Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023203.1 Corchorus olitorius cultivar O-4 contig23236, 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: 13913
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Found at i:2013 original size:12 final size:12
Alignment explanation
Indices: 1986--2019 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1976 GAAGTTCGTG
*
1986 TTTGAAGAC-CA
1 TTTGAAGACTTA
1997 TTTGAAGACTTA
1 TTTGAAGACTTA
2009 TTTGAAGACTT
1 TTTGAAGACTT
2020 TGAAGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTTA
Found at i:2023 original size:21 final size:23
Alignment explanation
Indices: 1986--2037 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
1976 GAAGTTCGTG
1986 TTTGAAGACCATTTGAAGACTTA
1 TTTGAAGACCATTTGAAGACTTA
*
2009 TTTGAAGA-C-TTTGAAGATTTA
1 TTTGAAGACCATTTGAAGACTTA
*
2030 TTTCAAGA
1 TTTGAAGA
2038 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 18 0.67
22 1 0.04
23 8 0.30
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (23 bp):
TTTGAAGACCATTTGAAGACTTA
Found at i:3803 original size:39 final size:40
Alignment explanation
Indices: 3713--3814 Score: 100
Period size: 39 Copynumber: 2.5 Consensus size: 40
3703 AAAAAAATTT
* *
3713 GTCTGCGTCTTTTCTTAAAAAATTTCGTTTTTAATTTTGA
1 GTCTGCATTTTTTCTTAAAAAATTTCGTTTTTAATTTTGA
* ** *
3753 GTCTGCGTTTTTTC-TAAAAAATTT-GTTTTGTGTTTTTGT
1 GTCTGCATTTTTTCTTAAAAAATTTCGTTTT-TAATTTTGA
* *
3792 GTTTGCATTTTTTTTTGAAAAAA
1 GTCTGCATTTTTTCTT-AAAAAA
3815 AAAAGAATCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
38 5 0.10
39 27 0.52
40 14 0.27
41 6 0.12
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.55
Consensus pattern (40 bp):
GTCTGCATTTTTTCTTAAAAAATTTCGTTTTTAATTTTGA
Found at i:3947 original size:35 final size:33
Alignment explanation
Indices: 3866--3947 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 33
3856 TCTGCGTCAC
* *
3866 AAAAAAAATTTTTGTTTTGCGTGTTCTAAAAAA
1 AAAAAAAATTCTTGTTCTGCGTGTTCTAAAAAA
* *
3899 AAAGAAAATTTCTTGTTCCTGCGT-TTTTAGAAAAGA
1 AAA-AAAAATTCTTGTT-CTGCGTGTTCTA-AAAA-A
3935 AAAAAAAATTCTT
1 AAAAAAAATTCTT
3948 TTATTTTCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 3 0.08
34 15 0.38
35 18 0.45
36 4 0.10
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.37
Consensus pattern (33 bp):
AAAAAAAATTCTTGTTCTGCGTGTTCTAAAAAA
Found at i:6980 original size:21 final size:21
Alignment explanation
Indices: 6956--7005 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
6946 CGCCCATTCA
**
6956 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
6977 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
6998 CCGTGCCA
1 CCGTGCCA
7006 TCGCCATTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:7391 original size:15 final size:16
Alignment explanation
Indices: 7363--7393 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7353 ATCTTTTTAA
7363 TTTTCCTTGCATTATT
1 TTTTCCTTGCATTATT
7379 TTTTCCTTG-ATTATT
1 TTTTCCTTGCATTATT
7394 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.13, C:0.16, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTTCCTTGCATTATT
Found at i:8896 original size:29 final size:31
Alignment explanation
Indices: 8844--8903 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
8834 GAAGTTCATG
*
8844 TTTGAAGACCATTTGAAGACTTATTTGAAGA
1 TTTGAAGACCATTTGAAGACTTATTTCAAGA
*
8875 TTTGAAGA-C-TTTGAAGATTTATTTCAAGA
1 TTTGAAGACCATTTGAAGACTTATTTCAAGA
8904 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
30 1 0.04
31 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (31 bp):
TTTGAAGACCATTTGAAGACTTATTTCAAGA
Found at i:13444 original size:28 final size:28
Alignment explanation
Indices: 13404--13500 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
13394 TCTATTTCTG
13404 ATTTTGGTCATTTTGCATGACCAGGGGC
1 ATTTTGGTCATTTTGCATGACCAGGGGC
*
13432 ATTTTGGTCATTTTGCATGACCATGGGC
1 ATTTTGGTCATTTTGCATGACCAGGGGC
* *
13460 ATTTTGGTCATTTTGTACAT--CTAGGGAC
1 ATTTTGGTCATTTTG--CATGACCAGGGGC
13488 ATTTTGGTCATTT
1 ATTTTGGTCATTT
13501 CAAGAACCTT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
28 60 0.95
30 3 0.05
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (28 bp):
ATTTTGGTCATTTTGCATGACCAGGGGC
Done.