Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011769.1 Kokia drynarioides strain JFW-HI SEQ_126764, 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: 9329
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:566 original size:6 final size:7
Alignment explanation
Indices: 547--573 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
537 AAATAATAAA
547 TATTTTT
1 TATTTTT
554 TATTTTT
1 TATTTTT
561 TATTTTT
1 TATTTTT
568 TATTTT
1 TATTTT
574 GTGGTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:1596 original size:89 final size:89
Alignment explanation
Indices: 1509--2023 Score: 357
Period size: 89 Copynumber: 5.8 Consensus size: 89
1499 GTAATTTTGG
* * *
1509 GAAAATTCGGGGTTAAAAATGGAATTTT-AAACATTT-GAGGGT-AAATGGTAATTTTTAGAAGT
1 GAAAATTTGGGGTTAAAAATGGAATTTTGGAA-GTTTAGAGGGTAAAATGGTAATTTTTAGAAGT
1571 TTCGGGGGTCAAAAATGGGATTTTT-
65 TTCGGGGGT-AAAAATGGGATTTTTA
* * * ** *
1596 GGAAGTTTGGAGGGT-AAAATGGTAATTTTTGGAAGTTCGGGGGGTAAAAAT-G-AGATTTTTAG
1 GAAAATTTGG-GGTTAAAAATGG-AA-TTTTGGAAGTTTAGAGGGT-AAAATGGTA-ATTTTTAG
*
1658 AAGTTTC-AGGGTCAAAAATGGGATTTTTA
61 AAGTTTCGGGGGT-AAAAATGGGATTTTTA
** * * * * *
1687 GAATTTTTGAGGTCAAAAAT-GAGATTTTTGAAGTTTAAAGGGTAAAATGGTAATTTTTGGAA--
1 GAAAATTTGGGGTTAAAAATGGA-ATTTTGGAAGTTTAGAGGGTAAAATGGTAATTTTTAGAAGT
*
1749 ATCGAGGGGTAAAAATGGGATTTTTA
65 TTCG-GGGGTAAAAATGGGATTTTTA
* * * * *
1775 G-AAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTTAGAGGGTAAAATGGTAATTTTTGGAAG
1 GAAAATTT-GGGGTTAAAAAT-GGAATTTTGGAAGTTTAGAGGGTAAAATGGTAATTTTTAGAAG
*
1839 TTT-GGGGGTAAAAATGGAATTTTTA
64 TTTCGGGGGTAAAAATGGGATTTTTA
* * * * * * *
1864 -AAAGTTTTGGGGTTAAAAATGGGATTTTGTAAGTTT-CATGGTCAAAAATGG-GATTTTTGGAA
1 GAAA-ATTTGGGGTTAAAAATGGAATTTTGGAAGTTTAGAGGGT--AAAATGGTAATTTTTAGAA
* * *
1926 GTTTCGAGGTTAAAAATGGGATTTATA
63 GTTTCGGGGGTAAAAATGGGATTTTTA
* ** * * * *
1953 G-AAGTTTCTAGGTCAAAAATGGGATTTTCGGAAG-TTCGAGGGTAAAAACGG-AATTTTTAGAA
1 GAAAATTT-GGGGTTAAAAATGGAATTTT-GGAAGTTTAGAGGGT-AAAATGGTAATTTTTAGAA
*
2015 GTCTCGGGG
63 GTTTCGGGG
2024 ACCTCCAGGG
Statistics
Matches: 343, Mismatches: 56, Indels: 56
0.75 0.12 0.12
Matches are distributed among these distances:
87 24 0.07
88 68 0.20
89 172 0.50
90 47 0.14
91 28 0.08
92 4 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (89 bp):
GAAAATTTGGGGTTAAAAATGGAATTTTGGAAGTTTAGAGGGTAAAATGGTAATTTTTAGAAGTT
TCGGGGGTAAAAATGGGATTTTTA
Found at i:1626 original size:30 final size:30
Alignment explanation
Indices: 1551--2016 Score: 320
Period size: 30 Copynumber: 15.6 Consensus size: 30
1541 ATTTGAGGGT
*
1551 AAATGGTAATTTTTAGAAGTTTCGG-GGGTCAA
1 AAATGG-AATTTTTGGAAGTTT-GGAGGGT-AA
*
1583 AAATGGGATTTTTGGAAGTTTGGAGGGT-A
1 AAATGGAATTTTTGGAAGTTTGGAGGGTAA
* *
1612 AAATGGTAATTTTTGGAAGTTCGGGGGGTAA
1 AAATGG-AATTTTTGGAAGTTTGGAGGGTAA
* *
1643 AAAT-GAGATTTTTAGAAGTTT-CAGGGTCAA
1 AAATGGA-ATTTTTGGAAGTTTGGAGGGT-AA
* * * *
1673 AAATGGGATTTTTAGAATTTTTGA-GGTCAA
1 AAATGGAATTTTTGGAAGTTTGGAGGGT-AA
**
1703 AAAT-GAGATTTTT-GAAGTTTAAAGGGT-A
1 AAATGGA-ATTTTTGGAAGTTTGGAGGGTAA
* *
1731 AAATGGTAATTTTTGGAA--ATCGAGGGGTAA
1 AAATGG-AATTTTTGGAAGTTTGGA-GGGTAA
* * *
1761 AAATGGGATTTTTAGAAGTTTCGA-GGTAAA
1 AAATGGAATTTTTGGAAGTTTGGAGGGT-AA
* *
1791 AAATGGGATTTTTGGAAGTTTAGAGGGT-A
1 AAATGGAATTTTTGGAAGTTTGGAGGGTAA
1820 AAATGGTAATTTTTGGAAGTTTGG-GGGTAA
1 AAATGG-AATTTTTGGAAGTTTGGAGGGTAA
** *
1850 AAATGGAATTTTTAAAAGTTTTGG-GGTTAA
1 AAATGGAATTTTTGGAAG-TTTGGAGGGTAA
* * * *
1880 AAATGGGA-TTTTGTAAGTTT-CATGGTCAA
1 AAATGGAATTTTTGGAAGTTTGGAGGGT-AA
* * *
1909 AAATGGGATTTTTGGAAGTTTCGAGGTTAA
1 AAATGGAATTTTTGGAAGTTTGGAGGGTAA
* * * **
1939 AAATGGGATTTATAGAAGTTTCTA-GGTCAA
1 AAATGGAATTTTTGGAAGTTTGGAGGGT-AA
* * *
1969 AAATGGGATTTTCGGAAG-TTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTGGAGGGTAA
* *
1998 AAACGGAATTTTTAGAAGT
1 AAATGGAATTTTTGGAAGT
2017 CTCGGGGACC
Statistics
Matches: 355, Mismatches: 51, Indels: 58
0.77 0.11 0.12
Matches are distributed among these distances:
28 12 0.03
29 103 0.29
30 200 0.56
31 34 0.10
32 6 0.02
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (30 bp):
AAATGGAATTTTTGGAAGTTTGGAGGGTAA
Found at i:1644 original size:118 final size:118
Alignment explanation
Indices: 1493--2016 Score: 414
Period size: 118 Copynumber: 4.4 Consensus size: 118
1483 TGTACGGGGC
* * * *
1493 AAAATGGTAATTTTGGGAAAATTC-GGGGTTAAAAATGGAATTTTA-AACATTTGAGGGT-AAAT
1 AAAATGGTAATTTTTGG-AAGTTCGGGGGGTAAAAATGGAATTTTAGAA-GTTTGAGGGTAAAAT
* *
1555 GGTAATTTTTAGAAGTTTCGGGGGTCAAAAATGGGATTTTTGGAAGTTTGGAGGGT
64 GG-GATTTTTAGAAGTTTAGGGGGTCAAAAATGGGATTTTTGGAAGTTTGGAGGGT
* *
1611 AAAATGGTAATTTTTGGAAGTTCGGGGGGTAAAAATGAGATTTTTAGAAGTTTCAGGGTCAAAAA
1 AAAATGGTAATTTTTGGAAGTTCGGGGGGTAAAAATG-GAATTTTAGAAGTTTGAGGGT--AAAA
** * * **
1676 TGGGATTTTTAGAA-TTTTTGAGGTCAAAAATGAGATTTTT-GAAGTTTAAAGGGT
63 TGGGATTTTTAGAAGTTTAGGGGGTCAAAAATGGGATTTTTGGAAGTTTGGAGGGT
* * *
1730 AAAATGGTAATTTTTGGAA-ATCGAGGGGTAAAAATGGGATTTTTAGAAGTTTCGA-GGTAAAAA
1 AAAATGGTAATTTTTGGAAGTTCGGGGGGTAAAAAT-GGAATTTTAGAAGTTT-GAGGGT--AAA
* * *
1793 ATGGGATTTTTGGAAGTTTAGAGGGT--AAAATGGTAATTTTTGGAAGTTTGG-GGGT
62 ATGGGATTTTTAGAAGTTTAGGGGGTCAAAAATGG-GATTTTTGGAAGTTTGGAGGGT
** ** * * * *
1848 AAAAATGG-AATTTTTAAAAGTTTTGGGGTTAAAAATGGGATTTT-GTAAGTTTCATGGTCAAAA
1 -AAAATGGTAATTTTTGGAAGTTCGGGGGGTAAAAATGGAATTTTAG-AAGTTTGAGGGT--AAA
* * * * * * **
1911 ATGGGATTTTTGGAAGTTT-CGAGGTTAAAAATGGGATTTATAGAAGTTTCTA-GGT
62 ATGGGATTTTTAGAAGTTTAGGGGGTCAAAAATGGGATTTTTGGAAGTTTGGAGGGT
* * * *
1966 CAAAAATGG-GATTTTCGGAAGTTC-GAGGGTAAAAACGGAATTTTTAGAAGT
1 --AAAATGGTAATTTTTGGAAGTTCGGGGGGTAAAAATGGAA-TTTTAGAAGT
2017 CTCGGGGACC
Statistics
Matches: 331, Mismatches: 54, Indels: 41
0.78 0.13 0.10
Matches are distributed among these distances:
117 16 0.05
118 162 0.49
119 112 0.34
120 25 0.08
121 10 0.03
122 6 0.02
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (118 bp):
AAAATGGTAATTTTTGGAAGTTCGGGGGGTAAAAATGGAATTTTAGAAGTTTGAGGGTAAAATGG
GATTTTTAGAAGTTTAGGGGGTCAAAAATGGGATTTTTGGAAGTTTGGAGGGT
Found at i:1823 original size:59 final size:60
Alignment explanation
Indices: 1559--2016 Score: 410
Period size: 59 Copynumber: 7.7 Consensus size: 60
1549 GTAAATGGTA
* * * * *
1559 ATTTTTAGAAGTTTCGGGGGTCAAAAATGGGATTTTTGGAAGTTTGGAGGGT-AAAATGGTA
1 ATTTTTGGAAGTTTCGAGGGT-AAAAATGGGATTTTTAGAAGTTTCGAGGGTAAAAATGG-G
* *
1620 ATTTTTGGAAG-TTCGGGGGGTAAAAATGAGATTTTTAGAAGTTTC-AGGGTCAAAAATGGG
1 ATTTTTGGAAGTTTC-GAGGGTAAAAATGGGATTTTTAGAAGTTTCGAGGGT-AAAAATGGG
* * * * ** *
1680 ATTTTTAGAATTTTTGA-GGTCAAAAATGAGATTTTT-GAAGTTTAAAGGGT-AAAATGGTA
1 ATTTTTGGAAGTTTCGAGGGT-AAAAATGGGATTTTTAGAAGTTTCGAGGGTAAAAATGG-G
*
1739 ATTTTTGGAA--ATCGAGGGGTAAAAATGGGATTTTTAGAAGTTTCGA-GGTAAAAAATGGG
1 ATTTTTGGAAGTTTCGA-GGGTAAAAATGGGATTTTTAGAAGTTTCGAGGGT-AAAAATGGG
* * * * *
1798 ATTTTTGGAAGTTTAGAGGGT-AAAATGGTAATTTTTGGAAGTTT-GGGGGTAAAAATGGA
1 ATTTTTGGAAGTTTCGAGGGTAAAAATGG-GATTTTTAGAAGTTTCGAGGGTAAAAATGGG
** * *
1857 ATTTTTAAAAGTTTTG-GGGTTAAAAATGGGA-TTTT-GTAAGTTTC-ATGGTCAAAAATGGG
1 ATTTTTGGAAGTTTCGAGGG-TAAAAATGGGATTTTTAG-AAGTTTCGAGGGT-AAAAATGGG
* * *
1916 ATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTATAGAAGTTTCTA-GGTCAAAAATGGG
1 ATTTTTGGAAGTTTCGAGGGTAAAAATGGGATTTTTAGAAGTTTCGAGGGT-AAAAATGGG
* * *
1976 ATTTTCGGAAG-TTCGAGGGTAAAAACGGAATTTTTAGAAGT
1 ATTTTTGGAAGTTTCGAGGGTAAAAATGGGATTTTTAGAAGT
2017 CTCGGGGACC
Statistics
Matches: 331, Mismatches: 41, Indels: 52
0.78 0.10 0.12
Matches are distributed among these distances:
57 4 0.01
58 40 0.12
59 134 0.40
60 123 0.37
61 30 0.09
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (60 bp):
ATTTTTGGAAGTTTCGAGGGTAAAAATGGGATTTTTAGAAGTTTCGAGGGTAAAAATGGG
Found at i:3793 original size:6 final size:6
Alignment explanation
Indices: 3779--3820 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
3769 AATTTGATAA
* *
3779 TAAATT TAAACT TAAATT TAAATT TAAA-A TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T
3821 TTAAACAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:3813 original size:17 final size:17
Alignment explanation
Indices: 3779--3849 Score: 81
Period size: 17 Copynumber: 4.1 Consensus size: 17
3769 AATTTGATAA
*
3779 TAAATTTAAACTTAAATT
1 TAAATTTAAA-ATAAATT
3797 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
* *
3814 TAAATTTTTAAACAAATT
1 TAAA-TTTAAAATAAATT
3832 T-AATCTTAAAATAAATT
1 TAAAT-TTAAAATAAATT
3849 T
1 T
3850 GAAGGGAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
16 1 0.02
17 23 0.50
18 22 0.48
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:3819 original size:35 final size:34
Alignment explanation
Indices: 3779--3849 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 34
3769 AATTTGATAA
3779 TAAA-TTTAAACTTAAATTTAAAT-TTAAAATAAATT
1 TAAATTTTAAAC--AAATTT-AATCTTAAAATAAATT
3814 TAAATTTTTAAACAAATTTAATCTTAAAATAAATT
1 TAAA-TTTTAAACAAATTTAATCTTAAAATAAATT
3849 T
1 T
3850 GAAGGGAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
34 3 0.09
35 23 0.70
37 7 0.21
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAATTTTAAACAAATTTAATCTTAAAATAAATT
Found at i:7457 original size:15 final size:16
Alignment explanation
Indices: 7423--7457 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
7413 CGAGCCTTTG
*
7423 GTTTTTTTAAAACAAG
1 GTTTTTTTAAAACAAA
7439 GTTTTTTTAAAA-AAA
1 GTTTTTTTAAAACAAA
7454 GTTT
1 GTTT
7458 ATCCCTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (16 bp):
GTTTTTTTAAAACAAA
Done.