Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014885.1 Corchorus olitorius cultivar O-4 contig14918, 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: 17248
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Found at i:4019 original size:16 final size:16
Alignment explanation
Indices: 3994--4037 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
3984 CGCCCGAACT
3994 CGAACCCGAAATTACC
1 CGAACCCGAAATTACC
* *
4010 CGAGCCCGAAAATACC
1 CGAACCCGAAATTACC
4026 CGAACCCGAAAT
1 CGAACCCGAAAT
4038 AATTTGAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.39, C:0.36, G:0.16, T:0.09
Consensus pattern (16 bp):
CGAACCCGAAATTACC
Found at i:4525 original size:31 final size:31
Alignment explanation
Indices: 4456--4527 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
4446 GTCTATCAAC
*
4456 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
**
4487 TAATAATTTGTTTAATTTAATG-C-TTAATTT
1 TTTTAATTTGTTTAATTTAA-GACTTTAATTT
4517 ATTTTAATTTG
1 -TTTTAATTTG
4528 CAATAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 6 0.18
31 27 0.79
32 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:4817 original size:13 final size:12
Alignment explanation
Indices: 4781--4827 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
4771 TCAATCTTTA
*
4781 TATATATTGATAA
1 TATATATT-ATAT
*
4794 TA-ATGTTATAT
1 TATATATTATAT
4805 TATATTATTATAT
1 TATA-TATTATAT
4818 TATATATTAT
1 TATATATTAT
4828 CGATAACCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:4976 original size:17 final size:17
Alignment explanation
Indices: 4956--5004 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
4946 AAATCAAACT
4956 CGAGCCCGAACTCGACC
1 CGAGCCCGAACTCGACC
* *
4973 CGAGCCCGAACCCTACC
1 CGAGCCCGAACTCGACC
*
4990 CGAGACCGAACTCGA
1 CGAGCCCGAACTCGA
5005 AAATACCGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.27, C:0.45, G:0.22, T:0.06
Consensus pattern (17 bp):
CGAGCCCGAACTCGACC
Found at i:5031 original size:16 final size:16
Alignment explanation
Indices: 5010--5059 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
5000 CTCGAAAATA
5010 CCGAACCCGACATAAC
1 CCGAACCCGACATAAC
*
5026 CCGAACCCGAAAATAA-
1 CCGAACCCG-ACATAAC
*
5042 CCGAACCCGACTTAAC
1 CCGAACCCGACATAAC
5058 CC
1 CC
5060 AAGCCCGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 4 0.14
16 20 0.69
17 5 0.17
ACGTcount: A:0.38, C:0.42, G:0.12, T:0.08
Consensus pattern (16 bp):
CCGAACCCGACATAAC
Found at i:5045 original size:32 final size:32
Alignment explanation
Indices: 4995--5081 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
4985 CTACCCGAGA
*
4995 CCGAACTCGAAAAT-ACCGAACCCGACATAAC
1 CCGAACCCGAAAATAACCGAACCCGACATAAC
*
5026 CCGAACCCGAAAATAACCGAACCCGACTTAAC
1 CCGAACCCGAAAATAACCGAACCCGACATAAC
*
5058 CC-AAGCCCGAAAATATCCGAACCC
1 CCGAA-CCCGAAAATAACCGAACCC
5082 AAAAAAGCCC
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
31 15 0.29
32 36 0.71
ACGTcount: A:0.40, C:0.38, G:0.13, T:0.09
Consensus pattern (32 bp):
CCGAACCCGAAAATAACCGAACCCGACATAAC
Found at i:6580 original size:16 final size:17
Alignment explanation
Indices: 6559--6593 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
6549 TAATAAACAA
6559 TAACATTGTCTC-AAGT
1 TAACATTGTCTCTAAGT
*
6575 TAACATTGTTTCTAAGT
1 TAACATTGTCTCTAAGT
6592 TA
1 TA
6594 GATAACTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (17 bp):
TAACATTGTCTCTAAGT
Done.