Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008604.1 Kokia drynarioides strain JFW-HI SEQ_123282, 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: 18256
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Found at i:68 original size:13 final size:12
Alignment explanation
Indices: 37--73 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
27 CTATTACAAG
37 TTGAATAATTAA
1 TTGAATAATTAA
*
49 TTTAATAATTGAA
1 TTGAATAATT-AA
62 TTGAATAATTAA
1 TTGAATAATTAA
74 CTACTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (12 bp):
TTGAATAATTAA
Found at i:9001 original size:16 final size:18
Alignment explanation
Indices: 8961--9011 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
8951 TAACTTTAAT
*
8961 AAAATTAGAATTAGATTGAA
1 AAAATTA-ATTTA-ATTGAA
8981 AAAATT-ATTTAATTG-A
1 AAAATTAATTTAATTGAA
8997 AAAATTAATTTAATT
1 AAAATTAATTTAATT
9012 AATTAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.24
17 12 0.41
18 4 0.14
20 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
AAAATTAATTTAATTGAA
Found at i:17005 original size:19 final size:21
Alignment explanation
Indices: 16970--17010 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
16960 AAAAATGAGC
16970 ATGTAAATTAAATAC-AAGTT
1 ATGTAAATTAAATACAAAGTT
16990 ATGT-AATT-AATGACAAAGTT
1 ATGTAAATTAAAT-ACAAAGTT
17010 A
1 A
17011 AATAACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.16
19 6 0.32
20 10 0.53
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (21 bp):
ATGTAAATTAAATACAAAGTT
Found at i:17062 original size:14 final size:14
Alignment explanation
Indices: 17033--17077 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
17023 CACGAACAAT
17033 TATACGAATGAATAAA
1 TATACGAA--AATAAA
17049 TATACGAAAATAAA
1 TATACGAAAATAAA
*
17063 TATAAGAAAAATAAA
1 TATACG-AAAATAAA
17078 ATATGAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 11 0.41
15 8 0.30
16 8 0.30
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (14 bp):
TATACGAAAATAAA
Found at i:17303 original size:28 final size:30
Alignment explanation
Indices: 17225--17481 Score: 173
Period size: 29 Copynumber: 8.8 Consensus size: 30
17215 GGAAAGTTTT
* *
17225 AGGGATAAAAAAGTTATTTTTGAGAAGTTCG
1 AGGGA-AAAAATGTAATTTTTGAGAAGTTCG
* * *
17256 AGAGTAAAAATGTGATTTTTG-GAAGTTCG
1 AGGGAAAAAATGTAATTTTTGAGAAGTTCG
*
17285 AGGGAAAAAATATAATTTTTG-GAAGCTT-G
1 AGGGAAAAAATGTAATTTTTGAGAAG-TTCG
*
17314 -GGG-AAAAATGTAATTTTTGAGAAGTTTG
1 AGGGAAAAAATGTAATTTTTGAGAAGTTCG
* *
17342 -GGG-GAAAATGTAATTTTTGAGAAGTTTG
1 AGGGAAAAAATGTAATTTTTGAGAAGTTCG
* ** * *
17370 GGGGTCAAAATGTGATTTTTG-GAAGTT-T
1 AGGGAAAAAATGTAATTTTTGAGAAGTTCG
* *
17398 AGGGATAAAAATGTGATTTTTGA-AAGTTTG
1 AGGGA-AAAAATGTAATTTTTGAGAAGTTCG
* * * *
17428 -GGAGAAAAAAACGTGATTTTTTGA-ATGTTCA
1 AGG-G-AAAAAATGT-AATTTTTGAGAAGTTCG
*
17459 AAGG-AAAAATGTAATTTTT-AGAA
1 AGGGAAAAAATGTAATTTTTGAGAA
17482 ATTTTAGGGG
Statistics
Matches: 186, Mismatches: 27, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
27 18 0.10
28 45 0.24
29 68 0.37
30 38 0.20
31 16 0.09
32 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.34
Consensus pattern (30 bp):
AGGGAAAAAATGTAATTTTTGAGAAGTTCG
Found at i:17347 original size:57 final size:56
Alignment explanation
Indices: 17212--17477 Score: 216
Period size: 59 Copynumber: 4.6 Consensus size: 56
17202 TAAAACGTAA
* * * * *
17212 TTTGGAAAGTTTTAGGGATAAAAAAGTTATTTTTGAGAAGTTCGAGAGTAAAAATGTGATT
1 TTTGG-AAGTTTGAGGGA-AAAAATGTAATTTTTG-GAAGTTTG-G-GGAAAAATGTGATT
* * * *
17273 TTTGGAAGTTCGAGGGAAAAAATATAATTTTTGGAAGCTTGGGGAAAAATGTAATT
1 TTTGGAAGTTTGAGGGAAAAAATGTAATTTTTGGAAGTTTGGGGAAAAATGTGATT
* *
17329 TTTGAGAAGTTTG-GGG-GAAAATGTAATTTTTGAGAAGTTTGGGGGTCAAAATGTGATT
1 TTTG-GAAGTTTGAGGGAAAAAATGTAATTTTTG-GAAGTTT-GGGG-AAAAATGTGATT
* * *
17387 TTTGGAAGTTT-AGGGATAAAAATGTGATTTTTGAAAGTTTGGGAGAAAAAAACGTGATT
1 TTTGGAAGTTTGAGGGA-AAAAATGTAATTTTTGGAAGTTTGGG-G--AAAAATGTGATT
* ** *
17446 TTTTGAATGTTCAAAGG-AAAAATGTAATTTTT
1 TTTGGAA-GTTTGAGGGAAAAAATGTAATTTTT
17478 AGAAATTTTA
Statistics
Matches: 169, Mismatches: 25, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
55 14 0.08
56 25 0.15
57 25 0.15
58 27 0.16
59 57 0.34
60 13 0.08
61 8 0.05
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (56 bp):
TTTGGAAGTTTGAGGGAAAAAATGTAATTTTTGGAAGTTTGGGGAAAAATGTGATT
Found at i:17373 original size:29 final size:28
Alignment explanation
Indices: 17261--17436 Score: 185
Period size: 29 Copynumber: 6.2 Consensus size: 28
17251 GTTCGAGAGT
* * *
17261 AAAAATGTGATTTTTGGAAGTTCGAGGGA
1 AAAAATGTAATTTTTGGAAGTTTG-GGGG
* *
17290 AAAAATATAATTTTTGGAAGCTT-GGGG
1 AAAAATGTAATTTTTGGAAGTTTGGGGG
17317 AAAAATGTAATTTTTGAGAAGTTTGGGGG
1 AAAAATGTAATTTTTG-GAAGTTTGGGGG
17346 -AAAATGTAATTTTTGAGAAGTTTGGGGG
1 AAAAATGTAATTTTTG-GAAGTTTGGGGG
* * **
17374 TCAAAATGTGATTTTTGGAAGTTTAGGGAT
1 -AAAAATGTAATTTTTGGAAGTTT-GGGGG
* * *
17404 AAAAATGTGATTTTTGAAAGTTTGGGAG
1 AAAAATGTAATTTTTGGAAGTTTGGGGG
17432 AAAAA
1 AAAAA
17437 AACGTGATTT
Statistics
Matches: 129, Mismatches: 13, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
27 18 0.14
28 43 0.33
29 51 0.40
30 17 0.13
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (28 bp):
AAAAATGTAATTTTTGGAAGTTTGGGGG
Found at i:17566 original size:30 final size:30
Alignment explanation
Indices: 17484--17566 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
17474 TTTTAGAAAT
* *
17484 TTTAGGGGTTAAATTACAATTTTGGAAAAG
1 TTTAGGGGTTAAAATATAATTTTGGAAAAG
*
17514 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
1 TTTAGGGGTTAAAATATAATTTTGGAAAAG
* *
17544 TTTAGGTGTTAAAATATGATTTT
1 TTTAGGGGTTAAAATATAATTTT
17567 TAGAAAGTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (30 bp):
TTTAGGGGTTAAAATATAATTTTGGAAAAG
Found at i:17574 original size:30 final size:30
Alignment explanation
Indices: 17464--17580 Score: 112
Period size: 30 Copynumber: 3.9 Consensus size: 30
17454 GTTCAAAGGA
* *
17464 AAAATGTAATTTTTAG-AAATTTTAGGGGTT
1 AAAATATAA-TTTTAGAAAAGTTTAGGGGTT
* * *
17494 AAATTACAATTTTGGAAAAGTTTAGGGGTT
1 AAAATATAATTTTAGAAAAGTTTAGGGGTT
* * *
17524 AAAATGTAATTTTGGAAAAGTTTAGGTGTT
1 AAAATATAATTTTAGAAAAGTTTAGGGGTT
* *
17554 AAAATATGATTTTTAG-AAAGTTCAGGG
1 AAAATAT-AATTTTAGAAAAGTTTAGGG
17581 ATCTTCTAGG
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
29 5 0.07
30 60 0.85
31 6 0.08
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (30 bp):
AAAATATAATTTTAGAAAAGTTTAGGGGTT
Done.