final size:25
Alignment explanation
Indices: 31--86 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
21 AAAAGTAACT
31 AAGAAAAATAAACGAAAATAAAAGAAA
1 AAGAAAAAT-AACGAAAA-AAAAGAAA
* *
58 AAGAAAAATAATGAAAAAAAATAAA
1 AAGAAAAATAACGAAAAAAAAGAAA
83 AAGA
1 AAGA
87 TAAGGGTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 11 0.41
26 7 0.26
27 9 0.33
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.09
Consensus pattern (25 bp):
AAGAAAAATAACGAAAAAAAAGAAA
Found at i:1786 original size:76 final size:76
Alignment explanation
Indices: 1649--1799 Score: 182
Period size: 76 Copynumber: 2.0 Consensus size: 76
1639 ACAAGGACCC
* *
1649 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
1714 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
1725 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
1787 GATGGGCTGTGTC
63 GATGGGCAGTGTC
1800 TTAGCTCATC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:9737 original size:25 final size:24
Alignment explanation
Indices: 9703--9752 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
9693 GTCCGCCCAT
*
9703 ATTAATTTTTTAAAATAAAATAATA
1 ATTAAATTTTTAAAATAAAA-AATA
**
9728 ATTAAATTTTTTTAATAAAAAATA
1 ATTAAATTTTTAAAATAAAAAATA
9752 A
1 A
9753 AATTTAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTAAATTTTTAAAATAAAAAATA
Found at i:10034 original size:37 final size:37
Alignment explanation
Indices: 9993--10208 Score: 225
Period size: 37 Copynumber: 5.8 Consensus size: 37
9983 GCAGTGATTT
* *
9993 GTAAGGAGAGCTCTTCGGTAAAGAGGGTGATGTCGCA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGTCGCA
* * *
10030 GTAAGGAGAGCTCTACAGTAAAGAGGGTGTTGTCGCA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGTCGCA
* * * *
10067 GTAAGGAGAGCTCTGCGGTGAAGAAGGTGCCGCCGCA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGTCGCA
* * * * **
10104 GTAAGGGGAGCTCAGCGGTAAAGAGGGTGTTATCATA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGTCGCA
* ** *
10141 GTAAGAAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGTCGCA
* ** *
10178 GTAAGGGGAGCTCTATGGTAAAAAGGGTGCT
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCT
10209 ACCGCAAGAT
Statistics
Matches: 146, Mismatches: 33, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 146 1.00
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.19
Consensus pattern (37 bp):
GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGTCGCA
Found at i:10115 original size:74 final size:74
Alignment explanation
Indices: 9993--10206 Score: 268
Period size: 74 Copynumber: 2.9 Consensus size: 74
9983 GCAGTGATTT
* * * * *
9993 GTAAGGAGAGCTCTTCGGTAAAGAGGGTGATGTCGCAGTAAGGAGAGCTCTACAGTAAAGAGGGT
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGCCGCAGTAAGGGGAGCTCTACGGTAAAGAGGGT
* *
10058 GTTGTCGCA
66 GTTATCACA
* * *
10067 GTAAGGAGAGCTCTGCGGTGAAGAAGGTGCCGCCGCAGTAAGGGGAGCTC-AGCGGTAAAGAGGG
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGCCGCAGTAAGGGGAGCTCTA-CGGTAAAGAGGG
*
10131 TGTTATCATA
65 TGTTATCACA
* * * * *
10141 GTAAGAAGAGCTCTGCGGTAAAGAGGGTGCTACCGCGGTAAGGGGAGCTCTATGGTAAAAAGGGT
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGCCGCAGTAAGGGGAGCTCTACGGTAAAGAGGGT
10206 G
66 G
10207 CTACCGCAAG
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
73 1 0.01
74 117 0.98
75 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.38, T:0.19
Consensus pattern (74 bp):
GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGCCGCAGTAAGGGGAGCTCTACGGTAAAGAGGGT
GTTATCACA
Found at i:10207 original size:111 final size:111
Alignment explanation
Indices: 9993--10203 Score: 253
Period size: 111 Copynumber: 1.9 Consensus size: 111
9983 GCAGTGATTT
** * * *
9993 GTAAGGAGAGCTCTTCGGTAAAGAGGGTGATGTCGCAGTAAGGAGAGCTCTACAGTAAAGAGGGT
1 GTAAGGAGAGCTCAGCGGTAAAGAGGGTGATATCACAGTAAGAAGAGCTCTACAGTAAAGAGGGT
* ** * *
10058 GTTGTCGCAGTAAGGAGAGCTCTGCGGTGAAGAAGGTGCCGCCGCA
66 GCTACCGCAGTAAGGAGAGCTCTACGGTGAAAAAGGTGCCGCCGCA
* * * * *
10104 GTAAGGGGAGCTCAGCGGTAAAGAGGGTGTTATCATAGTAAGAAGAGCTCTGCGGTAAAGAGGGT
1 GTAAGGAGAGCTCAGCGGTAAAGAGGGTGATATCACAGTAAGAAGAGCTCTACAGTAAAGAGGGT
* * *
10169 GCTACCGCGGTAAGGGGAGCTCTATGGT-AAAAAGG
66 GCTACCGCAGTAAGGAGAGCTCTACGGTGAAAAAGG
10204 GTGCTACCGC
Statistics
Matches: 82, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
110 6 0.07
111 76 0.93
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.19
Consensus pattern (111 bp):
GTAAGGAGAGCTCAGCGGTAAAGAGGGTGATATCACAGTAAGAAGAGCTCTACAGTAAAGAGGGT
GCTACCGCAGTAAGGAGAGCTCTACGGTGAAAAAGGTGCCGCCGCA
Found at i:12828 original size:35 final size:35
Alignment explanation
Indices: 12758--12829 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
12748 GAATGGGAAT
* *
12758 TTTCCCAATTTGAAAACTTAAAAGTTGATGGGAAC
1 TTTCCCAATTTGAAAACTTAAAACTTGATGAGAAC
*
12793 TTTCCCAATTTGAAAACTTAAAACTTGGTGAGAAC
1 TTTCCCAATTTGAAAACTTAAAACTTGATGAGAAC
12828 TT
1 TT
12830 AGAAAAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (35 bp):
TTTCCCAATTTGAAAACTTAAAACTTGATGAGAAC
Found at i:14274 original size:20 final size:19
Alignment explanation
Indices: 14249--14293 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
14239 ACTGACAGGC
*
14249 ACCTAATTGACCAAATTTAA
1 ACCTAATGGACCAAA-TTAA
*
14269 ACCTAAGGGACCAAATTAA
1 ACCTAATGGACCAAATTAA
14288 A-CTAAT
1 ACCTAAT
14294 CCAGGGGCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.18
19 5 0.23
20 13 0.59
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (19 bp):
ACCTAATGGACCAAATTAA
Done.