Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024569.1 Corchorus olitorius cultivar O-4 contig24602, 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: 2032
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Found at i:1746 original size:4 final size:4
Alignment explanation
Indices: 1733--2012 Score: 77
Period size: 4 Copynumber: 71.0 Consensus size: 4
1723 GACCAAAAAG
* * **
1733 ATTT -TTT ATTT ATTT A-CT ATTT ATATT -TTT ATTT ATTA ATTT AACT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
* * * **
1779 A-TT ATCT ATTT ATTT A-CT ATTT ATATT -TTT ATTT ATTA ATTT AACT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
* * * **
1825 A-TT ATCT ATTT ATTT A-CT ATTT ATCTT -TTT ATTT ATTA ATTT AGCT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
* * ** ** * *
1871 A-TT ATCT ATTT ATTT ACTATT ATCT ACTTT -TTT ACCT ACCT CTTT ATCT
1 ATTT ATTT ATTT ATTT A-T-TT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT
* * * ** *
1920 AATT ATCT ATAT ACCT ATTT ATCTT -TTT ATTT ATCT A-TT ATTTT CACTTT
1 ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT A-TTT -A-TTT
* * *
1970 ATTT -TCT ATTT ATTT ATTT ATTT ATCT A-TT ACTTT TTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT
2013 TAATATTTTT
Statistics
Matches: 197, Mismatches: 54, Indels: 50
0.65 0.18 0.17
Matches are distributed among these distances:
3 32 0.16
4 141 0.72
5 17 0.09
6 7 0.04
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (4 bp):
ATTT
Found at i:1765 original size:19 final size:19
Alignment explanation
Indices: 1741--1859 Score: 72
Period size: 19 Copynumber: 6.4 Consensus size: 19
1731 AGATTTTTTA
1741 TTTATTTACTATTTATATT
1 TTTATTTACTATTTATATT
* *
1760 TTTATTTATTAATTTA-ACT
1 TTTATTTACT-ATTTATATT
*
1779 ATTA--T-CTATTTAT-TT
1 TTTATTTACTATTTATATT
** *
1794 ACTATTTA-TATTTTTATT
1 TTTATTTACTATTTATATT
* *
1812 TATTAATTTAACTA-TTATCTA
1 T-TT-ATTT-ACTATTTATATT
*
1833 TTTATTTACTATTTATCTT
1 TTTATTTACTATTTATATT
1852 TTTATTTA
1 TTTATTTA
1860 TTAATTTAGC
Statistics
Matches: 76, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
15 9 0.12
16 1 0.01
17 8 0.11
18 6 0.08
19 33 0.43
20 11 0.14
21 6 0.08
22 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATTTACTATTTATATT
Found at i:1769 original size:27 final size:27
Alignment explanation
Indices: 1737--1821 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 27
1727 AAAAAGATTT
1737 TTTATTTATTTACTATTTATATTTTTA
1 TTTATTTATTTACTATTTATATTTTTA
* * *
1764 TTTATTAATTTAACTA-TTATCTATTTA
1 TTTATTTATTT-ACTATTTATATTTTTA
* *
1791 TTTA-CTATTTA-TATTTTTATTTATTAA
1 TTTATTTATTTACTATTTATATTT-TT-A
1818 TTTA
1 TTTA
1822 ACTATTATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
24 2 0.04
25 6 0.13
26 6 0.13
27 28 0.61
28 4 0.09
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTATTTATTTACTATTTATATTTTTA
Found at i:1806 original size:46 final size:46
Alignment explanation
Indices: 1739--1891 Score: 288
Period size: 46 Copynumber: 3.3 Consensus size: 46
1729 AAAGATTTTT
1739 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1785 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
* *
1831 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAGCTATTATC
1 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1877 TATTTATTTACTATT
1 TATTTATTTACTATT
1892 ATCTACTTTT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 105 1.00
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (46 bp):
TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
Found at i:1829 original size:27 final size:27
Alignment explanation
Indices: 1780--1867 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
1770 AATTTAACTA
* * *
1780 TTATCTATTTATTTACTATTTATATTT
1 TTATTTATTAATTTACTATTTATATAT
*
1807 TTATTTATTAATTTAACTA-TTATCTAT
1 TTATTTATTAATTT-ACTATTTATATAT
* * *
1834 TTATTTACT-ATTTATCTTTTTATTTAT
1 TTATTTATTAATTTA-CTATTTATATAT
*
1861 TAATTTA
1 TTATTTA
1868 GCTATTATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 39 0.78
28 4 0.08
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTTATTAATTTACTATTTATATAT
Found at i:1875 original size:19 final size:18
Alignment explanation
Indices: 1761--1893 Score: 71
Period size: 19 Copynumber: 7.2 Consensus size: 18
1751 ATTTATATTT
1761 TTATTTATTAATTTAACTA
1 TTATTTATTAATTT-ACTA
* *
1780 TTATCTATTTATTTACTA
1 TTATTTATTAATTTACTA
*
1798 TT-TATATT--TTTA-T-
1 TTATTTATTAATTTACTA
*
1811 TTATTAATTTAACTATTATCTA
1 TTATTTA-TTAA-T-TTA-CTA
* *
1833 TTTATTTACT-ATTTATCTTT
1 -TTATTTATTAATTTA-C-TA
1853 TTATTTATTAATTTAGCTA
1 TTATTTATTAATTTA-CTA
* *
1872 TTATCTATTTATTTACTA
1 TTATTTATTAATTTACTA
1890 TTAT
1 TTAT
1894 CTACTTTTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
13 2 0.02
14 3 0.03
15 6 0.07
17 5 0.06
18 14 0.16
19 42 0.47
20 8 0.09
21 2 0.02
22 1 0.01
23 6 0.07
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.62
Consensus pattern (18 bp):
TTATTTATTAATTTACTA
Found at i:1875 original size:27 final size:27
Alignment explanation
Indices: 1789--1886 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 27
1779 ATTATCTATT
* *
1789 TATTTA-CTATTTATATT-TTTATTTAT
1 TATTTATCTATTTAT-TTATTAATTTAC
* * *
1815 TAATTTAACTA-TTATCTATTTATTTAC
1 T-ATTTATCTATTTATTTATTAATTTAC
*
1842 TATTTATCTTTTTATTTATTAATTTAGC
1 TATTTATCTATTTATTTATTAATTTA-C
1870 TA-TTATCTATTTATTTA
1 TATTTATCTATTTATTTA
1887 CTATTATCTA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
26 9 0.15
27 45 0.75
28 6 0.10
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (27 bp):
TATTTATCTATTTATTTATTAATTTAC
Done.