Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005560.1 Kokia drynarioides strain JFW-HI SEQ_119668, 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: 2747
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Found at i:743 original size:41 final size:41
Alignment explanation
Indices: 698--904 Score: 290
Period size: 41 Copynumber: 5.1 Consensus size: 41
688 TTTAAATAAA
* * *
698 TTAGCAGCGCTTTCCCATAAGCGCCGCTATTGCTTTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACTT
* *
739 TTAGCGGCGCTTTCCCATAAGCGTCACTATTGCTCTGACTT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACTT
* *
780 TTAGCGGCACTTGCCCATAAGCGCCGCTATTGCTCTGACTT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACTT
* * * * *
821 TTAACGGTGCTTGCCCATAAGCGCCGCTATTGCTTTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACTT
*
862 TTAGCGGCGC-TTCCCATAAGCACCGCTATTGCTCTGACTT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACTT
902 TTA
1 TTA
905 TTGCTCTGAC
Statistics
Matches: 146, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 29 0.20
41 117 0.80
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACTT
Found at i:908 original size:15 final size:15
Alignment explanation
Indices: 888--919 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
878 TAAGCACCGC
*
888 TATTGCTCTGACTTT
1 TATTGCTCTGACCTT
903 TATTGCTCTGACCTT
1 TATTGCTCTGACCTT
918 TA
1 TA
920 GCGGCGCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.22, G:0.12, T:0.50
Consensus pattern (15 bp):
TATTGCTCTGACCTT
Found at i:959 original size:56 final size:55
Alignment explanation
Indices: 848--952 Score: 165
Period size: 55 Copynumber: 1.9 Consensus size: 55
838 TAAGCGCCGC
*
848 TATTGCTTTGACCTTTAGCGGCGCTTCCCATAAGCACCGCTATTGCTCTGACTTT
1 TATTGCTCTGACCTTTAGCGGCGCTTCCCATAAGCACCGCTATTGCTCTGACTTT
* **
903 TATTGCTCTGACCTTTAGCGGCGCTTTCCCTTAAGTGCCGCTATTGCTCT
1 TATTGCTCTGACCTTTAGCGGCGC-TTCCCATAAGCACCGCTATTGCTCT
953 ACCTTTTGCG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 23 0.51
56 22 0.49
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (55 bp):
TATTGCTCTGACCTTTAGCGGCGCTTCCCATAAGCACCGCTATTGCTCTGACTTT
Found at i:999 original size:96 final size:96
Alignment explanation
Indices: 807--990 Score: 219
Period size: 96 Copynumber: 1.9 Consensus size: 96
797 TAAGCGCCGC
* * *
807 TATTGCTCTGACTTTTAACGGTGCTTGCCCATAAGCGCCGCTATTGCTTTGACCTTTAGCGGCGC
1 TATTGCTCTGACCTTTAACGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* *
872 TTCCCATAAGCACCGCTATTGCTCTGACTTT
66 TTCACATAAACACCGCTATTGCTCTGACTTT
* * * * * *
903 TATTGCTCTGACCTTTAGCGGCGCTTTCCCTTAAGTGCCGCTATTGCTCT-ACCTTTTGCGGTG-
1 TATTGCTCTGACCTTTAACGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* *
966 TTTATATAAAAACACCGCTATTGCT
66 TTCACAT--AAACACCGCTATTGCT
991 TTACCTTTTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
94 4 0.05
95 11 0.15
96 58 0.79
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (96 bp):
TATTGCTCTGACCTTTAACGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
TTCACATAAACACCGCTATTGCTCTGACTTT
Found at i:1781 original size:17 final size:17
Alignment explanation
Indices: 1761--1820 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 17
1751 AGCGCATAAT
1761 TAAAATATAATTAAAAA
1 TAAAATATAATTAAAAA
* *
1778 TAAAATA-AAATAAAAC
1 TAAAATATAATTAAAAA
1794 TAAAA-ATAAATATGAAAAA
1 TAAAATAT-AAT-T-AAAAA
1813 T-AAATATA
1 TAAAATATA
1821 CTATTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
15 1 0.03
16 12 0.35
17 9 0.26
18 5 0.15
19 7 0.21
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
TAAAATATAATTAAAAA
Found at i:1786 original size:22 final size:22
Alignment explanation
Indices: 1761--1803 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1751 AGCGCATAAT
* *
1761 TAAAATATAATTAAAAATAAAA
1 TAAAATAAAACTAAAAATAAAA
1783 TAAAATAAAACTAAAAATAAA
1 TAAAATAAAACTAAAAATAAA
1804 TATGAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
TAAAATAAAACTAAAAATAAAA
Found at i:1813 original size:13 final size:13
Alignment explanation
Indices: 1795--1819 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1785 AAATAAAACT
1795 AAAAATAAATATG
1 AAAAATAAATATG
1808 AAAAATAAATAT
1 AAAAATAAATAT
1820 ACTATTTTTT
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAAATAAATATG
Found at i:1851 original size:11 final size:11
Alignment explanation
Indices: 1846--1884 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1836 CTTTTCAATT
1846 TTTTTTTCAAA
1 TTTTTTTCAAA
*
1857 TTTTTTTAAAA
1 TTTTTTTCAAA
*
1868 TTTTTTAC-AA
1 TTTTTTTCAAA
1878 TTTTTTT
1 TTTTTTT
1885 TAAAAACATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:1852 original size:12 final size:12
Alignment explanation
Indices: 1837--1885 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
1827 TTTTTTTAAC
*
1837 TTTTCAATTTTT
1 TTTTCAATATTT
1849 TTTTCAA-ATTT
1 TTTTCAATATTT
*
1860 TTTT-AAAATTT
1 TTTTCAATATTT
*
1871 TTTACAAT-TTT
1 TTTTCAATATTT
1882 TTTT
1 TTTT
1886 AAAAACATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 2 0.06
11 20 0.65
12 9 0.29
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCAATATTT
Found at i:1860 original size:20 final size:20
Alignment explanation
Indices: 1823--1860 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1813 TAAATATACT
* *
1823 ATTTTTTTTTTAACTTTTCA
1 ATTTTTTTTTCAAATTTTCA
1843 ATTTTTTTTTCAAATTTT
1 ATTTTTTTTTCAAATTTT
1861 TTTAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTTTTTCAAATTTTCA
Found at i:1886 original size:12 final size:12
Alignment explanation
Indices: 1837--1886 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
1827 TTTTTTTAAC
1837 TTTT-CAATTTT
1 TTTTACAATTTT
* *
1848 TTTTTCAAATTT
1 TTTTACAATTTT
*
1860 TTTTA-AA-ATT
1 TTTTACAATTTT
1870 TTTTACAATTTT
1 TTTTACAATTTT
1882 TTTTA
1 TTTTA
1887 AAAACATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 7 0.22
11 8 0.25
12 17 0.53
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTACAATTTT
Done.