Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012027.1 Corchorus olitorius cultivar O-4 contig12060, 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: 31058
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:8995 original size:52 final size:52
Alignment explanation
Indices: 8928--9184 Score: 327
Period size: 52 Copynumber: 4.9 Consensus size: 52
8918 GGAACTTTCT
* * * *
8928 CTAAATTGAACACTTTGAAGA-TCTAATGGGAACTTTCCCACTTTGGAAAGAC
1 CTAAATTGAACACTTTGAAAACT-TGATGGGAACTTTCCCACTTTGAAAAAAC
* * * *
8980 CTAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTGTGAAAAGAG
1 CTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAAAC
* * * *
9032 TTAAATTAAACGCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAAAG
1 CTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAAAC
* *
9084 TTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGCAAAAAC
1 CTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAAAC
* * ** *
9136 CTAAATTGAATATTTTGAAAACCCGATGGGAACTTTCCCGCTTTGAAAA
1 CTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
9185 CTTGAAAGGA
Statistics
Matches: 181, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
52 180 0.99
53 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (52 bp):
CTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAAAC
Found at i:9688 original size:18 final size:19
Alignment explanation
Indices: 9665--9703 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9655 ATTTAACAAT
9665 ATTTAAAG-AAATATAAAC
1 ATTTAAAGAAAATATAAAC
*
9683 ATTTAAGGAAAATATAAAC
1 ATTTAAAGAAAATATAAAC
9702 AT
1 AT
9704 GGGTGCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (19 bp):
ATTTAAAGAAAATATAAAC
Found at i:11197 original size:12 final size:12
Alignment explanation
Indices: 11180--11216 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 12
11170 TAAAAGACTC
11180 AAAACCTTTTTG
1 AAAACCTTTTTG
11192 AAAACCTATTTTTG
1 AAAACC--TTTTTG
11206 AAAACCTTTTT
1 AAAACCTTTTT
11217 TTGAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 11 0.48
14 12 0.52
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43
Consensus pattern (12 bp):
AAAACCTTTTTG
Found at i:11218 original size:15 final size:14
Alignment explanation
Indices: 11186--11238 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
11176 ACTCAAAACC
*
11186 TTTTTGAAAACCTA
1 TTTTTGAAAACCTT
11200 TTTTTGAAAACCTT
1 TTTTTGAAAACCTT
*
11214 TTTTTGAAAACAATT
1 TTTTTGAAAAC-CTT
*
11229 TTCTTGAAAA
1 TTTTTGAAAA
11239 ACGTCTCTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
14 24 0.69
15 11 0.31
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACCTT
Found at i:12762 original size:154 final size:154
Alignment explanation
Indices: 12477--12788 Score: 545
Period size: 154 Copynumber: 2.0 Consensus size: 154
12467 ACTAATGCAC
* *
12477 AATGAATGCATGATCATATATACAAGTTGATGGTTTGACAACTCTACAACTCTTGTAACTGTGCA
1 AATGAATGCATGATCAAATATACAAGTTGATGGCTTGACAACTCTACAACTCTTGTAACTGTGCA
12542 TGCAAAACGCAAGTGACGTGGCATTCAAAGTCTCATGTCGATGGATACATAGAAAAGATGCATGA
66 TGCAAAACGCAAGTGACGTGGCATTCAAAGTCTCATGTCGATGGATACATAGAAAAGATGCATGA
12607 CATGGCAAACTATGTTGATGAGCA
131 CATGGCAAACTATGTTGATGAGCA
* * *
12631 AATGTATGCATGATCAAATATACAAGTTGATGGCTTGACAACTTTACGACTCTTGTAACTGTGCA
1 AATGAATGCATGATCAAATATACAAGTTGATGGCTTGACAACTCTACAACTCTTGTAACTGTGCA
* *
12696 TGCAAAATGCAAGTGACGTGGCATTCAAAGTCTCATG-CTGATGGATACATAGAAAAGATGTATG
66 TGCAAAACGCAAGTGACGTGGCATTCAAAGTCTCATGTC-GATGGATACATAGAAAAGATGCATG
12760 ACATGGCAAACTATGTTGATGAGCA
130 ACATGGCAAACTATGTTGATGAGCA
12785 AATG
1 AATG
12789 CGTGAGCATG
Statistics
Matches: 150, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
153 1 0.01
154 149 0.99
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (154 bp):
AATGAATGCATGATCAAATATACAAGTTGATGGCTTGACAACTCTACAACTCTTGTAACTGTGCA
TGCAAAACGCAAGTGACGTGGCATTCAAAGTCTCATGTCGATGGATACATAGAAAAGATGCATGA
CATGGCAAACTATGTTGATGAGCA
Found at i:14202 original size:29 final size:29
Alignment explanation
Indices: 14170--14228 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
14160 AAACTTTTTC
14170 CGTCTTTTATTGATCTTCTAACCTTGTGA
1 CGTCTTTTATTGATCTTCTAACCTTGTGA
14199 CGTCTTTTATTGATCTTCTAACCTTGTGA
1 CGTCTTTTATTGATCTTCTAACCTTGTGA
14228 C
1 C
14229 TAAGTCTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.22, G:0.14, T:0.47
Consensus pattern (29 bp):
CGTCTTTTATTGATCTTCTAACCTTGTGA
Found at i:16024 original size:166 final size:166
Alignment explanation
Indices: 15750--16082 Score: 666
Period size: 166 Copynumber: 2.0 Consensus size: 166
15740 TTTCGTTCCA
15750 TCAATGAACCTCTGCTTCGAAGTAATTCCAGTTAGGTGTATTAAAAATCAAAATAATCAATGATT
1 TCAATGAACCTCTGCTTCGAAGTAATTCCAGTTAGGTGTATTAAAAATCAAAATAATCAATGATT
15815 GGTGGTATATTAAAAATTAGTCAACATTTTATGCAGTGGTGATAATTATCCTTTTCAAGTGTAAT
66 GGTGGTATATTAAAAATTAGTCAACATTTTATGCAGTGGTGATAATTATCCTTTTCAAGTGTAAT
15880 GGTTATATTGTGTGTGAAGACAATTTTATCCCCCTT
131 GGTTATATTGTGTGTGAAGACAATTTTATCCCCCTT
15916 TCAATGAACCTCTGCTTCGAAGTAATTCCAGTTAGGTGTATTAAAAATCAAAATAATCAATGATT
1 TCAATGAACCTCTGCTTCGAAGTAATTCCAGTTAGGTGTATTAAAAATCAAAATAATCAATGATT
15981 GGTGGTATATTAAAAATTAGTCAACATTTTATGCAGTGGTGATAATTATCCTTTTCAAGTGTAAT
66 GGTGGTATATTAAAAATTAGTCAACATTTTATGCAGTGGTGATAATTATCCTTTTCAAGTGTAAT
16046 GGTTATATTGTGTGTGAAGACAATTTTATCCCCCTT
131 GGTTATATTGTGTGTGAAGACAATTTTATCCCCCTT
16082 T
1 T
16083 TATATCGTCT
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 167 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (166 bp):
TCAATGAACCTCTGCTTCGAAGTAATTCCAGTTAGGTGTATTAAAAATCAAAATAATCAATGATT
GGTGGTATATTAAAAATTAGTCAACATTTTATGCAGTGGTGATAATTATCCTTTTCAAGTGTAAT
GGTTATATTGTGTGTGAAGACAATTTTATCCCCCTT
Found at i:17179 original size:21 final size:23
Alignment explanation
Indices: 17129--17176 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
17119 GAAGGGAGAA
* *
17129 AAGAAGCAACCATTGTAGAGAGG
1 AAGAAACAACCATTGCAGAGAGG
17152 AAGAAACAACCATTGCAGAGAGG
1 AAGAAACAACCATTGCAGAGAGG
17175 AA
1 AA
17177 AACGCAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.15, G:0.27, T:0.10
Consensus pattern (23 bp):
AAGAAACAACCATTGCAGAGAGG
Found at i:27546 original size:32 final size:32
Alignment explanation
Indices: 27505--27565 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
27495 AAATATGTTT
*
27505 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGTCGATTCAATTA
*
27537 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGATATAATAGTCGATTCAA
27566 AAGTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Done.