Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018730.1 Corchorus olitorius cultivar O-4 contig18763, 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: 8250
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.21
Found at i:1951 original size:21 final size:21
Alignment explanation
Indices: 1911--1951 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1901 TACAGCTGCA
*
1911 CCACACACACATATGAATATT
1 CCACACACACATATCAATATT
1932 CCACACACACAT-TCACATAT
1 CCACACACACATATCA-ATAT
1952 GAATATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.41, C:0.34, G:0.02, T:0.22
Consensus pattern (21 bp):
CCACACACACATATCAATATT
Found at i:1969 original size:19 final size:19
Alignment explanation
Indices: 1945--2041 Score: 89
Period size: 19 Copynumber: 5.3 Consensus size: 19
1935 CACACACATT
1945 CACATATGAATATTCTACA
1 CACATATGAATATTCTACA
**
1964 CACATACAAATA-TCTCACA
1 CACATATGAATATTCT-ACA
*
1983 CATATATGAATACTT-TACA
1 CACATATGAATA-TTCTACA
*
2002 CACATACGAATATT-T-CA
1 CACATATGAATATTCTACA
2019 CAC--ATGAATATTCTACA
1 CACATATGAATATTCTACA
*
2036 TACATA
1 CACATA
2042 CGGGGTACTC
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
15 8 0.13
16 1 0.02
17 9 0.15
18 6 0.10
19 36 0.58
20 1 0.02
21 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (19 bp):
CACATATGAATATTCTACA
Found at i:1976 original size:25 final size:27
Alignment explanation
Indices: 1912--1967 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1902 ACAGCTGCAC
*
1912 CACACACACATATGAATATTCCACACA
1 CACATACACATATGAATATTCCACACA
* *
1939 CACATTCACATATGAATATTCTACACA
1 CACATACACATATGAATATTCCACACA
1966 CA
1 CA
1968 TACAAATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.30, G:0.04, T:0.23
Consensus pattern (27 bp):
CACATACACATATGAATATTCCACACA
Found at i:1982 original size:17 final size:17
Alignment explanation
Indices: 1962--2023 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
1952 GAATATTCTA
*
1962 CACACATACAAATATCT
1 CACACATACAAATATTT
*
1979 CACACATATATGAATACTTT
1 CACACATACA--AATA-TTT
*
1999 ACACACATACGAATATTT
1 -CACACATACAAATATTT
2017 CACACAT
1 CACACAT
2024 GAATATTCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 16 0.43
18 3 0.08
19 8 0.22
20 2 0.05
21 8 0.22
ACGTcount: A:0.44, C:0.26, G:0.03, T:0.27
Consensus pattern (17 bp):
CACACATACAAATATTT
Found at i:1992 original size:38 final size:36
Alignment explanation
Indices: 1945--2042 Score: 121
Period size: 38 Copynumber: 2.7 Consensus size: 36
1935 CACACACATT
1945 CACATATGAATATTCTACACACATACAAATATCTCA
1 CACATATGAATATTCTACACACATACAAATATCTCA
* *
1981 CACATATATGAATACTT-TACACACATACGAATATTTCA
1 CAC--ATATGAATA-TTCTACACACATACAAATATCTCA
*
2019 CAC--ATGAATATTCTACATACATAC
1 CACATATGAATATTCTACACACATAC
2043 GGGGTACTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
33 2 0.04
34 17 0.31
36 3 0.05
38 31 0.56
39 2 0.04
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (36 bp):
CACATATGAATATTCTACACACATACAAATATCTCA
Found at i:2040 original size:17 final size:17
Alignment explanation
Indices: 1945--2040 Score: 56
Period size: 17 Copynumber: 5.4 Consensus size: 17
1935 CACACACATT
*
1945 CACATATGAATATTCTA
1 CACACATGAATATTCTA
*
1962 CACACAT-ACAAATATCTCA
1 CACACATGA-ATAT-TCT-A
*
1981 CACATATATGAATACTT-TA
1 CAC--ACATGAATA-TTCTA
2000 CACACATACGAATATT-T-
1 CACACAT--GAATATTCTA
2017 CACACATGAATATTCTA
1 CACACATGAATATTCTA
*
2034 CATACAT
1 CACACAT
2041 ACGGGGTACT
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
15 7 0.11
16 2 0.03
17 25 0.40
18 6 0.10
19 13 0.21
20 1 0.02
21 6 0.10
22 2 0.03
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (17 bp):
CACACATGAATATTCTA
Found at i:2115 original size:16 final size:16
Alignment explanation
Indices: 2094--2126 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2084 CACACACATG
2094 AGTATTCCACAAATAA
1 AGTATTCCACAAATAA
*
2110 AGTATTCCACACATAA
1 AGTATTCCACAAATAA
2126 A
1 A
2127 AAAGGGCCAC
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:0.48, C:0.21, G:0.06, T:0.24
Consensus pattern (16 bp):
AGTATTCCACAAATAA
Done.