Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004471.1 Kokia drynarioides strain JFW-HI SEQ_117890, 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: 2687
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Found at i:54 original size:29 final size:27
Alignment explanation
Indices: 7--325 Score: 128
Period size: 29 Copynumber: 10.9 Consensus size: 27
1 ATCTAA
7 GGGTAAAATGGTAATTTTTTGAAAGTTCG
1 GGGTAAAATGG-AA-TTTTTGAAAGTTCG
*
36 GGGTCAAAAATGGAATTTTTGGAAA-TTAAG
1 GGGT--AAAATGGAATTTTT-GAAAGTT-CG
* *
66 AGGTAAAATGGTAAATTTTGGAAA-TTCG
1 GGGTAAAATGG--AATTTTTGAAAGTTCG
* * *
94 AGTGTAAAATAGTAATTTTTGAAAACTTC-
1 -GGGTAAAAT-GGAATTTTTG-AAAGTTCG
* *
123 GCGTCAAGAAT-GATATTTTTGGAAGTTCGG
1 GGGT-AA-AATGGA-ATTTTTGAAAGTTC-G
* *
153 GGGTAAAATGGTAATTTTTGGAAGTTTGG
1 GGGTAAAATGG-AATTTTTGAAAG-TTCG
* * * *
182 GGGAAAAAATGTGATTTTTTGGAAATTTAG
1 GGG-TAAAATG-GAATTTTT-GAAAGTTCG
* *
212 GGGTAAAATGTAATTTTTGGAAAGTTCAA
1 GGGTAAAATGGAATTTTT-GAAAGTTC-G
** *
241 GGGTAAAAATATAATTTGTGTG-AAGCTCG
1 GGGT-AAAATGGAATTT-T-TGAAAGTTCG
* *
270 AGGGTAAAATGTAATTTTTGTGAAGTTCG
1 -GGGTAAAATGGAATTTTTG-AAAGTTCG
*
299 AGGGTCAAAATGTG-ATTTTTTAAAGTT
1 -GGGT-AAAATG-GAATTTTTGAAAGTT
326 TGGGAGTCAA
Statistics
Matches: 227, Mismatches: 33, Indels: 60
0.71 0.10 0.19
Matches are distributed among these distances:
27 2 0.01
28 41 0.18
29 91 0.40
30 79 0.35
31 13 0.06
32 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (27 bp):
GGGTAAAATGGAATTTTTGAAAGTTCG
Found at i:158 original size:87 final size:88
Alignment explanation
Indices: 9--175 Score: 214
Period size: 87 Copynumber: 1.9 Consensus size: 88
1 ATCTAAGG
* * *
9 GTAAAATGGTAATTTTTTGAAAGTTCGGGGTCAAAAATGGAATTTTTGGAAATTAAGAGGTAAAA
1 GTAAAATAGTAATTTTTTGAAACTTCGGCGTCAAAAATGGAATTTTTGGAAATTAAGAGGTAAAA
74 TGGTAAATTTTGGAAATTCGAGT
66 TGGTAAATTTTGGAAATTCGAGT
* * ** *
97 GTAAAATAGTAA-TTTTTGAAAACTTC-GCGTCAAGAAT-GATATTTTTGGAAGTTCGGGGGTAA
1 GTAAAATAGTAATTTTTTG-AAACTTCGGCGTCAAAAATGGA-ATTTTTGGAAATTAAGAGGTAA
*
159 AATGGTAATTTTTGGAA
64 AATGGTAAATTTTGGAA
176 GTTTGGGGGA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
86 2 0.03
87 49 0.72
88 17 0.25
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.35
Consensus pattern (88 bp):
GTAAAATAGTAATTTTTTGAAACTTCGGCGTCAAAAATGGAATTTTTGGAAATTAAGAGGTAAAA
TGGTAAATTTTGGAAATTCGAGT
Found at i:219 original size:59 final size:58
Alignment explanation
Indices: 133--355 Score: 177
Period size: 59 Copynumber: 3.8 Consensus size: 58
123 GCGTCAAGAA
* * * *
133 TGATATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGG-AAGTTTGGGGGAAAAAATG
1 TGAT-TTTTTGGAAATT-TGGGGTAAAAT-GTAATTTTTGGAAAGTTCGAGGGAAAAAATG
* * *
193 TGATTTTTTGGAAATTTAGGGGTAAAATGTAATTTTTGGAAAGTTCAAGGGTAAAAATA
1 TGATTTTTTGGAAATTT-GGGGTAAAATGTAATTTTTGGAAAGTTCGAGGGAAAAAATG
* * ** * **
252 T-AATTTGTGTGAAGCTCGAGGGTAAAATGTAATTTTTGTG-AAGTTCGAGGGTCAAAATG
1 TGATTTTTTG-GAAATTTG-GGGTAAAATGTAATTTTTG-GAAAGTTCGAGGGAAAAAATG
* *
311 TGATTTTTT--AAAGTTTGGGAGTCAAATTATAATTTTTGGAAAGTT
1 TGATTTTTTGGAAA-TTTGGG-GT-AAAATGTAATTTTTGGAAAGTT
356 TGGGGGACAA
Statistics
Matches: 131, Mismatches: 22, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
57 4 0.03
58 23 0.18
59 94 0.72
60 10 0.08
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (58 bp):
TGATTTTTTGGAAATTTGGGGTAAAATGTAATTTTTGGAAAGTTCGAGGGAAAAAATG
Found at i:356 original size:30 final size:30
Alignment explanation
Indices: 320--382 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
310 GTGATTTTTT
* *
320 AAAGTTTGGGAGTCAAATTATAATTTTTGG
1 AAAGTTTGGGAGACAAATCATAATTTTTGG
* *
350 AAAGTTTGGGGGACAAATCATGATTTTTGG
1 AAAGTTTGGGAGACAAATCATAATTTTTGG
380 AAA
1 AAA
383 AATTAGGGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAGTTTGGGAGACAAATCATAATTTTTGG
Found at i:1993 original size:46 final size:46
Alignment explanation
Indices: 1933--2033 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
1923 TTAGACTTTT
* * * * *
1933 TAAATTAAAGTTTAAAATTAAGTTTAAAACC-ATTTCAAATTTAA-A
1 TAAATTTAACTTTAAAAATAAATTTAAAACCGATTT-AAACTTAATA
1978 CTAAATTTAACTTTAAAAATAAATTTAAAACCGATTTAAACTTAATA
1 -TAAATTTAACTTTAAAAATAAATTTAAAACCGATTTAAACTTAATA
2025 TAAATTTAA
1 TAAATTTAA
2034 AATCAAAAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
46 43 0.90
47 5 0.10
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (46 bp):
TAAATTTAACTTTAAAAATAAATTTAAAACCGATTTAAACTTAATA
Found at i:2581 original size:78 final size:78
Alignment explanation
Indices: 2483--2687 Score: 209
Period size: 78 Copynumber: 2.6 Consensus size: 78
2473 TGATCGGGTG
* * * * * **
2483 AGAGATTGACTGATAATGATCTGCCTCAAGCTCGAGGGAAGAGATCGAATGACTGCGATTTGGCC
1 AGAGATTGTCTGATGATGATCTGCCTCAAGCTTGAGGGAAGAGATCGAATGACTGCAATCTACCC
2548 CAGGCTCCAGGTA
66 CAGGCTCCAGGTA
* * * * * **
2561 AGAGATTGTCTGATGGTGATCTGCCT-TAGCCTTGAGGTAAGATATTGAATGGTTGCAATCTACC
1 AGAGATTGTCTGATGATGATCTGCCTCAAG-CTTGAGGGAAGAGATCGAATGACTGCAATCTACC
**
2625 CCAGGCTCGGGGTA
65 CCAGGCTCCAGGTA
*
2639 AGAGATT-TGCTGATGATGATCTGCCACAAGCTTG-GGGTAAGAGATCGAA
1 AGAGATTGT-CTGATGATGATCTGCCTCAAGCTTGAGGG-AAGAGATCGAA
Statistics
Matches: 101, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
77 5 0.05
78 94 0.93
79 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (78 bp):
AGAGATTGTCTGATGATGATCTGCCTCAAGCTTGAGGGAAGAGATCGAATGACTGCAATCTACCC
CAGGCTCCAGGTA
Done.