Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005848.1 Kokia drynarioides strain JFW-HI SEQ_120148, 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: 4563
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1619 original size:30 final size:30
Alignment explanation
Indices: 1585--1717 Score: 96
Period size: 30 Copynumber: 4.5 Consensus size: 30
1575 TAGAAATCAT
* *
1585 ATTTTGACCCTCGAACTTTCAAAAAATATC
1 ATTTTGACCCTCAAACTTTCAAAAATTATC
* * *
1615 ATTTTTTA-CCTTAAACTTTCCAAAAATTACC
1 A-TTTTGACCCTCAAACTTT-CAAAAATTATC
** * *
1646 ATTTT-ACCC-CGGA-TGTCCAAAATTA-C
1 ATTTTGACCCTCAAACTTTCAAAAATTATC
*
1672 AATTTTGACCCTAAAACTTTCAAAAATTATC
1 -ATTTTGACCCTCAAACTTTCAAAAATTATC
* *
1703 ATTTTTACCCCCAAA
1 ATTTTGACCCTCAAA
1718 TATCCAGAAT
Statistics
Matches: 77, Mismatches: 18, Indels: 16
0.69 0.16 0.14
Matches are distributed among these distances:
26 1 0.01
27 13 0.17
28 6 0.08
29 3 0.04
30 38 0.49
31 16 0.21
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (30 bp):
ATTTTGACCCTCAAACTTTCAAAAATTATC
Found at i:1689 original size:58 final size:57
Alignment explanation
Indices: 1627--1903 Score: 299
Period size: 58 Copynumber: 4.8 Consensus size: 57
1617 TTTTTACCTT
* *
1627 AAACTTTCCAAAAATTACCATTTTA-CCCCGGATGTCCAAAATTACAATTTTGACCCTA
1 AAAC-TTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAATTACATTTTTGACCC-A
* * * * * *
1685 AAACTTTCAAAAATTATCATTTTTACCCCCAAATATCCAGAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCA-TTTTACCCCCGAATGTCCAAAATTACATTTTTGA-CCCA
* * * * *
1744 AAACTTCTAAAAATTACTATTTTACCCCCTAATGTCCAAAAATTCCATTTTTGACCCG
1 AAACTTCCAAAAATTACCATTTTACCCCCGAATGTCC-AAAATTACATTTTTGACCCA
* *
1802 AAACTTCCAAAAATTACCATTTTACCCCTCGAATGTCTAAAA--ACTATTTTTGACCACG
1 AAACTTCCAAAAATTACCATTTTACCCC-CGAATGTCCAAAATTAC-ATTTTTGACC-CA
* * *
1860 AACCTTCCAAAAATTACCATTTTACCCTCGAGTGTCCAAAATTA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAATTA
1904 TCGTTTTACC
Statistics
Matches: 185, Mismatches: 25, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
56 1 0.01
57 34 0.18
58 86 0.46
59 61 0.33
60 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (57 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGAATGTCCAAAATTACATTTTTGACCCA
Found at i:1770 original size:29 final size:30
Alignment explanation
Indices: 1627--1829 Score: 142
Period size: 29 Copynumber: 7.0 Consensus size: 30
1617 TTTTTACCTT
1627 AAACTTTCCAAAAATTACCATTTT-ACCCC-
1 AAAC-TTCCAAAAATTACCATTTTGACCCCA
** * *
1656 GGA-TGTCC-AAAATTACAATTTTGACCCTA
1 AAACT-TCCAAAAATTACCATTTTGACCCCA
* * * *
1685 AAACTTTCAAAAATTATCATTTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTGACCCCA
*
1715 AAA-TATCC-AGAATT-CCATTTTTGACCCCA
1 AAACT-TCCAAAAATTACCA-TTTTGACCCCA
* * *
1744 AAACTTCTAAAAATTACTATTTT-ACCCCC
1 AAACTTCCAAAAATTACCATTTTGACCCCA
* *
1773 TAA-TGTCCAAAAATT-CCATTTTTGA-CCCG
1 AAACT-TCCAAAAATTACCA-TTTTGACCCCA
1802 AAACTTCCAAAAATTACCATTTT-ACCCC
1 AAACTTCCAAAAATTACCATTTTGACCCC
1830 TCGAATGTCT
Statistics
Matches: 132, Mismatches: 26, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
27 14 0.11
28 13 0.10
29 66 0.50
30 37 0.28
31 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTACCATTTTGACCCCA
Found at i:1897 original size:29 final size:29
Alignment explanation
Indices: 1633--1930 Score: 117
Period size: 29 Copynumber: 10.3 Consensus size: 29
1623 CCTTAAACTT
*
1633 TCCAAAAATTACCATTTTACCC-CGGATG
1 TCCAAAAATTACCATTTTACCCTCGAATG
* **
1661 TCC-AAAATTACAATTTTGACCCTAAAACT-
1 TCCAAAAATTACCATTTT-ACCCTCGAA-TG
* * * * *
1690 TTCAAAAATTATCATTTTTACCCCCAAATA
1 TCCAAAAATTACCA-TTTTACCCTCGAATG
* *
1720 TCC-AGAATT-CCATTTTTGACCC-CAAAACT-
1 TCCAAAAATTACCA-TTTT-ACCCTC-GAA-TG
* * * *
1749 TCTAAAAATTACTATTTTACCCCCTAATG
1 TCCAAAAATTACCATTTTACCCTCGAATG
1778 TCCAAAAATT-CCATTTTTGA-CC-CGAAACT-
1 TCCAAAAATTACCA-TTTT-ACCCTCG-AA-TG
1807 TCCAAAAATTACCATTTTACCCCTCGAATG
1 TCCAAAAATTACCATTTTA-CCCTCGAATG
* * * *
1837 TCTAAAAACTA--TTTTTGA-CCACGAACCT-
1 TCCAAAAATTACCATTTT-ACCCTCGAA--TG
*
1865 TCCAAAAATTACCATTTTACCCTCGAGTG
1 TCCAAAAATTACCATTTTACCCTCGAATG
* * **
1894 TCC-AAAATTATCGTTTTA-CCTCCGAACA
1 TCCAAAAATTACCATTTTACCCT-CGAATG
1922 TCCAAAAAT
1 TCCAAAAAT
1931 CACTTTTTTA
Statistics
Matches: 206, Mismatches: 33, Indels: 61
0.69 0.11 0.20
Matches are distributed among these distances:
27 22 0.11
28 53 0.26
29 67 0.33
30 56 0.27
31 8 0.04
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCTCGAATG
Done.