Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011349.1 Kokia drynarioides strain JFW-HI SEQ_126329, 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: 12116
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:3624 original size:29 final size:30
Alignment explanation
Indices: 3575--3867 Score: 330
Period size: 30 Copynumber: 9.9 Consensus size: 30
3565 GGAAATTTTA
* *
3575 GGGTAAAAAATGGGATTTTTTGGAAG-TTCG
1 GGGTTAAAAAT-GGAATTTTTGGAAGTTTCG
*
3605 GGGTTAAAAATGGGATTTTTGGAAGTTTCG
1 GGGTTAAAAATGGAATTTTTGGAAGTTTCG
* *
3635 GAGTTAAAAATGGAATTTTTGAAAGTTTCG
1 GGGTTAAAAATGGAATTTTTGGAAGTTTCG
* * *
3665 GGGTCAAAAATGGAATTTTTAGAAGTTTAG
1 GGGTTAAAAATGGAATTTTTGGAAGTTTCG
3695 GGG-TAAAAATGGAATTTTTGGAAGTTTCG
1 GGGTTAAAAATGGAATTTTTGGAAGTTTCG
* *
3724 GGGTCAAAAATGGGATTTTTGGAAG-TTCG
1 GGGTTAAAAATGGAATTTTTGGAAGTTTCG
* *
3753 GAGG-TAAAAAT-GAAATTTTAGAAGTTTCG
1 G-GGTTAAAAATGGAATTTTTGGAAGTTTCG
** *
3782 GGGACAAAAATGGGATTTTTGGAAG-TTCG
1 GGGTTAAAAATGGAATTTTTGGAAGTTTCG
* * *
3811 GGGGTAAAAATGAAATTTTTGAAAGTTTCG
1 GGGTTAAAAATGGAATTTTTGGAAGTTTCG
* *
3841 TGGTCAAAAAT-GAGATTTTTGGAAGTT
1 GGGTTAAAAATGGA-ATTTTTGGAAGTT
3868 AGGGACCTCC
Statistics
Matches: 221, Mismatches: 34, Indels: 16
0.82 0.13 0.06
Matches are distributed among these distances:
28 12 0.05
29 85 0.38
30 124 0.56
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.33
Consensus pattern (30 bp):
GGGTTAAAAATGGAATTTTTGGAAGTTTCG
Found at i:3705 original size:59 final size:59
Alignment explanation
Indices: 3571--3871 Score: 378
Period size: 59 Copynumber: 5.1 Consensus size: 59
3561 TTTGGGAAAT
* * *
3571 TTTA-GGGTAAAAAATGGGATTTTTTGGAAG-TTCGGGGTTAAAAATGGGATTTTTGGAAG
1 TTTAGGGGT-AAAAAT-GGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * *
3630 TTTCGGAGTTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAG
1 TTTAGG-GGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
*
3690 TTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
1 TTTAGGGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * *
3749 -TTCGGAGGTAAAAATGAAATTTTAG-AAGTTTCGGGGACAAAAATGGGATTTTTGGAAG
1 TTTAGG-GGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
** * * *
3807 TTCGGGGGTAAAAATGAAATTTTTGAAAGTTTCGTGGTCAAAAATGAGATTTTTGGAAG
1 TTTAGGGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
3866 -TTAGGG
1 TTTAGGG
3872 ACCTCCAAGG
Statistics
Matches: 212, Mismatches: 24, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
58 58 0.27
59 114 0.54
60 38 0.18
61 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
TTTAGGGGTAAAAATGGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
Found at i:4804 original size:13 final size:13
Alignment explanation
Indices: 4788--4816 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4778 TTATTTACCC
4788 TTTTTA-TTTATT
1 TTTTTATTTTATT
4800 TTTTTATTTTATT
1 TTTTTATTTTATT
4813 TTTT
1 TTTT
4817 AAAAGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:5605 original size:17 final size:17
Alignment explanation
Indices: 5568--5683 Score: 151
Period size: 17 Copynumber: 6.6 Consensus size: 17
5558 TTATTTATTT
5568 TAAATTTTAAATTTGAAAA
1 TAAA-TTTAAATTT-AAAA
* *
5587 TAATTTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
5604 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
5622 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
5639 TAAATTTAAAATTTTAAA
1 TAAATTT-AAATTTAAAA
* *
5657 CAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
5674 TAAATTTAAA
1 TAAATTTAAA
5684 GGGAGTATAG
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
17 43 0.51
18 39 0.46
19 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:5614 original size:35 final size:34
Alignment explanation
Indices: 5568--5683 Score: 153
Period size: 35 Copynumber: 3.3 Consensus size: 34
5558 TTATTTATTT
* *
5568 TAAATTTTAAATTTGAAAATAATTTTAAACTTAAAA
1 TAAA-TTTAAATTTTAAAATAA-TTTAAATTTAAAA
5604 TAAATTTAAATTTTAAAATAAATTTAAATTTAAAA
1 TAAATTTAAATTTTAAAAT-AATTTAAATTTAAAA
*
5639 TAAATTTAAAATTTTAAACA-AATTTAATTTTAAAA
1 TAAATTT-AAATTTTAAA-ATAATTTAAATTTAAAA
5674 TAAATTTAAA
1 TAAATTTAAA
5684 GGGAGTATAG
Statistics
Matches: 74, Mismatches: 3, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
34 3 0.04
35 54 0.73
36 16 0.22
37 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (34 bp):
TAAATTTAAATTTTAAAATAATTTAAATTTAAAA
Found at i:5615 original size:24 final size:24
Alignment explanation
Indices: 5588--5637 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5578 ATTTGAAAAT
*
5588 AATTTTAAACTTAAA-ATAAATTTA
1 AATTTTAAA-ATAAATATAAATTTA
*
5612 AATTTTAAAATAAATTTAAATTTA
1 AATTTTAAAATAAATATAAATTTA
5636 AA
1 AA
5638 ATAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTTTAAAATAAATATAAATTTA
Found at i:6141 original size:92 final size:90
Alignment explanation
Indices: 5964--6158 Score: 207
Period size: 92 Copynumber: 2.1 Consensus size: 90
5954 TTAATATAAT
* * * * * *
5964 ATTTGGTATCTAAATTTGATAATTTTTCTTAATTTGGTATCTAAATTTTTTTGGTCTAATTTAGT
1 ATTTGGTACCTAAATTTGACAATTTTTCTTAAGTTGGTATCTAAACTTTTTGGGTCCAATTTAGT
**
6029 ACTCAAACTTCATACTTTTTTTTTTTA
66 ACTCAAACTTCATAC--TTTTTTCCTA
* * *
6056 ATTTGGTACCTAAATTTGACACTTTTTTTTAAGTTGGTATTTAAACTTTTTGGAGTCCAATTTAG
1 ATTTGGTACCTAAATTTGACAATTTTTCTTAAGTTGGTATCTAAACTTTTTGG-GTCCAATTTAG
* *
6121 TAC-CTGAACTT--GACTCTTTTTCCTA
65 TACTC-AAACTTCATACT-TTTTTCCTA
6146 ATTTGGTACCTAA
1 ATTTGGTACCTAA
6159 TTTTTTTTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
89 1 0.01
90 20 0.23
91 2 0.02
92 46 0.53
93 18 0.21
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (90 bp):
ATTTGGTACCTAAATTTGACAATTTTTCTTAAGTTGGTATCTAAACTTTTTGGGTCCAATTTAGT
ACTCAAACTTCATACTTTTTTCCTA
Found at i:6372 original size:31 final size:31
Alignment explanation
Indices: 6336--6426 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
6326 AAAAAAGCTT
6336 AGGTACCAAATTAGGAAAAAATGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAATGTCAAGTTC
* ** *
6367 AGGTACCAAATTGGGTCCAAAA----AAGTTT
1 AGGTACCAAATTAGG-AAAAAATGTCAAGTTC
6395 AGGTACCAAATTAGGAAAAAATGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAATGTCAAGTTC
6426 A
1 A
6427 ATTATTAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
27 4 0.09
28 19 0.40
31 20 0.43
32 4 0.09
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (31 bp):
AGGTACCAAATTAGGAAAAAATGTCAAGTTC
Found at i:6402 original size:59 final size:58
Alignment explanation
Indices: 6326--6494 Score: 207
Period size: 59 Copynumber: 2.9 Consensus size: 58
6316 TTAAATCTAA
* * *
6326 AAAAAAGCTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGGTCC
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGATACCAAATTAGGT-C
**
6385 AAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCA-ATTATTAAATTAGGTC
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGA-TACCAAATTAGGTC
* ** * *
6443 AAAAAA-TTTAGATACCAAATTAAAAAAAAACTTTCAAATTCAGATACCAAAT
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAAA-TGTCAAGTTCAGATACCAAAT
6495 ATTATATTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
57 21 0.22
58 22 0.23
59 52 0.55
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (58 bp):
AAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGATACCAAATTAGGTC
Done.