Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008352.1 Kokia drynarioides strain JFW-HI SEQ_123019, 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: 13429
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:2219 original size:41 final size:42
Alignment explanation
Indices: 2172--2362 Score: 153
Period size: 41 Copynumber: 4.7 Consensus size: 42
2162 CTATTGCTTA
* *
2172 ACCTTTAGCGACGCTTTCCCATAAGCACT-GCTAATTCTCTG
1 ACCTTTAGCGACGCTTTCTCATAAGCACTCGCTAATGCTCTG
* * * *
2213 ACCTTTAGCGGCGCTTTCTCATATGC-GTCACTAATGCTCTG
1 ACCTTTAGCGACGCTTTCTCATAAGCACTCGCTAATGCTCTG
** * * * * * *
2254 ATTTTTGGTGGCGTTTTCTTATAAGCAC-CG-TAGTGCTCTG
1 ACCTTTAGCGACGCTTTCTCATAAGCACTCGCTAATGCTCTG
* * *
2294 ACCTTTAGCGACTCTTTCTCATAAGC-GTCGCTAATACTCTG
1 ACCTTTAGCGACGCTTTCTCATAAGCACTCGCTAATGCTCTG
*
2335 ACCTTTACCTG-CGCTTT-TCCATAAGCAC
1 ACCTTTAGC-GACGCTTTCT-CATAAGCAC
2363 CACTAAAGAT
Statistics
Matches: 113, Mismatches: 30, Indels: 13
0.72 0.19 0.08
Matches are distributed among these distances:
40 31 0.27
41 81 0.72
42 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.35
Consensus pattern (42 bp):
ACCTTTAGCGACGCTTTCTCATAAGCACTCGCTAATGCTCTG
Found at i:2359 original size:81 final size:81
Alignment explanation
Indices: 2183--2368 Score: 196
Period size: 81 Copynumber: 2.3 Consensus size: 81
2173 CCTTTAGCGA
* * * * *
2183 CGCTTTCCCATAAGCACTGCTAATTCTCTGACCTTTAGCGGCGCTTTCTCATATGCGTCACTAAT
1 CGCTTTTCCATAAGCACCGCTAATGCTCTGACCTTTAGCGACGCTTTCTCATAAGCGTCACTAAT
* * ***
2248 GCTCTGATTTTTGGTG
66 ACTCTGACTTTACCTG
* * * *
2264 -GCGTTTTCTTATAAGCACCG-TAGTGCTCTGACCTTTAGCGACTCTTTCTCATAAGCGTCGCTA
1 CGC-TTTTC-CATAAGCACCGCTAATGCTCTGACCTTTAGCGACGCTTTCTCATAAGCGTCACTA
2327 ATACTCTGACCTTTACCTG
64 ATACTCTGA-CTTTACCTG
*
2346 CGCTTTTCCATAAGCACCACTAA
1 CGCTTTTCCATAAGCACCGCTAA
2369 AGATCAAAGC
Statistics
Matches: 83, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
80 2 0.02
81 58 0.70
82 21 0.25
83 2 0.02
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (81 bp):
CGCTTTTCCATAAGCACCGCTAATGCTCTGACCTTTAGCGACGCTTTCTCATAAGCGTCACTAAT
ACTCTGACTTTACCTG
Found at i:3781 original size:41 final size:41
Alignment explanation
Indices: 3720--3937 Score: 292
Period size: 41 Copynumber: 5.3 Consensus size: 41
3710 TAAATTAACT
* * * * *
3720 TTTAGCGGGGTTTTCTCATAAACGCCTCTATTACTCTGATC
1 TTTAGCGGTGCTTTCCCATAAACGCCGCTATTACTCTGACC
*
3761 TTTAGCGGCGCTTTCCCATAAACGCCGCTATTACTCTGACC
1 TTTAGCGGTGCTTTCCCATAAACGCCGCTATTACTCTGACC
* * *
3802 TTTAGCGGTGCTTTCACATAAATGCCGCTATTACTCTAACC
1 TTTAGCGGTGCTTTCCCATAAACGCCGCTATTACTCTGACC
* * *
3843 TTTAGCGGTGCTTTCCCATAATCGCCGCTAATGCTCTGACC
1 TTTAGCGGTGCTTTCCCATAAACGCCGCTATTACTCTGACC
* * *
3884 TTTAGCGGTGCTTTCCCATAATCGCCGCTAATGCTCTGACC
1 TTTAGCGGTGCTTTCCCATAAACGCCGCTATTACTCTGACC
*
3925 TTTAGCGGCGCTT
1 TTTAGCGGTGCTT
3938 ATGTAAAAAC
Statistics
Matches: 161, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 161 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.33
Consensus pattern (41 bp):
TTTAGCGGTGCTTTCCCATAAACGCCGCTATTACTCTGACC
Found at i:3953 original size:41 final size:41
Alignment explanation
Indices: 3753--3987 Score: 122
Period size: 41 Copynumber: 5.8 Consensus size: 41
3743 GCCTCTATTA
* * * * * *
3753 CTCTGATCTTTAGCGGCGCTT-TCCCATAAACGCCGCTATTA
1 CTCTGACCTTTAGCGGCGCTTAT-GCAAAAACCCCGCTAATG
* ** * *
3794 CTCTGACCTTTAGCGGTGCTT-T-CACATAAATGCCGCTATTA
1 CTCTGACCTTTAGCGGCGCTTATGCA-A-AAACCCCGCTAATG
* * * * * *
3835 CTCTAACCTTTAGCGGTGCTT-TCCCATAATCGCCGCTAATG
1 CTCTGACCTTTAGCGGCGCTTAT-GCAAAAACCCCGCTAATG
* * * * *
3876 CTCTGACCTTTAGCGGTGCTT-TCCCATAATCGCCGCTAATG
1 CTCTGACCTTTAGCGGCGCTTAT-GCAAAAACCCCGCTAATG
* *
3917 CTCTGACCTTTAGCGGCGCTTATGTAAAAACCCCGCTATTG
1 CTCTGACCTTTAGCGGCGCTTATGCAAAAACCCCGCTAATG
* * * * *
3958 CT-TTACCTTTTGCGACGTTTATGGAAAAAC
1 CTCTGACCTTTAGCGGCGCTTATGCAAAAAC
3988 GCTGCTATTG
Statistics
Matches: 166, Mismatches: 23, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.01
40 23 0.14
41 138 0.83
42 1 0.01
43 2 0.01
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (41 bp):
CTCTGACCTTTAGCGGCGCTTATGCAAAAACCCCGCTAATG
Found at i:3980 original size:40 final size:40
Alignment explanation
Indices: 3908--4008 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 40
3898 CCCATAATCG
* * * * *
3908 CCGCTAATGCTCTGACCTTTAGCGGCGCTTATGTAAAAACC
1 CCGCTATTGCT-TTACCTTTTGCGACGCTTATGGAAAAACC
* *
3949 CCGCTATTGCTTTACCTTTTGCGACGTTTATGGAAAAACG
1 CCGCTATTGCTTTACCTTTTGCGACGCTTATGGAAAAACC
*
3989 CTGCTATTG-TTTCACCTTTT
1 CCGCTATTGCTTT-ACCTTTT
4009 TTGCGGTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.06
40 38 0.75
41 10 0.20
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (40 bp):
CCGCTATTGCTTTACCTTTTGCGACGCTTATGGAAAAACC
Found at i:4301 original size:16 final size:18
Alignment explanation
Indices: 4262--4295 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4252 TAAGTTTATA
4262 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
4279 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
4296 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:6467 original size:21 final size:20
Alignment explanation
Indices: 6439--6483 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
6429 CTATGTTTAT
*
6439 AAAAGGTGTTTTG-AAGAAGA
1 AAAAGGTGTTTGGCAAG-AGA
6459 AAAATGGTGTTTGGCAAGAGA
1 AAAA-GGTGTTTGGCAAGAGA
6480 AAAA
1 AAAA
6484 ATGAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.29, T:0.22
Consensus pattern (20 bp):
AAAAGGTGTTTGGCAAGAGA
Found at i:6952 original size:19 final size:21
Alignment explanation
Indices: 6928--6968 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6918 ATATTCTTAT
*
6928 AAAAATT-AA-AAATATATAA
1 AAAAATTCAATAAATACATAA
6947 AAAAATTCAATAAATACATAA
1 AAAAATTCAATAAATACATAA
6968 A
1 A
6969 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 10 0.53
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAATTCAATAAATACATAA
Found at i:9072 original size:24 final size:25
Alignment explanation
Indices: 9044--9091 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
9034 ATATTAATAA
*
9044 AATC-AAGATTCTTTCACACCAAAT
1 AATCAAAGATTATTTCACACCAAAT
* *
9068 AATCAAATATTATTTCACATCAAA
1 AATCAAAGATTATTTCACACCAAA
9092 CATGTTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (25 bp):
AATCAAAGATTATTTCACACCAAAT
Found at i:12442 original size:29 final size:29
Alignment explanation
Indices: 12391--12872 Score: 409
Period size: 29 Copynumber: 16.4 Consensus size: 29
12381 AAAATGGTGG
**
12391 TTTTGGAAGGTTCGAAGTCAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGTCAAAAATGGGAT
* *
12421 TTTTGGAAGTTCGAGGTAAAAAATGGGAT
1 TTTTGGAAGTTCGGGGTCAAAAATGGGAT
*
12450 TTTTGGAAGTTCGGGGT--AAAATGGTAAT
1 TTTTGGAAGTTCGGGGTCAAAAATGG-GAT
* *
12478 TTTTAGATGGTTCGGGGTCAAAAATGGGAT
1 TTTTGGA-AGTTCGGGGTCAAAAATGGGAT
* * *
12508 TTTTGGATGTTTGGGGGT--AAAATGGTAAT
1 TTTTGGAAG-TTCGGGGTCAAAAATGG-GAT
* * *
12537 TTTTGAAAGGTTCGAGGTCAAAAATGAGAT
1 TTTTGGAA-GTTCGGGGTCAAAAATGGGAT
* *
12567 TTTTGGATGTTCGGGGGT--AAAATGGTAAT
1 TTTTGGAAGTTC-GGGGTCAAAAATGG-GAT
12596 TTTTGGAAGGTTCGGGGTCAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGTCAAAAATGGGAT
* *
12626 TTTTGGAAGTTTGGGGGT--AAAATGGTAAT
1 TTTTGGAAG-TTCGGGGTCAAAAATGG-GAT
*
12655 TTTTGGAAGGTTCGAGGTCAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGTCAAAAATGGGAT
**
12685 TTTTGGAAGTTCGGGGGT--AAAATAGTAAT
1 TTTTGGAAGTTC-GGGGTCAAAAAT-GGGAT
*
12714 TTTTGAAAGGTTCGGGGTCAAAAAT-GGAT
1 TTTTGGAA-GTTCGGGGTCAAAAATGGGAT
**
12743 TTTTGGAAGTTCGAGGGT--AAAATGATATT
1 TTTTGGAAGTTCG-GGGTCAAAAATGGGA-T
*
12772 TTTTGTAAGGTTCGGGGTCAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGTCAAAAATGGGAT
*
12802 TTTTGGAAGTTCGGGGGT--AAAATGGTAAT
1 TTTTGGAAGTTC-GGGGTCAAAAATGG-GAT
* * * *
12831 TTTCGAAAGGTTCGAGGTAAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGTCAAAAATGGGAT
12861 TTTTGGAAGTTC
1 TTTTGGAAGTTC
12873 AGGGACCTTT
Statistics
Matches: 368, Mismatches: 49, Indels: 71
0.75 0.10 0.15
Matches are distributed among these distances:
27 12 0.03
28 46 0.12
29 158 0.43
30 106 0.29
31 46 0.12
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (29 bp):
TTTTGGAAGTTCGGGGTCAAAAATGGGAT
Found at i:12455 original size:59 final size:58
Alignment explanation
Indices: 12411--12872 Score: 651
Period size: 59 Copynumber: 7.9 Consensus size: 58
12401 TTCGAAGTCA
* *
12411 AAAATGG-GATTTTTGGAA-GTTCGAGGTAAAAAATGGGATTTTTGGAAGTTCGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGT
* * * * *
12467 AAAATGGTAATTTTTAGATGGTTCGGGGTCAAAAATGGGATTTTTGGATGTTTGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGT
* * *
12526 AAAATGGTAATTTTTGAAAGGTTCGAGGTCAAAAATGAGATTTTTGGATGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC-GGGGT
* *
12585 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGT
12644 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC-GGGGT
* * *
12703 AAAATAGTAATTTTTGAAAGGTTCGGGGTCAAAAAT-GGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGT
* * * *
12761 AAAATGATATTTTTTGTAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC-GGGGT
* * *
12820 AAAATGGTAATTTTCGAAAGGTTCGAGGTAAAAAATGGGATTTTTGGAAGTTC
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC
12873 AGGGACCTTT
Statistics
Matches: 364, Mismatches: 33, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
56 7 0.02
57 9 0.02
58 83 0.23
59 262 0.72
60 3 0.01
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGT
Found at i:12784 original size:176 final size:177
Alignment explanation
Indices: 12419--12872 Score: 716
Period size: 176 Copynumber: 2.6 Consensus size: 177
12409 CAAAAATGGG
* * *
12419 ATTTTTGGAA-GTTCGAGGTAAAAAATGGGATTTTTGGAAG-TTCGGGGTAAAATGGTAATTTTT
1 ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTT
* * * * * *
12482 AGATGGTTCGGGGTCAAAAATGGGATTTTTGGATGTTTGGGGGTAAAATGGTAATTTTTGAAAGG
66 GGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGAAAGG
* * *
12547 TTCGAGGTCAAAAATGAGATTTTTGGATGTTCGGGGGTAAAATGGTA
131 TTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGATA
12594 ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTT
1 ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTT
12659 GGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGAAAGG
66 GGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGAAAGG
*
12724 TTCGGGGTCAAAAATG-GATTTTTGGAAGTTCGAGGGTAAAATGATA
131 TTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGATA
* * * *
12770 TTTTTTGTAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTC
1 ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTT
* *
12835 GAAAGGTTCGAGGTAAAAAATGGGATTTTTGGAAGTTC
66 GGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC
12873 AGGGACCTTT
Statistics
Matches: 258, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
175 10 0.04
176 152 0.59
177 96 0.37
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (177 bp):
ATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTT
GGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGAAAGG
TTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGATA
Done.