Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010148.1 Corchorus capsularis cultivar CVL-1 contig10169, 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: 26129
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4875 original size:73 final size:72
Alignment explanation
Indices: 4789--4935 Score: 206
Period size: 73 Copynumber: 2.0 Consensus size: 72
4779 TTGAGGACAT
*
4789 GAAGGACCCAAGAAACCATTTACGTAAACTTTCGAATTCAAATTG-GTATTGGACGTGTATATGT
1 GAAGGACCCAAGAAACCATTTACGTAAACTTTCGAATTCAAATTGAGT-TTGG-CATGTATATGT
4853 GCCGGTTTG
64 GCCGGTTTG
* * * *
4862 GAAGGACCCAAGAAACCTTTTAGGTAGACTTTCGGATTCAAATTGATGTTTGGCATGTATATGTG
1 GAAGGACCCAAGAAACCATTTACGTAAACTTTCGAATTCAAATTGA-GTTTGGCATGTATATGTG
*
4927 CCTGTTTG
65 CCGGTTTG
4935 G
1 G
4936 TCGGGCCTTG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
73 60 0.91
74 4 0.06
75 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (72 bp):
GAAGGACCCAAGAAACCATTTACGTAAACTTTCGAATTCAAATTGAGTTTGGCATGTATATGTGC
CGGTTTG
Found at i:10720 original size:3 final size:3
Alignment explanation
Indices: 10714--10763 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
10704 TTCTTCCTTG
* *
10714 TCT TCT TCT TCC TCT TCC TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
10762 TC
1 TC
10764 ATGTATGACT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:11782 original size:13 final size:14
Alignment explanation
Indices: 11764--11792 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
11754 AGCCTTTCGG
11764 TTTCTTTTTT-TTT
1 TTTCTTTTTTCTTT
11777 TTTCTTTTTTCTTT
1 TTTCTTTTTTCTTT
11791 TT
1 TT
11793 GGCGGCTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTCTTTTTTCTTT
Found at i:11784 original size:7 final size:7
Alignment explanation
Indices: 11764--11792 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
11754 AGCCTTTCGG
11764 TTTCTTT
1 TTTCTTT
11771 TTT-TTT
1 TTTCTTT
11777 TTTCTTT
1 TTTCTTT
11784 TTTCTTT
1 TTTCTTT
11791 TT
1 TT
11793 GGCGGCTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTCTTT
Found at i:13298 original size:60 final size:60
Alignment explanation
Indices: 13203--13362 Score: 221
Period size: 60 Copynumber: 2.7 Consensus size: 60
13193 TGAGATAGAT
* ** * * * * *
13203 ACTTATTTGATCGGTTTGGCAAACGTTAGGTCCTTATTTTGCCAAATTCAAAGATCATAC
1 ACTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCAGAC
*
13263 ACTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAAATCAGAC
1 ACTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCAGAC
* *
13323 CCTTATTTGAGCATTTTGTCAAACGTTAGGCCCTTATTTG
1 ACTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
13363 AACAATTAGC
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 88 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (60 bp):
ACTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATCAGAC
Found at i:13302 original size:31 final size:30
Alignment explanation
Indices: 13264--13363 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 30
13254 AGATCATACA
13264 CTTATTTGAGCATTTTGGCAAACATTAGGCC
1 CTTATTTGAGCATTTT-GCAAACATTAGGCC
** * * * *
13295 CTTATTTG-GCCAAATT-AAAAAATCAGACC
1 CTTATTTGAG-CATTTTGCAAACATTAGGCC
*
13324 CTTATTTGAGCATTTTGTCAAACGTTAGGCC
1 CTTATTTGAGCATTTTG-CAAACATTAGGCC
13355 CTTATTTGA
1 CTTATTTGA
13364 ACAATTAGCC
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
29 21 0.40
30 2 0.04
31 29 0.56
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (30 bp):
CTTATTTGAGCATTTTGCAAACATTAGGCC
Found at i:14078 original size:45 final size:45
Alignment explanation
Indices: 14028--14113 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
14018 ACTTCTCCAA
* * * *
14028 CTCATCATTAATCCGGGGTAGGGATTTTTTAGTAATTCCACCCAC
1 CTCATCATTAATCCGAGGTAGAGATCTTTCAGTAATTCCACCCAC
* *
14073 CTCATCATTAATTCGAGGTAGATATCTTTCAGTAATTCCAC
1 CTCATCATTAATCCGAGGTAGAGATCTTTCAGTAATTCCAC
14114 TACTCTATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (45 bp):
CTCATCATTAATCCGAGGTAGAGATCTTTCAGTAATTCCACCCAC
Found at i:14313 original size:2 final size:2
Alignment explanation
Indices: 14306--14331 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14296 ATATGTAGTG
14306 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
14332 ATTATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14843 original size:42 final size:42
Alignment explanation
Indices: 14792--14874 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
14782 GATTTGTAAA
*
14792 TTTGAAAAATTCGTAGGTGAA-AGTCCAACTGATTCGTAAAAG
1 TTTGAAAAATTCGCAGGTGAATA-TCCAACTGATTCGTAAAAG
*
14834 TTTGAAAAATTCGCAGGTGAATATCCAATTGATTCGTAAAA
1 TTTGAAAAATTCGCAGGTGAATATCCAACTGATTCGTAAAA
14875 CTTGAAAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (42 bp):
TTTGAAAAATTCGCAGGTGAATATCCAACTGATTCGTAAAAG
Found at i:20819 original size:41 final size:41
Alignment explanation
Indices: 20765--20851 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
20755 TCATAATGAT
* *
20765 ATATCGTTCAAAAATAAATCCTTAAAAAAATACATTCTTAA
1 ATATCCTTAAAAAATAAATCCTTAAAAAAATACATTCTTAA
** *
20806 ATATCCTTAAAAAATAAATCCTTTTAAAAATATATTCTTAA
1 ATATCCTTAAAAAATAAATCCTTAAAAAAATACATTCTTAA
*
20847 TTATC
1 ATATC
20852 ATTCAACAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.48, C:0.14, G:0.01, T:0.37
Consensus pattern (41 bp):
ATATCCTTAAAAAATAAATCCTTAAAAAAATACATTCTTAA
Found at i:25585 original size:16 final size:17
Alignment explanation
Indices: 25561--25594 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
25551 GAGGACTAGC
*
25561 TGAGGTGGCA-AAGGAG
1 TGAGCTGGCACAAGGAG
25577 TGAGCTGGCACAAGGAG
1 TGAGCTGGCACAAGGAG
25594 T
1 T
25595 TTGTTGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.12, G:0.44, T:0.15
Consensus pattern (17 bp):
TGAGCTGGCACAAGGAG
Done.