Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022906.1 Corchorus olitorius cultivar O-4 contig22939, 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: 14765
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Found at i:3740 original size:15 final size:15
Alignment explanation
Indices: 3720--3751 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3710 CCTTGGGGGT
3720 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
3735 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
3750 TC
1 TC
3752 CACTTAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (15 bp):
TCAAAATCAACAAGC
Found at i:4443 original size:66 final size:65
Alignment explanation
Indices: 4337--4462 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 65
4327 AGTAATTCTG
* *
4337 AACCTGATTTGAGTGTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACCA
1 AACCTAATTTAAGTGTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACCA
** * * *
4402 AACCTAATTTAAGTGTTGTTTGTGATGACACT-AAATTTGTTTTAGGTGTTGTTTGTGATGA
1 AACCTAATTTAAGTG-TGTTTGCAATGACA-TGAAATCTGTTTTAGATGTTGTTAGTGATGA
4463 AACAAATTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
65 13 0.25
66 38 0.73
67 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (65 bp):
AACCTAATTTAAGTGTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACCA
Found at i:4476 original size:33 final size:32
Alignment explanation
Indices: 4368--4510 Score: 126
Period size: 33 Copynumber: 4.3 Consensus size: 32
4358 CAATGACATG
* * *
4368 AAATCTGTTTTAGATGTTGTTAGTGATGATACC
1 AAATCTGTTTTAGGTGTTGTTTGTGATGA-AAC
* ** * *
4401 AAACCTAATTTAAGTGTTGTTTGTGATGACAC
1 AAATCTGTTTTAGGTGTTGTTTGTGATGAAAC
*
4433 TAAATTTGTTTTAGGTGTTGTTTGTGATGAAAC
1 -AAATCTGTTTTAGGTGTTGTTTGTGATGAAAC
* **
4466 AAATTCTGTTTT-GGATGCTAATTGTGATGAAAAC
1 AAA-TCTGTTTTAGG-TGTTGTTTGTGATG-AAAC
4500 AAATCTGTTTT
1 AAATCTGTTTT
4511 GGTTGATCAT
Statistics
Matches: 88, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
32 6 0.07
33 75 0.85
34 7 0.08
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (32 bp):
AAATCTGTTTTAGGTGTTGTTTGTGATGAAAC
Found at i:7960 original size:20 final size:20
Alignment explanation
Indices: 7937--7974 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7927 GAAGAGTTTA
*
7937 AAGCCATCGGAGATCATTTG
1 AAGCCATCAGAGATCATTTG
*
7957 AAGCCATTAGAGATCATT
1 AAGCCATCAGAGATCATT
7975 AACAAAGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AAGCCATCAGAGATCATTTG
Found at i:13017 original size:16 final size:16
Alignment explanation
Indices: 12992--13024 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12982 GGCCCTTTTT
12992 TTTATGTGTGGAATAC
1 TTTATGTGTGGAATAC
*
13008 TTTATTTGTGGAATAC
1 TTTATGTGTGGAATAC
13024 T
1 T
13025 CGTGTGTGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (16 bp):
TTTATGTGTGGAATAC
Found at i:13106 original size:15 final size:16
Alignment explanation
Indices: 13076--13128 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
13066 AGTACCCCGT
*
13076 ATGTATGTAGAATATTC
1 ATGTGTGTA-AATATTC
13093 ATGTGTG-AAATATTC
1 ATGTGTGTAAATATTC
13108 GTATGTGTGTAAAGTATTC
1 --ATGTGTGTAAA-TATTC
13127 AT
1 AT
13129 ATTTGTGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 7 0.23
16 1 0.03
17 15 0.48
18 3 0.10
19 5 0.16
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.42
Consensus pattern (16 bp):
ATGTGTGTAAATATTC
Found at i:13125 original size:19 final size:18
Alignment explanation
Indices: 13073--13136 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
13063 TGGAGTACCC
*
13073 CGTATGTATGTAGAATATT
1 CGTATGTGTGTA-AATATT
13092 C--ATGTGTG-AAATATT
1 CGTATGTGTGTAAATATT
13107 CGTATGTGTGTAAAGTATT
1 CGTATGTGTGTAAA-TATT
* *
13126 CATATTTGTGT
1 CGTATGTGTGT
13137 GAGATATTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 7 0.18
16 1 0.03
17 13 0.34
18 3 0.08
19 14 0.37
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (18 bp):
CGTATGTGTGTAAATATT
Found at i:13144 original size:19 final size:19
Alignment explanation
Indices: 13094--13144 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
13084 AGAATATTCA
*
13094 TGTGTGAAATATTCGTATG
1 TGTGTGAAATATTCATATG
*
13113 TGTGT-AAAGTATTCATATT
1 TGTGTGAAA-TATTCATATG
*
13132 TGTGTGAGATATT
1 TGTGTGAAATATT
13145 AGAATATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.11
19 22 0.81
20 2 0.07
ACGTcount: A:0.27, C:0.04, G:0.24, T:0.45
Consensus pattern (19 bp):
TGTGTGAAATATTCATATG
Done.