Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016185.1 Corchorus olitorius cultivar O-4 contig16218, 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: 6850
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3635 original size:84 final size:85
Alignment explanation
Indices: 3493--3658 Score: 289
Period size: 84 Copynumber: 2.0 Consensus size: 85
3483 ATCACCTACG
*
3493 GTTCTTACAAACCATTGCTCCATTTTATGCCGTTGGATACGAAAGCTATAAATAATGACCGTTAG
1 GTTCTTACAAACCATTGCTCCATTTTATGCCGTTAGATACGAAAGCTATAAATAATGACCGTTAG
3558 ATTGTTTGACAAATTAATAA
66 ATTGTTTGACAAATTAATAA
* * *
3578 GTTCTTACAAACCATTG-TTCATTTTATGCCGTTAGATATGAAAGTTATAAATAATGACCGTTAG
1 GTTCTTACAAACCATTGCTCCATTTTATGCCGTTAGATACGAAAGCTATAAATAATGACCGTTAG
3642 ATTGTTTGACAAATTAA
66 ATTGTTTGACAAATTAA
3659 AAGGAGTGTT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 60 0.78
85 17 0.22
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (85 bp):
GTTCTTACAAACCATTGCTCCATTTTATGCCGTTAGATACGAAAGCTATAAATAATGACCGTTAG
ATTGTTTGACAAATTAATAA
Found at i:3687 original size:29 final size:28
Alignment explanation
Indices: 3637--3692 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
3627 AATAATGACC
3637 GTTAGATTGTTTGACAAATTAAAAGGAGT
1 GTTAGATTGTTTGACAAATT-AAAGGAGT
**
3666 GTTAGATTGTTTGACATGTTAAAGGAG
1 GTTAGATTGTTTGACAAATTAAAGGAG
3693 GGAATTGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (28 bp):
GTTAGATTGTTTGACAAATTAAAGGAGT
Found at i:3954 original size:13 final size:13
Alignment explanation
Indices: 3936--3961 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3926 AATCTCATAT
3936 CTCTAATATATAA
1 CTCTAATATATAA
3949 CTCTAATATATAA
1 CTCTAATATATAA
3962 AGGTGTGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
CTCTAATATATAA
Found at i:4876 original size:133 final size:133
Alignment explanation
Indices: 4633--4889 Score: 304
Period size: 133 Copynumber: 1.9 Consensus size: 133
4623 TTAGGGTTTA
** * * * * *
4633 ACTATCAAAATTTGTTGTTTGACCATGCATATGCAATTAAATGTTTTGTGTGGTTTGACAATCGG
1 ACTATCAAAATTTGGGGTTTAACCATGCATATACAATGAAATGCTTTATGTGGTTTGACAATCGG
* * *
4698 ACTTTGGAATTTAACCATCATCCTTTGGAATTTGATCATGTATGTATAATGATGTTTTTTGAGAT
66 ACTTTGGAATTTAACCATCATCCTTTGGAATTTGACCATGCATGTACAATGATGTTTTTTGAGAT
4763 TCG
131 TCG
* * * *
4766 ACTATTAAAATTTGGGGTTTAATCATGCATATATAATGAAATGCTTTATGTGGTTTGACTATC-G
1 ACTATCAAAATTTGGGGTTTAACCATGCATATACAATGAAATGCTTTATGTGGTTTGACAATCGG
* * **
4830 AGCTTTGTG-ATTTAACTATCATCTTTTGGGGTTT-AGCCATGCATGTACAATGATGTTTTT
66 A-CTTTG-GAATTTAACCATCATCCTTTGGAATTTGA-CCATGCATGTACAATGATGTTTTT
4890 GGGGTTTGAC
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
132 3 0.03
133 99 0.96
134 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (133 bp):
ACTATCAAAATTTGGGGTTTAACCATGCATATACAATGAAATGCTTTATGTGGTTTGACAATCGG
ACTTTGGAATTTAACCATCATCCTTTGGAATTTGACCATGCATGTACAATGATGTTTTTTGAGAT
TCG
Found at i:5044 original size:56 final size:55
Alignment explanation
Indices: 4978--5155 Score: 147
Period size: 56 Copynumber: 3.3 Consensus size: 55
4968 CAATGATGTT
* *
4978 TTTTGGGGTTTGACTGTGCATATACAATGAAAATTTTTTGTGATTTGACTATTGAA
1 TTTTGAGGTTTGACTATGCATATACAATGAAAATTTTTTGTG-TTTGACTATTGAA
* ** *
5034 TTTTGAGGTTTGA-TCATGCATATGCAATG---ATGTTTTTG-G-GGGACTATTAAAA
1 TTTTGAGGTTTGACT-ATGCATATACAATGAAAAT-TTTTTGTGTTTGACTATT-GAA
* * *
5086 TATTG-GGTTTGACCATGCATATACAATGAAATGTTTTTTGTGGTTTGACTATTGAA
1 TTTTGAGGTTTGACTATGCATATACAATGAAA-ATTTTTTGT-GTTTGACTATTGAA
*
5142 GTTT-AGGGTTTGAC
1 TTTTGA-GGTTTGAC
5156 CATCATTCTT
Statistics
Matches: 94, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
51 27 0.29
52 6 0.06
53 3 0.03
54 12 0.13
55 2 0.02
56 29 0.31
57 15 0.16
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.43
Consensus pattern (55 bp):
TTTTGAGGTTTGACTATGCATATACAATGAAAATTTTTTGTGTTTGACTATTGAA
Found at i:5062 original size:90 final size:90
Alignment explanation
Indices: 4833--5075 Score: 246
Period size: 90 Copynumber: 2.7 Consensus size: 90
4823 ACTATCGAGC
* * * * *
4833 TTTGTGATTTAACTATC-ATCTTTTGGGGTTT-AGCCATGCATGTACAATGATG-TTTTTGGGGT
1 TTTGTGATTTGACTATCGAAC-TTTGAGGTTTGA-CCATGCATATGCAATGATGTTTTTTGGGGT
*
4895 TTGACCATGCATATACTATAAAATGTTTT
64 TTGACCATGCATATACAATAAAA--TTTT
* * *
4924 TTTGTGGTTTGACTATCGAACTTTGGGGTTTGACCAT-C-TACGCACAATGATGTTTTTTGGGGT
1 TTTGTGATTTGACTATCGAACTTTGAGGTTTGACCATGCATATG--CAATGATGTTTTTTGGGGT
**
4987 TTGACTGTGCATATACAATGAAAA-TTT
64 TTGACCATGCATATACAAT-AAAATTTT
* * * *
5014 TTTGTGATTTGACTATTGAATTTTGAGGTTTGATCATGCATATGCAATGATGTTTTTGGGGG
1 TTTGTGATTTGACTATCGAACTTTGAGGTTTGACCATGCATATGCAATGATGTTTTTTGGGG
5076 ACTATTAAAA
Statistics
Matches: 128, Mismatches: 16, Indels: 17
0.80 0.10 0.11
Matches are distributed among these distances:
89 1 0.01
90 53 0.41
91 38 0.30
92 32 0.25
93 4 0.03
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (90 bp):
TTTGTGATTTGACTATCGAACTTTGAGGTTTGACCATGCATATGCAATGATGTTTTTTGGGGTTT
GACCATGCATATACAATAAAATTTT
Found at i:6158 original size:2 final size:2
Alignment explanation
Indices: 6151--6185 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6141 GTTCAATGCT
6151 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6186 TCAATAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6332 original size:386 final size:378
Alignment explanation
Indices: 5625--6392 Score: 1428
Period size: 386 Copynumber: 2.0 Consensus size: 378
5615 TTAAATGCCT
5625 AAAGATTAGATTTGAAGAAAACACATATATGTATAGATCCTACATTTGAAGAAGACATATCACAT
1 AAAGATTAGATTTGAAGAAAACACATATATGTATAGATCCTACATTTGAAGAAGACATATCACAT
5690 ATGTATGATGTAGAAATTTATAATTTCAACAATTTCTAGTGTATATCATATGTGAATTGAAACAA
66 ATGTATGATGTAGAAATTTATAATTTCAACAATTTCTAGTGTATATCATATGTGAATTGAAACAA
*
5755 ATTAATAAGTTCAATGCATATATATATATATGTATATATATATATTCAATAAGAAGCATTATTGA
131 ATTAATAAGTTCAATGCATATATATATATATATATATATATATATTCAATAAGAAGCATTATTGA
*
5820 TTCTCAAATTCGAACTCATTACTCATTAATTCATTTTTATATATATTGTGGTGCATATATAATAT
196 TTCTCAAATTCAAACTCATTACTCATTAATTCATTTTTATATATATTGTGGTGCATATATAATAT
5885 CTTTTGTTACCTTATATGTTTTGTCAAAACTCATCAACTAGATATTAATTCATATTCAATTCACT
261 CTTTTGTTACCTTATATGTTTTGTCAAAACTCATCAACTAGATATTAATTCATATTCAATTCACT
5950 CATTATCACTCCAGTTTTAATTCTTTGTTATAGTTAATTGTATTTTTTCATTG
326 CATTATCACTCCAGTTTTAATTCTTTGTTATAGTTAATTGTATTTTTTCATTG
6003 AAAGATTAGATTTGAAGAAAACACATATATGTATAGATCCTACATTTGAAGAAGACATATCACAT
1 AAAGATTAGATTTGAAGAAAACACATATATGTATAGATCCTACATTTGAAGAAGACATATCACAT
6068 ATGTATGATGTAGAAATTTATAATTTCAACAATTTCTAGTGTATATCATATGTGAATTGAAACAA
66 ATGTATGATGTAGAAATTTATAATTTCAACAATTTCTAGTGTATATCATATGTGAATTGAAACAA
6133 ATTAATAAGTTCAATGCTTATATATATATATATATATATATATATATATATATTCAATAAGAAGC
131 ATTAATAAGTTCAATGC--------ATATATATATATATATATATATATATATTCAATAAGAAGC
6198 ATTATTGATTCTCAAATTCAAACTCATTACTCATTAATTCATTTTTATATATATTGTGGTGCATA
188 ATTATTGATTCTCAAATTCAAACTCATTACTCATTAATTCATTTTTATATATATTGTGGTGCATA
6263 TATAATATCTTTTGTTACCTTATATGTTTTGTCAAAACTCATCAACTAGATATTAATTCATATTC
253 TATAATATCTTTTGTTACCTTATATGTTTTGTCAAAACTCATCAACTAGATATTAATTCATATTC
* *
6328 AATTCACTCATTATCACTCCATTTTTAATTCTTTGTTATAGTTAATTGTGTTTTTTCATTG
318 AATTCACTCATTATCACTCCAGTTTTAATTCTTTGTTATAGTTAATTGTATTTTTTCATTG
6389 AAAG
1 AAAG
6393 GTCCAAATGA
Statistics
Matches: 378, Mismatches: 4, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
378 147 0.39
386 231 0.61
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (378 bp):
AAAGATTAGATTTGAAGAAAACACATATATGTATAGATCCTACATTTGAAGAAGACATATCACAT
ATGTATGATGTAGAAATTTATAATTTCAACAATTTCTAGTGTATATCATATGTGAATTGAAACAA
ATTAATAAGTTCAATGCATATATATATATATATATATATATATATTCAATAAGAAGCATTATTGA
TTCTCAAATTCAAACTCATTACTCATTAATTCATTTTTATATATATTGTGGTGCATATATAATAT
CTTTTGTTACCTTATATGTTTTGTCAAAACTCATCAACTAGATATTAATTCATATTCAATTCACT
CATTATCACTCCAGTTTTAATTCTTTGTTATAGTTAATTGTATTTTTTCATTG
Done.