Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009832.1 Corchorus olitorius cultivar O-4 contig09864, 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: 3760
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Found at i:1776 original size:27 final size:27
Alignment explanation
Indices: 1724--1874 Score: 102
Period size: 23 Copynumber: 6.2 Consensus size: 27
1714 AAGATAATAA
* * *
1724 TAATACATAAATAGAT-AATAACTAAAT
1 TAATAAATAAAAAGATAAAT-AGTAAAT
*
1751 TAATAAAGAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
*
1775 -AATAAATAAATA-AT-AAT--TAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
1797 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
1821 -AATAAATAGATA-AT-AAT--TAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
1843 TAATAAATAAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
*
1870 AAATA
1 TAATA
1875 GACAATAGTT
Statistics
Matches: 95, Mismatches: 12, Indels: 34
0.67 0.09 0.24
Matches are distributed among these distances:
19 2 0.02
21 8 0.08
22 4 0.04
23 41 0.43
24 4 0.04
25 8 0.08
27 25 0.26
28 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:1787 original size:19 final size:19
Alignment explanation
Indices: 1765--1970 Score: 104
Period size: 19 Copynumber: 11.5 Consensus size: 19
1755 AAAGAAAAAG
1765 ATAAATAGTAAATAAATAA
1 ATAAATAGTAAATAAATAA
* *
1784 AT-AATAATTAAATTAATAA
1 ATAAAT-AGTAAATAAATAA
* *
1803 ATAAAAAGATAAAT-AGTAA
1 ATAAATAG-TAAATAAATAA
1822 ATAAATAG---AT-AATAA
1 ATAAATAGTAAATAAATAA
* *
1837 TTAAATTAATAAATAAA-AA
1 ATAAA-TAGTAAATAAATAA
*
1856 GATAAATAGTAAATAAATAG
1 -ATAAATAGTAAATAAATAA
* *
1876 A-CAATAGTTAA-AAATAA
1 ATAAATAGTAAATAAATAA
* **
1893 ATAAAAAGATAAAT-AGCAA
1 ATAAATAG-TAAATAAATAA
*
1912 ATAAATAG---AT-AATAG
1 ATAAATAGTAAATAAATAA
* *
1927 TTAAA-A-TAAATAAAAAA
1 ATAAATAGTAAATAAATAA
*
1944 ATAAATAGTAAATAAATAG
1 ATAAATAGTAAATAAATAA
1963 AT-AATAGT
1 ATAAATAGT
1971 TTAAAAAAAT
Statistics
Matches: 138, Mismatches: 30, Indels: 39
0.67 0.14 0.19
Matches are distributed among these distances:
14 1 0.01
15 18 0.13
16 4 0.03
17 13 0.09
18 22 0.16
19 66 0.48
20 14 0.10
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (19 bp):
ATAAATAGTAAATAAATAA
Found at i:1788 original size:46 final size:46
Alignment explanation
Indices: 1707--2009 Score: 383
Period size: 46 Copynumber: 6.7 Consensus size: 46
1697 AATAGGTAGC
* * *
1707 TAAA-AAAAAGATAATAATAATACATAAATAGATAATAACTAAATTAA
1 TAAATAAAAAGAT-A-AATAGTAAATAAATAGATAATAATTAAATTAA
* *
1754 TAAAGAAAAAGATAAATAGTAAATAAATAAATAATAATTAAATTAA
1 TAAATAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
1800 TAAATAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
1 TAAATAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
* *
1846 TAAATAAAAAGATAAATAGTAAATAAATAGACAATAGTTAAA--AA
1 TAAATAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
* *
1890 TAAATAAAAAGATAAATAGCAAATAAATAGATAATAGTT-AA--AA
1 TAAATAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
* * *
1933 TAAATAAAAAAATAAATAGTAAATAAATAGATAATAGTTTAA--AA
1 TAAATAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
* *
1977 -AAATAAAAAAAATAAATAGTGAATAAATA-ATAA
1 TAAAT-AAAAAGATAAATAGTAAATAAATAGATAA
2010 AAAAAATCTT
Statistics
Matches: 240, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
43 49 0.20
44 66 0.28
46 112 0.47
47 5 0.02
48 8 0.03
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (46 bp):
TAAATAAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAA
Found at i:1960 original size:27 final size:27
Alignment explanation
Indices: 1746--1966 Score: 95
Period size: 27 Copynumber: 8.6 Consensus size: 27
1736 AGATAATAAC
* * *
1746 TAAATTAATAAAGAAAAAGATAAATAG
1 TAAATAAATAAATAAAAAAATAAATAG
1773 TAAATAAATAAAT-----AAT-AAT--
1 TAAATAAATAAATAAAAAAATAAATAG
* *
1792 TAAATTAATAAATAAAAAGATAAATAG
1 TAAATAAATAAATAAAAAAATAAATAG
*
1819 TAAATAAATAGAT-----AAT-AAT--
1 TAAATAAATAAATAAAAAAATAAATAG
* *
1838 TAAATTAATAAATAAAAAGATAAATAG
1 TAAATAAATAAATAAAAAAATAAATAG
*
1865 TAAATAAATAGACAATAGTTAAAAATAAATA-
1 TAAATAAAT--A-AATA--AAAAAATAAATAG
* **
1896 -AAA-AGATAAAT-AGCAAATAAATAG
1 TAAATAAATAAATAAAAAAATAAATAG
1920 ATAATAGTTAAAATAAATAAAAAAATAAATAG
1 -TAA-A--T-AAATAAATAAAAAAATAAATAG
*
1952 TAAATAAATAGATAA
1 TAAATAAATAAATAA
1967 TAGTTTAAAA
Statistics
Matches: 142, Mismatches: 22, Indels: 60
0.63 0.10 0.27
Matches are distributed among these distances:
19 23 0.16
21 6 0.04
22 4 0.03
23 9 0.06
24 4 0.03
25 6 0.04
26 5 0.04
27 41 0.29
28 1 0.01
29 4 0.03
30 8 0.06
31 10 0.07
32 21 0.15
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (27 bp):
TAAATAAATAAATAAAAAAATAAATAG
Found at i:1966 original size:8 final size:8
Alignment explanation
Indices: 1644--1957 Score: 108
Period size: 8 Copynumber: 40.1 Consensus size: 8
1634 ATAAAAAAAA
1644 AGATAAAT
1 AGATAAAT
* *
1652 AGATATAG
1 AGATAAAT
1660 AGATAAAT
1 AGATAAAT
1668 AGATAAAT
1 AGATAAAT
* *
1676 AGATACAG
1 AGATAAAT
1684 AGA-ATAAT
1 AGATA-AAT
1692 AGATAAAT
1 AGATAAAT
* **
1700 AGGTAGCT
1 AGATAAAT
* *
1708 A-AAAAAA
1 AGATAAAT
1715 AGAT-AAT
1 AGATAAAT
1722 A-AT-AAT
1 AGATAAAT
*
1728 ACATAAAT
1 AGATAAAT
1736 AGAT-AAT
1 AGATAAAT
1743 A-ACTAAATT
1 AGA-TAAA-T
1752 A-AT-AA-
1 AGATAAAT
1757 AGA-AAA-
1 AGATAAAT
1763 AGATAAAT
1 AGATAAAT
1771 AG-TAAAT
1 AGATAAAT
*
1778 AAATAAAT
1 AGATAAAT
*
1786 A-ATAATT
1 AGATAAAT
* *
1793 AAATTAAT
1 AGATAAAT
* *
1801 AAATAAAA
1 AGATAAAT
1809 AGATAAAT
1 AGATAAAT
1817 AG-TAAAT
1 AGATAAAT
* *
1824 AAATAGAT
1 AGATAAAT
*
1832 A-ATAATT
1 AGATAAAT
* *
1839 AAATTAAT
1 AGATAAAT
* *
1847 AAATAAAA
1 AGATAAAT
1855 AGATAAAT
1 AGATAAAT
1863 AGTAAATAAAT
1 AG---ATAAAT
*
1874 AGA-CAAT
1 AGATAAAT
*
1881 AGTTAAAAAT
1 AG--ATAAAT
* *
1891 AAATAAAA
1 AGATAAAT
1899 AGATAAAT
1 AGATAAAT
1907 AGCAAATAAAT
1 AG---ATAAAT
1918 AGAT-AAT
1 AGATAAAT
*
1925 AGTTAAAAT
1 AGAT-AAAT
* *
1934 AAATAAAA
1 AGATAAAT
*
1942 AAATAAAT
1 AGATAAAT
1950 AG-TAAAT
1 AGATAAAT
1957 A
1 A
1958 AATAGATAAT
Statistics
Matches: 229, Mismatches: 50, Indels: 55
0.69 0.15 0.16
Matches are distributed among these distances:
5 1 0.00
6 13 0.06
7 58 0.25
8 127 0.55
9 10 0.04
10 4 0.02
11 16 0.07
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (8 bp):
AGATAAAT
Done.