Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023158.1 Corchorus olitorius cultivar O-4 contig23191, 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: 17258
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:777 original size:2 final size:2
Alignment explanation
Indices: 770--825 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
760 TAATTTAAGT
770 TA TA TA TA TA TA TA TA -A T- TA T- TA -A T- TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
806 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
826 CTACTTTGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
1 6 0.12
2 42 0.88
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1775 original size:68 final size:68
Alignment explanation
Indices: 1665--1972 Score: 355
Period size: 69 Copynumber: 4.6 Consensus size: 68
1655 TAAAGCTCTA
* * *
1665 TTTTCTATTTCCAAAAAATACTCTTTCGGCCGAAGGGTCATTTTCGTCTTTTTGTATTTAAGTTT
1 TTTTCAATTTCC-AAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTATTTAAGTTT
1730 AGTG
65 AGTG
* *
1734 TTTTCAATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC--CTT-T-TTTCAG--TA
1 TTTTCAATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTATTTAAGTTTA
1793 -T-
66 GTG
* * * * * * *
1794 TTTCT-ATTTCCAAAAAATACTCTTTCGGTTGAAGGGTCATTTTCGTCTTTTTGCATTTTAGTTT
1 TTT-TCAATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTATTTAAGTTT
*
1858 AGTA
65 AGTG
** * *
1862 TTTTCTTTTTTCCAAAAATACCCTTTCGGTTGAAGGGTCATTTTCGTCGTTTTGTATTTAAGTTT
1 TTTTC-AATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTATTTAAGTTT
1927 AGTG
65 AGTG
* *
1931 TTTTCCATTTCCAAAAATACCCTTTCGGTCGAATGGTCATTT
1 TTTTCAATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTT
1973 AAGTTTAGTA
Statistics
Matches: 203, Mismatches: 25, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
60 40 0.20
61 2 0.01
62 4 0.02
64 10 0.05
65 1 0.00
66 4 0.02
67 2 0.01
68 69 0.34
69 71 0.35
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (68 bp):
TTTTCAATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTATTTAAGTTTA
GTG
Found at i:2030 original size:17 final size:15
Alignment explanation
Indices: 2000--2033 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
1990 TTTTACCATA
2000 TAAAATATATAAATC
1 TAAAATATATAAATC
2015 TAAAATAATAATAAATC
1 TAAAAT-AT-ATAAATC
2032 TA
1 TA
2034 TCACAAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 2 0.12
17 9 0.53
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAATATATAAATC
Found at i:2921 original size:98 final size:98
Alignment explanation
Indices: 2752--2948 Score: 385
Period size: 98 Copynumber: 2.0 Consensus size: 98
2742 AGAAATCTTT
*
2752 AACTAATATCTACAACAAGTCACAATAGTAACAAAGAACTCTAAATGATACGTAACATATCCCAA
1 AACTAATATCCACAACAAGTCACAATAGTAACAAAGAACTCTAAATGATACGTAACATATCCCAA
2817 ATATAGCAAAGAAATCTCCGACTAACATTAACA
66 ATATAGCAAAGAAATCTCCGACTAACATTAACA
2850 AACTAATATCCACAACAAGTCACAATAGTAACAAAGAACTCTAAATGATACGTAACATATCCCAA
1 AACTAATATCCACAACAAGTCACAATAGTAACAAAGAACTCTAAATGATACGTAACATATCCCAA
2915 ATATAGCAAAGAAATCTCCGACTAACATTAACA
66 ATATAGCAAAGAAATCTCCGACTAACATTAACA
2948 A
1 A
2949 CAAGTCATAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.21
Consensus pattern (98 bp):
AACTAATATCCACAACAAGTCACAATAGTAACAAAGAACTCTAAATGATACGTAACATATCCCAA
ATATAGCAAAGAAATCTCCGACTAACATTAACA
Found at i:4265 original size:2 final size:2
Alignment explanation
Indices: 4260--4288 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4250 ACACACACAC
4260 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4289 AAGGCATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6661 original size:30 final size:32
Alignment explanation
Indices: 6611--6672 Score: 110
Period size: 30 Copynumber: 2.0 Consensus size: 32
6601 TATACCAAAG
6611 CCTACTATATATCAACACACAAGGCTGATATA
1 CCTACTATATATCAACACACAAGGCTGATATA
6643 CCTACTATATATC-A-ACACAAGGCTGATATA
1 CCTACTATATATCAACACACAAGGCTGATATA
6673 TCAAAAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 16 0.53
31 1 0.03
32 13 0.43
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (32 bp):
CCTACTATATATCAACACACAAGGCTGATATA
Found at i:6714 original size:2 final size:2
Alignment explanation
Indices: 6707--6734 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6697 AACCTACTAG
6707 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
6735 CCTAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8706 original size:24 final size:24
Alignment explanation
Indices: 8658--8707 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
8648 GGGAGGAGGA
*
8658 GTGTTGCTTGGTGAAGGAGGTTGT
1 GTGTTGCTTGGTGAAGGAGGCTGT
*
8682 GTGTTGCTTGGT-ACAGGGGGCTGT
1 GTGTTGCTTGGTGA-AGGAGGCTGT
8706 GT
1 GT
8708 AGGGGGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.10, C:0.08, G:0.46, T:0.36
Consensus pattern (24 bp):
GTGTTGCTTGGTGAAGGAGGCTGT
Found at i:9329 original size:22 final size:22
Alignment explanation
Indices: 9268--9331 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
9258 GACCCATGAG
*
9268 AAAAATCAAAACCATTTTCATA
1 AAAAATCAAAACCAATTTCATA
* * *
9290 TAAAAT-GAAA--GA-TT-ATA
1 AAAAATCAAAACCAATTTCATA
9307 AAAAATCAAAACCAATTTCATA
1 AAAAATCAAAACCAATTTCATA
9329 AAA
1 AAA
9332 GAAATGTAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 10
0.64 0.15 0.21
Matches are distributed among these distances:
17 8 0.27
18 5 0.17
20 1 0.03
21 5 0.17
22 11 0.37
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.25
Consensus pattern (22 bp):
AAAAATCAAAACCAATTTCATA
Found at i:9346 original size:38 final size:38
Alignment explanation
Indices: 9268--9347 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 38
9258 GACCCATGAG
* **
9268 AAAAATCAAAACCATTTTCATATAAAATGAAAGATTATA
1 AAAAATCAAAACCAATTTCA-ATAAAATGAAAGAAGATA
9307 AAAAATCAAAACCAATTTC-ATAAAA-GAAATGTAAGATA
1 AAAAATCAAAACCAATTTCAATAAAATGAAA-G-AAGATA
9345 AAA
1 AAA
9348 TAATTCACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 4 0.11
37 7 0.19
38 7 0.19
39 18 0.50
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.24
Consensus pattern (38 bp):
AAAAATCAAAACCAATTTCAATAAAATGAAAGAAGATA
Found at i:9497 original size:45 final size:45
Alignment explanation
Indices: 9412--9506 Score: 115
Period size: 45 Copynumber: 2.1 Consensus size: 45
9402 ACTATCAAAA
9412 ATGAAGAGAAGAGAGAGCAGCGCAGACCAAAGAAAGAGAACAGA-G
1 ATGAAGAGAAGAGAGAGCAGCGCAGACCAAAGAAAGAGAACA-ACG
* * *
9457 ATGAAGAGAAGAGGGAGC-GACGCAGGCCAAAGGATA-AGAACAACG
1 ATGAAGAGAAGAGAGAGCAG-CGCAGACCAAA-GAAAGAGAACAACG
9502 ATGAA
1 ATGAA
9507 AAAAAATTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
44 2 0.05
45 39 0.89
46 3 0.07
ACGTcount: A:0.48, C:0.14, G:0.34, T:0.04
Consensus pattern (45 bp):
ATGAAGAGAAGAGAGAGCAGCGCAGACCAAAGAAAGAGAACAACG
Done.