Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014534.1 Corchorus capsularis cultivar CVL-1 contig14555, 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: 52440
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5185 original size:2 final size:2
Alignment explanation
Indices: 5180--5216 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5170 TATTTTCCGA
5180 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5217 CTAATATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14732 original size:32 final size:31
Alignment explanation
Indices: 14688--14758 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 31
14678 CGCTCTAGTG
14688 GGGCGGCTTGACCATGGTAAGTCGCCCTCCT
1 GGGCGGCTTGACCATGGTAAGTCGCCCTCCT
14719 GGGACGGCTTGACCATGGTAAGTCGCCCTCCT
1 GGG-CGGCTTGACCATGGTAAGTCGCCCTCCT
14751 AGGGCGGC
1 -GGGCGGC
14759 ACGGGTCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
31 3 0.08
32 32 0.84
33 3 0.08
ACGTcount: A:0.14, C:0.31, G:0.35, T:0.20
Consensus pattern (31 bp):
GGGCGGCTTGACCATGGTAAGTCGCCCTCCT
Found at i:15965 original size:13 final size:13
Alignment explanation
Indices: 15949--15979 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
15939 GATAACCCTT
15949 GTTTATAAAAGGA
1 GTTTATAAAAGGA
*
15962 GTTTATAAAATGA
1 GTTTATAAAAGGA
15975 GTTTA
1 GTTTA
15980 ATATAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (13 bp):
GTTTATAAAAGGA
Found at i:16870 original size:15 final size:15
Alignment explanation
Indices: 16850--16882 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
16840 AAGAGAAATC
16850 AAAAAGGAA-AAAACA
1 AAAAAGGAATAAAA-A
16865 AAAAAGGAATAAAAA
1 AAAAAGGAATAAAAA
16880 AAA
1 AAA
16883 GTGATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAGGAATAAAAA
Found at i:17897 original size:3 final size:3
Alignment explanation
Indices: 17889--17916 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17879 AAGTAAGATT
17889 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
17917 CCTGATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:19767 original size:12 final size:12
Alignment explanation
Indices: 19752--19782 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19742 TCCTTGTGCA
19752 TTTATAAATGTG
1 TTTATAAATGTG
*
19764 TTTAAAAATGTG
1 TTTATAAATGTG
19776 TTTATAA
1 TTTATAA
19783 TTTAAATCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (12 bp):
TTTATAAATGTG
Found at i:30232 original size:42 final size:42
Alignment explanation
Indices: 30174--30259 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
30164 CACCTCTCCG
*
30174 CCGCTACCGTTGCCACCACGAACCGGGGCATAAGAGCCCTTT
1 CCGCTACCGTTGCCACCACGAACCGAGGCATAAGAGCCCTTT
* *
30216 CCGCTACCGTTGCCACCACGACCCGAGGCGTAAGAGCCCTTT
1 CCGCTACCGTTGCCACCACGAACCGAGGCATAAGAGCCCTTT
30258 CC
1 CC
30260 TTTCCCCTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.20, C:0.41, G:0.23, T:0.16
Consensus pattern (42 bp):
CCGCTACCGTTGCCACCACGAACCGAGGCATAAGAGCCCTTT
Found at i:34789 original size:10 final size:10
Alignment explanation
Indices: 34774--34800 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
34764 TAGTAGCACT
34774 AGCAGCAGCC
1 AGCAGCAGCC
34784 AGCAGCAGCC
1 AGCAGCAGCC
34794 AGCAGCA
1 AGCAGCA
34801 ACATCAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.33, C:0.37, G:0.30, T:0.00
Consensus pattern (10 bp):
AGCAGCAGCC
Found at i:44865 original size:12 final size:12
Alignment explanation
Indices: 44848--44872 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44838 GGCTCCTTAG
44848 CACTTTGCATAT
1 CACTTTGCATAT
44860 CACTTTGCATAT
1 CACTTTGCATAT
44872 C
1 C
44873 CTTCATCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (12 bp):
CACTTTGCATAT
Found at i:47213 original size:1 final size:1
Alignment explanation
Indices: 47207--47243 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
47197 TTATTTTAAT
*
47207 AAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
47244 CCGAAAATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:50860 original size:6 final size:6
Alignment explanation
Indices: 50851--50875 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
50841 CATTTTCGCC
50851 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
50876 ATGGTTGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:51561 original size:6 final size:6
Alignment explanation
Indices: 51550--51574 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
51540 ACAGCGCATT
51550 CGAGTC CGAGTC CGAGTC CGAGTC C
1 CGAGTC CGAGTC CGAGTC CGAGTC C
51575 ATCTCTGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (6 bp):
CGAGTC
Done.