Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020338.1 Corchorus olitorius cultivar O-4 contig20371, 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: 37097
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:764 original size:46 final size:46
Alignment explanation
Indices: 697--788 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
687 TCCTACATGA
*
697 GTCAGGGTTAGCTTCGGATTAGTCGGATACAATATAACTATTAAAG
1 GTCAGGATTAGCTTCGGATTAGTCGGATACAATATAACTATTAAAG
743 GTCAGGATTAGCTTCGGATTAGTCGGATACAATATAACTATTAAAG
1 GTCAGGATTAGCTTCGGATTAGTCGGATACAATATAACTATTAAAG
789 CTCGACCGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (46 bp):
GTCAGGATTAGCTTCGGATTAGTCGGATACAATATAACTATTAAAG
Found at i:11722 original size:19 final size:20
Alignment explanation
Indices: 11692--11750 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
11682 ACCGACCGTT
*
11692 TATTAATATATATAATTAAATA
1 TATT-ATATATATAATTATA-A
*
11714 TATTATATATAT-ATGATAA
1 TATTATATATATAATTATAA
11733 TATTATATATATAATTAT
1 TATTATATATATAATTAT
11751 TAAACGGTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 13 0.39
20 8 0.24
21 8 0.24
22 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTATATATATAATTATAA
Found at i:11739 original size:15 final size:15
Alignment explanation
Indices: 11691--11752 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
11681 AACCGACCGT
11691 TTATTA-ATATAT-A
1 TTATTATATATATAA
*
11704 TAATTA-A-ATAT-A
1 TTATTATATATATAA
11716 TTATATATATATGATAA
1 TTAT-TATATAT-ATAA
11733 -TATTATATATATAA
1 TTATTATATATATAA
11747 TTATTA
1 TTATTA
11753 AACGGTCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
12 8 0.20
13 8 0.20
14 5 0.12
15 14 0.34
16 5 0.12
17 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TTATTATATATATAA
Found at i:12766 original size:13 final size:13
Alignment explanation
Indices: 12750--12774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12740 TAAGCCAGAG
12750 TTTTAATTAGTTA
1 TTTTAATTAGTTA
12763 TTTTAATTAGTT
1 TTTTAATTAGTT
12775 TAAAATAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTTAATTAGTTA
Found at i:28895 original size:30 final size:31
Alignment explanation
Indices: 28835--28895 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
28825 CAGGGTGAAG
* *
28835 GAGGAAGATTGGGAATTAAAAAATTGTGTTT
1 GAGGAAGATTGGGAATTAAAAAACTATGTTT
28866 GAGGAA-ACTTGGGAATT-AAAAACTATGTTT
1 GAGGAAGA-TTGGGAATTAAAAAACTATGTTT
28896 TTGTAAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.31
Consensus pattern (31 bp):
GAGGAAGATTGGGAATTAAAAAACTATGTTT
Found at i:30047 original size:25 final size:27
Alignment explanation
Indices: 29997--30049 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 27
29987 TCCTTTGATT
*
29997 TAAACTATTCATTTGAAATTGTTTGCA
1 TAAACTATTCATTTGAAATTGCTTGCA
30024 TAAA-TATTCATTT-AAATTGCTTGCA
1 TAAACTATTCATTTGAAATTGCTTGCA
30049 T
1 T
30050 TTAGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 12 0.48
26 9 0.36
27 4 0.16
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (27 bp):
TAAACTATTCATTTGAAATTGCTTGCA
Found at i:30585 original size:184 final size:184
Alignment explanation
Indices: 30276--30645 Score: 731
Period size: 184 Copynumber: 2.0 Consensus size: 184
30266 CACAAAAAAT
30276 GGAAATTAAGAACATTAAAAAAAATGAGGATTCATGTTTCTTTTCTCAATAAGTACATTGATTAC
1 GGAAATTAAGAACATTAAAAAAAATGAGGATTCATGTTTCTTTTCTCAATAAGTACATTGATTAC
30341 AATTGTTTCCTAAGGATCTTGCAGCCTTCATCATGTAATGGGCTTTATAGCGCTGCCTTGTTCTA
66 AATTGTTTCCTAAGGATCTTGCAGCCTTCATCATGTAATGGGCTTTATAGCGCTGCCTTGTTCTA
*
30406 CAGATATCTTCAATAGAGTTTTGCCTGTCAAACAAAGGTAATACAGTCCCCCAG
131 CAGATATCTTCAATAGAATTTTGCCTGTCAAACAAAGGTAATACAGTCCCCCAG
30460 GGAAATTAAGAACATTAAAAAAAATGAGGATTCATGTTTCTTTTCTCAATAAGTACATTGATTAC
1 GGAAATTAAGAACATTAAAAAAAATGAGGATTCATGTTTCTTTTCTCAATAAGTACATTGATTAC
30525 AATTGTTTCCTAAGGATCTTGCAGCCTTCATCATGTAATGGGCTTTATAGCGCTGCCTTGTTCTA
66 AATTGTTTCCTAAGGATCTTGCAGCCTTCATCATGTAATGGGCTTTATAGCGCTGCCTTGTTCTA
30590 CAGATATCTTCAATAGAATTTTGCCTGTCAAACAAAGGTAATACAGTCCCCCAG
131 CAGATATCTTCAATAGAATTTTGCCTGTCAAACAAAGGTAATACAGTCCCCCAG
30644 GG
1 GG
30646 TAATAGGTAG
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 185 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (184 bp):
GGAAATTAAGAACATTAAAAAAAATGAGGATTCATGTTTCTTTTCTCAATAAGTACATTGATTAC
AATTGTTTCCTAAGGATCTTGCAGCCTTCATCATGTAATGGGCTTTATAGCGCTGCCTTGTTCTA
CAGATATCTTCAATAGAATTTTGCCTGTCAAACAAAGGTAATACAGTCCCCCAG
Done.