Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001986.1 Corchorus olitorius cultivar O-4 contig01986, 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: 2595
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Found at i:830 original size:15 final size:14
Alignment explanation
Indices: 798--835 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
788 AGAACTTGAC
798 TTTTTTTT-AGATG
1 TTTTTTTTAAGATG
*
811 TTTTTTTTAAGATT
1 TTTTTTTTAAGATG
825 TATTTTTTTAA
1 T-TTTTTTTAA
836 AAGGATTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 5 0.23
15 9 0.41
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (14 bp):
TTTTTTTTAAGATG
Found at i:851 original size:24 final size:24
Alignment explanation
Indices: 822--868 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
812 TTTTTTTAAG
*
822 ATTTATTTTTTTAAAAGGATTAGT
1 ATTTATTTTTGTAAAAGGATTAGT
846 ATTTATTTTTGTAAAAGGATTAG
1 ATTTATTTTTGTAAAAGGATTAG
869 GGTATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTTATTTTTGTAAAAGGATTAGT
Found at i:876 original size:24 final size:24
Alignment explanation
Indices: 825--876 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
815 TTTTAAGATT
* * *
825 TATTTTTTTAAAAGGATTAGTATT
1 TATTTTTGTAAAAGGATTAGGATA
*
849 TATTTTTGTAAAAGGATTAGGGTA
1 TATTTTTGTAAAAGGATTAGGATA
873 TATT
1 TATT
877 AAGAGATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (24 bp):
TATTTTTGTAAAAGGATTAGGATA
Found at i:1626 original size:23 final size:23
Alignment explanation
Indices: 1596--1645 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
1586 GATGTTTTTT
1596 TTAGATTTATTTTT-TAAAAGGA
1 TTAGATTTATTTTTGTAAAAGGA
1618 TTAGTATTTATTTTTGTAAAAGGA
1 TTAG-ATTTATTTTTGTAAAAGGA
1642 TTAG
1 TTAG
1646 GGTATATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 4 0.15
23 10 0.38
24 12 0.46
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (23 bp):
TTAGATTTATTTTTGTAAAAGGA
Found at i:1653 original size:24 final size:23
Alignment explanation
Indices: 1603--1653 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
1593 TTTTTAGATT
* *
1603 TATTTTTTAAAAGGATTAGTATT
1 TATTTTTTAAAAGGATTAGGATA
*
1626 TATTTTTGTAAAAGGATTAGGGTA
1 TATTTTT-TAAAAGGATTAGGATA
1650 TATT
1 TATT
1654 AAGAGATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (23 bp):
TATTTTTTAAAAGGATTAGGATA
Found at i:1788 original size:6 final size:6
Alignment explanation
Indices: 1770--1799 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1760 GTTTAGACTT
1770 ATATAG TATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATA
1800 TATAATTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:1794 original size:12 final size:13
Alignment explanation
Indices: 1770--1803 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1760 GTTTAGACTT
1770 ATATAGTATATAG
1 ATATAGTATATAG
1783 ATATAG-ATATAG
1 ATATAGTATATAG
1795 ATATA-TATA
1 ATATAGTATA
1804 ATTCGTCGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (13 bp):
ATATAGTATATAG
Found at i:2127 original size:19 final size:19
Alignment explanation
Indices: 2103--2159 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
2093 AATAACTCTA
2103 ATATGTATTTATCAAATCC
1 ATATGTATTTATCAAATCC
* *
2122 ATATGTATTTA-AAAATCTA
1 ATATGTATTTATCAAATC-C
2141 ATATGTATTTATCAAATCC
1 ATATGTATTTATCAAATCC
2160 GATTAACATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.16
19 22 0.69
20 5 0.16
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (19 bp):
ATATGTATTTATCAAATCC
Done.