Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022345.1 Corchorus olitorius cultivar O-4 contig22378, 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: 19395
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3548 original size:21 final size:21
Alignment explanation
Indices: 3522--3571 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3512 CGGCCATTCA
**
3522 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
3543 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
3564 CCGTGCCA
1 CCGTGCCA
3572 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:3948 original size:15 final size:14
Alignment explanation
Indices: 3928--3957 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3918 ATCTTTTTAA
3928 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
3943 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
3957 T
1 T
3958 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:6851 original size:15 final size:16
Alignment explanation
Indices: 6823--6862 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
6813 TTACTTTGCT
6823 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
6839 TTGTTTT-TAGTTTAA
1 TTGTTTTCTAGTTTAA
*
6854 TTGCTTTCT
1 TTGTTTTCT
6863 GTCAATCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:9356 original size:41 final size:42
Alignment explanation
Indices: 9285--9378 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 42
9275 TTCAATATAA
* * * *
9285 TCCCTGATCTA-AGGTAACATTTGTTAATTGATTCAGTTTTG
1 TCCCTGATTTAGAGGTAACATTTATTAATTGATTCAATTTCG
* *
9326 TCCCTGATTTAGA-GTAATATTTATTTATTGATTCAATTTCG
1 TCCCTGATTTAGAGGTAACATTTATTAATTGATTCAATTTCG
9367 -CCCTTGATTTAG
1 TCCC-TGATTTAG
9379 GATTTTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 3 0.07
41 41 0.91
42 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (42 bp):
TCCCTGATTTAGAGGTAACATTTATTAATTGATTCAATTTCG
Found at i:10577 original size:22 final size:23
Alignment explanation
Indices: 10542--10585 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
10532 AGAGATAGAA
*
10542 AAAAGATCAAAAAAAAAGAAGAG
1 AAAAGATCAAAAAAAAAAAAGAG
*
10565 AAAA-ATCAGAAAAAAAAAAGA
1 AAAAGATCAAAAAAAAAAAAGA
10586 TGCAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (23 bp):
AAAAGATCAAAAAAAAAAAAGAG
Found at i:15956 original size:33 final size:34
Alignment explanation
Indices: 15888--15978 Score: 112
Period size: 33 Copynumber: 2.7 Consensus size: 34
15878 TTTTTACCAA
* *
15888 TTTTACTTTAATTATCAAATACCAATTTTACTCT
1 TTTTACTATAATTACCAAATACCAATTTTACTCT
* *
15922 TTTTACTATATTTACCAAATATCAA-TTTACTCT
1 TTTTACTATAATTACCAAATACCAATTTTACTCT
* * *
15955 TTTTATTCTAATTACCGAATACCA
1 TTTTACTATAATTACCAAATACCA
15979 TTTAACTTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
33 27 0.56
34 21 0.44
ACGTcount: A:0.33, C:0.19, G:0.01, T:0.47
Consensus pattern (34 bp):
TTTTACTATAATTACCAAATACCAATTTTACTCT
Found at i:16025 original size:17 final size:17
Alignment explanation
Indices: 16003--16056 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
15993 CCAAATTTCA
16003 TTTTACCATTTTACTCT
1 TTTTACCATTTTACTCT
*
16020 TTTTA-C-TTTAATCTCT
1 TTTTACCATTTTA-CTCT
*
16036 TTTTACCATATTACTCT
1 TTTTACCATTTTACTCT
16053 TTTT
1 TTTT
16057 GTTTTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 14 0.45
18 3 0.10
ACGTcount: A:0.19, C:0.20, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTACCATTTTACTCT
Found at i:16093 original size:26 final size:27
Alignment explanation
Indices: 16033--16093 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
16023 TACTTTAATC
*
16033 TCTTTTTACCATATTACTCTTTTTGTT
1 TCTTTTTACCAAATTACTCTTTTTGTT
** * *
16060 T-TAATTACCAAATTTC-CTTTTTTTT
1 TCTTTTTACCAAATTACTCTTTTTGTT
16085 TCTTTTTAC
1 TCTTTTTAC
16094 TTTGATTACC
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
25 9 0.35
26 16 0.62
27 1 0.04
ACGTcount: A:0.18, C:0.18, G:0.02, T:0.62
Consensus pattern (27 bp):
TCTTTTTACCAAATTACTCTTTTTGTT
Done.