Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020439.1 Corchorus olitorius cultivar O-4 contig20472, 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: 27385
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:1989 original size:29 final size:28
Alignment explanation
Indices: 1952--2059 Score: 81
Period size: 29 Copynumber: 3.8 Consensus size: 28
1942 CATTTTACAT
* *
1952 GTCCTGGGGCATTCTGGTCATCCTTCTAG
1 GTCCAGGGGCATTCTGGTCATCATTC-AG
* * * *
1981 GTCCAGGGGGCATTGTGATCATTATTCAT
1 GTCCA-GGGGCATTCTGGTCATCATTCAG
* ** *
2010 GTCCAGGGGCATTTTGGTCATTTTTCAT
1 GTCCAGGGGCATTCTGGTCATCATTCAG
* *
2038 GTTCAGGGGGCATTTTGGTCAT
1 GTCCA-GGGGCATTCTGGTCAT
2060 TTCAAGTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
28 24 0.36
29 26 0.39
30 17 0.25
ACGTcount: A:0.15, C:0.19, G:0.29, T:0.37
Consensus pattern (28 bp):
GTCCAGGGGCATTCTGGTCATCATTCAG
Found at i:2060 original size:29 final size:29
Alignment explanation
Indices: 1936--2061 Score: 130
Period size: 28 Copynumber: 4.4 Consensus size: 29
1926 ATCAAATCGC
* * *
1936 TTTGCTCATTTTACATGTCC-TGGGGCAT
1 TTTGGTCATTTTTCATGTCCAGGGGGCAT
* ** *
1964 TCTGGTCATCCTTCTAGGTCCAGGGGGCAT
1 TTTGGTCATTTTTC-ATGTCCAGGGGGCAT
* * *
1994 TGTGATCATTATTCATGTCCA-GGGGCAT
1 TTTGGTCATTTTTCATGTCCAGGGGGCAT
*
2022 TTTGGTCATTTTTCATGTTCAGGGGGCAT
1 TTTGGTCATTTTTCATGTCCAGGGGGCAT
2051 TTTGGTCATTT
1 TTTGGTCATTT
2062 CAAGTTTATT
Statistics
Matches: 79, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
28 33 0.42
29 29 0.37
30 17 0.22
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.40
Consensus pattern (29 bp):
TTTGGTCATTTTTCATGTCCAGGGGGCAT
Found at i:7536 original size:109 final size:109
Alignment explanation
Indices: 7345--7567 Score: 401
Period size: 109 Copynumber: 2.0 Consensus size: 109
7335 AAGTTGGAGA
7345 AAGAAAGATGCACAATGTCGAAGATCAACATTACAACTGAAAAGATCAAGATTATCCGAGAGAGA
1 AAGAAAGATGCACAATGTCGAAGATCAACATTACAACTGAAAAGATCAAGATTATCCGAGAGAGA
*
7410 CTGAAAGCAGTACAAGACAGGCAGAAAAGTTATGCGGATAATCG
66 CTGAAAGCAGCACAAGACAGGCAGAAAAGTTATGCGGATAATCG
* *
7454 AAGAAAGATGCACGATGTCGAAGATCGACATTACAACTGAAAAGATCAAGATTATCCGAGAGAGA
1 AAGAAAGATGCACAATGTCGAAGATCAACATTACAACTGAAAAGATCAAGATTATCCGAGAGAGA
* *
7519 TTGAAAGCAGCACAAGACAGGCAGAAAAGTTATGTGGATAATCG
66 CTGAAAGCAGCACAAGACAGGCAGAAAAGTTATGCGGATAATCG
7563 AAGAA
1 AAGAA
7568 GGGATCTTGA
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.17
Consensus pattern (109 bp):
AAGAAAGATGCACAATGTCGAAGATCAACATTACAACTGAAAAGATCAAGATTATCCGAGAGAGA
CTGAAAGCAGCACAAGACAGGCAGAAAAGTTATGCGGATAATCG
Found at i:17830 original size:87 final size:87
Alignment explanation
Indices: 17702--17916 Score: 317
Period size: 87 Copynumber: 2.5 Consensus size: 87
17692 AACCCAGAGT
17702 ATGCAAAAATGACCAAAATGCCCCTGG--ATGCACAAATATGACCAAAATGCCCCTAGATACGCA
1 ATGCAAAAATGACCAAAATGCCCCTGGACATGCA-AAA-ATGACCAAAATGCCCCTAGATACGCA
*
17765 AAAATGACCAAAATGCCCCTGGAC
64 AAAATGACCAAAATACCCCTGGAC
* * * *
17789 ATGCAAACATGATCAAAATGCCCCTGGACATGCAAAAATGACCAAAATGCCCCTGGATGCGCAAA
1 ATGCAAAAATGACCAAAATGCCCCTGGACATGCAAAAATGACCAAAATGCCCCTAGATACGCAAA
* *
17854 TATGACCAAAATACCCCTGGAT
66 AATGACCAAAATACCCCTGGAC
* *
17876 ACGCAAAAATGACCAAAATGCCCCTGGACATGCAAACATGA
1 ATGCAAAAATGACCAAAATGCCCCTGGACATGCAAAAATGA
17917 TCAATTAAGA
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
87 107 0.93
88 3 0.03
89 5 0.04
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (87 bp):
ATGCAAAAATGACCAAAATGCCCCTGGACATGCAAAAATGACCAAAATGCCCCTAGATACGCAAA
AATGACCAAAATACCCCTGGAC
Found at i:17910 original size:29 final size:29
Alignment explanation
Indices: 17702--17916 Score: 281
Period size: 29 Copynumber: 7.4 Consensus size: 29
17692 AACCCAGAGT
17702 ATGCAAAAATGACCAAAATGCCCCTGG--
1 ATGCAAAAATGACCAAAATGCCCCTGGAC
* *
17729 ATGCACAAATATGACCAAAATGCCCCTAGAT
1 ATGCA-AAA-ATGACCAAAATGCCCCTGGAC
*
17760 ACGCAAAAATGACCAAAATGCCCCTGGAC
1 ATGCAAAAATGACCAAAATGCCCCTGGAC
* *
17789 ATGCAAACATGATCAAAATGCCCCTGGAC
1 ATGCAAAAATGACCAAAATGCCCCTGGAC
*
17818 ATGCAAAAATGACCAAAATGCCCCTGGAT
1 ATGCAAAAATGACCAAAATGCCCCTGGAC
** * * *
17847 GCGCAAATATGACCAAAATACCCCTGGAT
1 ATGCAAAAATGACCAAAATGCCCCTGGAC
*
17876 ACGCAAAAATGACCAAAATGCCCCTGGAC
1 ATGCAAAAATGACCAAAATGCCCCTGGAC
*
17905 ATGCAAACATGA
1 ATGCAAAAATGA
17917 TCAATTAAGA
Statistics
Matches: 164, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 5 0.03
28 3 0.02
29 149 0.91
30 3 0.02
31 4 0.02
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (29 bp):
ATGCAAAAATGACCAAAATGCCCCTGGAC
Found at i:26577 original size:32 final size:33
Alignment explanation
Indices: 26526--26591 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
26516 GATATCAACT
*
26526 ACTTTTTTTACTTGATTTATTATTTTTTTCTCTA
1 ACTTTTTTTACTT-ATTTATTATTTTCTTCTCTA
*
26560 ACTTTTTTTACTT-TTTATTCTTTTCTTCTCTA
1 ACTTTTTTTACTTATTTATTATTTTCTTCTCTA
26592 TTTTCTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 17 0.57
34 13 0.43
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (33 bp):
ACTTTTTTTACTTATTTATTATTTTCTTCTCTA
Done.