Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006533.1 Kokia drynarioides strain JFW-HI SEQ_121117, 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: 16168
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:8557 original size:30 final size:30
Alignment explanation
Indices: 8503--8858 Score: 304
Period size: 29 Copynumber: 12.3 Consensus size: 30
8493 AGATGCTTGG
*
8503 GGGT-AAAATGGTGATTTTTG-GAAGTTCGA
1 GGGTAAAAAT-GTAATTTTTGAGAAGTTCGA
* *
8532 GGGTAAAAATATAATTTTTGAGAAGTT-TA
1 GGGTAAAAATGTAATTTTTGAGAAGTTCGA
*
8561 GGGGTAAAAATGTGATTTTTG-GAAGTAT-GA
1 -GGGTAAAAATGTAATTTTTGAGAAGT-TCGA
* *
8591 GGGTAAAAATGTGATTTTTG-GAAGTAC-A
1 GGGTAAAAATGTAATTTTTGAGAAGTTCGA
* *
8619 GGGTAAAAATATGATTTTTGA-AAGTTCG-
1 GGGTAAAAATGTAATTTTTGAGAAGTTCGA
** *
8647 GGGGCAAAATGTAGTTTTTG-GAAGTTCG-
1 GGGTAAAAATGTAATTTTTGAGAAGTTCGA
8675 GGGT-AAAATGTAATTTTTGAGAAGTTCGA
1 GGGTAAAAATGTAATTTTTGAGAAGTTCGA
* * *
8704 -GG-CAAAATGTATTTTTTGAGAAGTTCGG
1 GGGTAAAAATGTAATTTTTGAGAAGTTCGA
* *
8732 GGGT-AAAATATATTTTTTG-GAAAGTTCGA
1 GGGTAAAAATGTAATTTTTGAG-AAGTTCGA
* *
8761 GGGTAAAAATGTGATTTTT-AAAAGTTCG-
1 GGGTAAAAATGTAATTTTTGAGAAGTTCGA
8789 GGGTAAAAAATGTAATTTTTGGAGAAG-T-GTA
1 GGGT-AAAAATGTAATTTTT-GAGAAGTTCG-A
* *
8820 GGGTCAAAATGTAATTTTT-AGAAAGTTTGA
1 GGGTAAAAATGTAATTTTTGAG-AAGTTCGA
*
8850 GGGTCAAAA
1 GGGTAAAAA
8859 CGTGATTTCT
Statistics
Matches: 276, Mismatches: 27, Indels: 47
0.79 0.08 0.13
Matches are distributed among these distances:
27 14 0.05
28 90 0.33
29 95 0.34
30 68 0.25
31 9 0.03
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTTGAGAAGTTCGA
Found at i:8758 original size:57 final size:57
Alignment explanation
Indices: 8516--8842 Score: 272
Period size: 59 Copynumber: 5.7 Consensus size: 57
8506 TAAAATGGTG
* * *
8516 ATTTTTGG-AAGTTCGAGGGTAAAAATATAATTTTTGAGAAGTTTAGGGGTAAAAATGT
1 ATTTTTGGAAAGTTCGAGGGTAAAAATGT-ATTTTTGAGAAG-TTCGGGGTAAAAATAT
* *
8574 GATTTTTGG-AAGTAT-GAGGGTAAAAATGTGATTTTTG-GAAGTACAGGGTAAAAATAT
1 -ATTTTTGGAAAGT-TCGAGGGTAAAAATGT-ATTTTTGAGAAGTTCGGGGTAAAAATAT
** *
8631 GATTTTT-GAAAGTTCG-GGGGCAAAATGTAGTTTTTG-GAAGTTCGGGGT-AAAATGT
1 -ATTTTTGGAAAGTTCGAGGGTAAAAATGTA-TTTTTGAGAAGTTCGGGGTAAAAATAT
*
8686 AATTTTT-GAGAAGTTCGA-GG-CAAAATGTATTTTTTGAGAAGTTCGGGGGT-AAAATAT
1 -ATTTTTGGA-AAGTTCGAGGGTAAAAATGTA-TTTTTGAGAAGTTC-GGGGTAAAAATAT
* *
8743 ATTTTTTGGAAAGTTCGAGGGTAAAAATGTGATTTTT-AAAAGTTCGGGGTAAAAAATGT
1 A-TTTTTGGAAAGTTCGAGGGTAAAAATGT-ATTTTTGAGAAGTTCGGGGT-AAAAATAT
*
8802 AATTTTTGGAGAAG-T-GTAGGGTCAAAATGTAATTTTT-AGAA
1 -ATTTTTGGA-AAGTTCG-AGGGTAAAAATGT-ATTTTTGAGAA
8843 AGTTTGAGGG
Statistics
Matches: 230, Mismatches: 20, Indels: 36
0.80 0.07 0.13
Matches are distributed among these distances:
55 30 0.13
56 45 0.20
57 53 0.23
58 16 0.07
59 80 0.35
60 6 0.03
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35
Consensus pattern (57 bp):
ATTTTTGGAAAGTTCGAGGGTAAAAATGTATTTTTGAGAAGTTCGGGGTAAAAATAT
Found at i:8877 original size:30 final size:29
Alignment explanation
Indices: 8795--8881 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
8785 TTCGGGGTAA
* * * *
8795 AAAATGTAATTTTTGGAGAAGTGTAGGGTC
1 AAAACGTAATTTCTAGA-AAGTTTAGGGTC
* *
8825 AAAATGTAATTTTTAGAAAGTTTGAGGGTC
1 AAAACGTAATTTCTAGAAAGTTT-AGGGTC
*
8855 AAAACGTGATTTCTA-AATAGTTTAGGG
1 AAAACGTAATTTCTAGAA-AGTTTAGGG
8882 ACCTTCTAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
29 11 0.22
30 39 0.78
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAACGTAATTTCTAGAAAGTTTAGGGTC
Found at i:10902 original size:17 final size:17
Alignment explanation
Indices: 10880--10944 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
10870 TAGAAAAATT
10880 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
10897 TTTAAATTTAAAAATAAT
1 TTTAAATTT-AAAATAAA
*
10915 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
10932 TTAAAAATTAAAA
1 TTTAAATTTAAAA
10945 ATTTGGTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
17 27 0.64
18 15 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:10926 original size:35 final size:35
Alignment explanation
Indices: 10879--10946 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
10869 TTAGAAAAAT
* * *
10879 TTTTAAATTTAAAATAAATTTAAATTTAAAAATAA
1 TTTTAAACTTAAAATAAATTAAAAATTAAAAATAA
10914 TTTTAAACTTAAAATAAATTAAAAATTAAAAAT
1 TTTTAAACTTAAAATAAATTAAAAATTAAAAAT
10947 TTGGTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (35 bp):
TTTTAAACTTAAAATAAATTAAAAATTAAAAATAA
Found at i:10945 original size:18 final size:18
Alignment explanation
Indices: 10883--10946 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
10873 AAAAATTTTT
*
10883 AAATTTAAAATAAATTTA
1 AAATTAAAAATAAATTTA
* *
10901 AATTTAAAAATAATTTTA
1 AAATTAAAAATAAATTTA
* *
10919 AACTT-AAAATAAATTAA
1 AAATTAAAAATAAATTTA
10936 AAATTAAAAAT
1 AAATTAAAAAT
10947 TTGGTTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
17 14 0.37
18 24 0.63
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTAAAAATAAATTTA
Found at i:13549 original size:47 final size:50
Alignment explanation
Indices: 13479--13581 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 50
13469 ATCTTTAACA
* * *
13479 AATAATTCATTCATTAATTAATAATATAATGGTT-AAAA-AAACTCAAAC
1 AATAATTAATTAATTAATTAATAATATAATGATTCAAAAGAAACTCAAAC
*
13527 -ATAATTAATTAATTAATTAATAATATAATGATTCAAAAGAAACTGAAAC
1 AATAATTAATTAATTAATTAATAATATAATGATTCAAAAGAAACTCAAAC
13576 AATAAT
1 AATAAT
13582 CCCTAAACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
47 30 0.62
48 4 0.08
49 9 0.19
50 5 0.10
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (50 bp):
AATAATTAATTAATTAATTAATAATATAATGATTCAAAAGAAACTCAAAC
Done.