Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016855.1 Corchorus olitorius cultivar O-4 contig16888, 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: 12545
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:564 original size:73 final size:72
Alignment explanation
Indices: 450--584 Score: 209
Period size: 73 Copynumber: 1.9 Consensus size: 72
440 GAAAATGACA
* *
450 GGAACTTTCCCTAAATTGAAAACTAAAACTTGGTGGGAACTTTCCCAATTCAAAAACTTTGAAAA
1 GGAACTTTCCCTAAATTGAAAACTAAAACTAGGTGGAAACTTTCCCAATTCAAAAACTTTGAAAA
515 TCGAATG
66 TCGAATG
* *
522 GGAACTTTCCC-AATTTGAAAACTTAAAAACTAGGTGGAAACTTTCCCAATTTAAAAACTTTGA
1 GGAACTTTCCCTAAATTGAAAAC-T-AAAACTAGGTGGAAACTTTCCCAATTCAAAAACTTTGA
585 CCTGATAAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
71 10 0.18
72 12 0.21
73 35 0.61
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (72 bp):
GGAACTTTCCCTAAATTGAAAACTAAAACTAGGTGGAAACTTTCCCAATTCAAAAACTTTGAAAA
TCGAATG
Found at i:571 original size:36 final size:35
Alignment explanation
Indices: 450--581 Score: 133
Period size: 36 Copynumber: 3.7 Consensus size: 35
440 GAAAATGACA
* * *
450 GGAACTTTCCCTAAATTGAAAAC-TAAAACTTGGTG
1 GGAACTTTCCC-AATTTAAAAACTTAAAACTAGGTG
* * *
485 GGAACTTTCCCAATTCAAAAACTTTGAAAA-TCGAATG
1 GGAACTTTCCCAATTTAAAAAC-TT-AAAACTAG-GTG
*
522 GGAACTTTCCCAATTTGAAAACTTAAAAACTAGGTG
1 GGAACTTTCCCAATTTAAAAACTT-AAAACTAGGTG
*
558 GAAACTTTCCCAATTTAAAAACTT
1 GGAACTTTCCCAATTTAAAAACTT
582 TGACCTGATA
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
34 8 0.10
35 11 0.14
36 33 0.41
37 28 0.35
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (35 bp):
GGAACTTTCCCAATTTAAAAACTTAAAACTAGGTG
Found at i:6008 original size:15 final size:15
Alignment explanation
Indices: 5988--6031 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
5978 CATTTCCATT
5988 AGGTTTAAGCTTAAA
1 AGGTTTAAGCTTAAA
*
6003 AGGTTTCA-CTTAAA
1 AGGTTTAAGCTTAAA
*
6017 AGGTTTAAGTTTAAA
1 AGGTTTAAGCTTAAA
6032 TTGAGCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (15 bp):
AGGTTTAAGCTTAAA
Found at i:6827 original size:32 final size:32
Alignment explanation
Indices: 6786--6863 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
6776 CACATGTAAA
* **
6786 ATTTTGAAAAAAGTTTGAGGACTTATTTGGTC
1 ATTTTGAAAAAAGGTAAAGGACTTATTTGGTC
**
6818 ATTTTG-AAAAAGGTAAAGGGTTTATTTGGTC
1 ATTTTGAAAAAAGGTAAAGGACTTATTTGGTC
6849 ATTTT-AAAAAAGGTA
1 ATTTTGAAAAAAGGTA
6864 GAGGGCAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
31 34 0.85
32 6 0.15
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (32 bp):
ATTTTGAAAAAAGGTAAAGGACTTATTTGGTC
Found at i:6843 original size:31 final size:31
Alignment explanation
Indices: 6808--6868 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
6798 GTTTGAGGAC
*
6808 TTATTTGGTCATTTTGAAAAAGGTAAAGGGT
1 TTATTTGGTCATTTTAAAAAAGGTAAAGGGT
*
6839 TTATTTGGTCATTTTAAAAAAGGTAGAGGG
1 TTATTTGGTCATTTTAAAAAAGGTAAAGGG
6869 CAAAAAGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (31 bp):
TTATTTGGTCATTTTAAAAAAGGTAAAGGGT
Found at i:7744 original size:13 final size:13
Alignment explanation
Indices: 7726--7752 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7716 AAATGGAAAA
7726 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
7739 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
7752 T
1 T
7753 TCCGTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:10626 original size:58 final size:58
Alignment explanation
Indices: 10530--10642 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 58
10520 ATTAATCAAA
*
10530 TATCAAGTGACATGTTCTTTATTAGATGCATAAGAAAAGACGTTTTCGGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAGAAAAGACGTTTTAGGACCGAGACT
* *
10588 TATCGAGTGACATGTTTTTTTATTAGATGTC-TAA-AAAAGACGTTTTAGGACCGAG
1 TATCAAGTGACATG-TTCTTTATTAGATG-CATAAGAAAAGACGTTTTAGGACCGAG
10643 GCATGATGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 33 0.66
59 16 0.32
60 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAGAAAAGACGTTTTAGGACCGAGACT
Found at i:11961 original size:36 final size:36
Alignment explanation
Indices: 11914--11983 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
11904 TTCAATAACC
*
11914 TTACATCTTTTGT-GATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAG-TTTTGATTATCATATTTCTTA
*
11950 TTACATTTTTTGTAGTTTTGATTATCATATTTCT
1 TTACATCTTTTGTAGTTTTGATTATCATATTTCT
11984 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAGTTTTGATTATCATATTTCTTA
Done.