Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002195.1 Kokia drynarioides strain JFW-HI SEQ_114174, 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: 5785
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Found at i:661 original size:6 final size:6
Alignment explanation
Indices: 650--726 Score: 65
Period size: 6 Copynumber: 13.7 Consensus size: 6
640 TAGATTTGAA
* * *
650 TAAATT TAAATT TAAA-- TAATTT TAAATT TAAA-A TAAATT TAAACT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * *
695 TAAAAT T-AATT TAACTT TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
727 CCTAAAACAA
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
4 3 0.05
5 12 0.22
6 40 0.73
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:662 original size:16 final size:16
Alignment explanation
Indices: 638--726 Score: 97
Period size: 17 Copynumber: 5.4 Consensus size: 16
628 CATTATTTAT
* *
638 TTTAGATTTGAATAAA
1 TTTAAATTTAAATAAA
*
654 TTTAAATTTAAATAAT
1 TTTAAATTTAAATAAA
670 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
* *
687 TTTAAACTTAAAATTAA
1 TTTAAA-TTTAAATAAA
*
704 TTTAACTTTAAAATAAA
1 TTTAAATTT-AAATAAA
721 TTTAAA
1 TTTAAA
727 CCTAAAACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
16 24 0.40
17 34 0.57
18 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:685 original size:17 final size:17
Alignment explanation
Indices: 648--743 Score: 122
Period size: 17 Copynumber: 5.7 Consensus size: 17
638 TTTAGATTTG
648 AATAAATTTAAATTT-A
1 AATAAATTTAAATTTAA
*
664 AATAATTTTAAATTTAA
1 AATAAATTTAAATTTAA
*
681 AATAAATTTAAACTTAA
1 AATAAATTTAAATTTAA
* *
698 AATTAATTTAACTTTAA
1 AATAAATTTAAATTTAA
**
715 AATAAATTTAAACCTAA
1 AATAAATTTAAATTTAA
*
732 AACAAATTTAAA
1 AATAAATTTAAA
744 AATAAGTTCA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
16 14 0.21
17 54 0.79
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:688 original size:11 final size:11
Alignment explanation
Indices: 672--726 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
662 TAAATAATTT
672 TAAATTTAAAA
1 TAAATTTAAAA
*
683 TAAATTTAAACT
1 TAAATTTAAA-A
* **
695 TAAAATTAATT
1 TAAATTTAAAA
*
706 TAACTTTAAAA
1 TAAATTTAAAA
717 TAAATTTAAA
1 TAAATTTAAA
727 CCTAAAACAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
11 27 0.77
12 8 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:4134 original size:21 final size:22
Alignment explanation
Indices: 4078--4137 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
4068 CGATCTGAGG
*
4078 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
4099 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
4121 AAAAA-AATAGAAAATAG
1 AAAAATAAAAGAAAATAG
4138 GAAAGTCGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:4639 original size:49 final size:49
Alignment explanation
Indices: 4567--4660 Score: 188
Period size: 49 Copynumber: 1.9 Consensus size: 49
4557 GCGTCAATCA
4567 CGTATTACAGAGAATTGATGAATACTCGGGTTGAAAAGAGTTAAGATCC
1 CGTATTACAGAGAATTGATGAATACTCGGGTTGAAAAGAGTTAAGATCC
4616 CGTATTACAGAGAATTGATGAATACTCGGGTTGAAAAGAGTTAAG
1 CGTATTACAGAGAATTGATGAATACTCGGGTTGAAAAGAGTTAAG
4661 CACGGATTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.27
Consensus pattern (49 bp):
CGTATTACAGAGAATTGATGAATACTCGGGTTGAAAAGAGTTAAGATCC
Found at i:4957 original size:36 final size:36
Alignment explanation
Indices: 4916--5012 Score: 167
Period size: 36 Copynumber: 2.7 Consensus size: 36
4906 CTTATGGGGA
*
4916 AGCGCCGCTAAAGGTCAGAGCAATAAAGACCAGAGC
1 AGCGCCGCTAAAGGTTAGAGCAATAAAGACCAGAGC
*
4952 AGCGCCGCTAAAGGTTAGAGCAATAAAGATCAGAGC
1 AGCGCCGCTAAAGGTTAGAGCAATAAAGACCAGAGC
*
4988 AGCGCCGCTAAATGTTAGAGCAATA
1 AGCGCCGCTAAAGGTTAGAGCAATA
5013 GCGGCGCTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (36 bp):
AGCGCCGCTAAAGGTTAGAGCAATAAAGACCAGAGC
Found at i:5052 original size:41 final size:41
Alignment explanation
Indices: 4880--5217 Score: 317
Period size: 41 Copynumber: 8.5 Consensus size: 41
4870 TACATAAACA
* * * *
4880 CCGCAAAAGGT-AGAGCAATAGCAGTGCTTATGGGGAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
** * *
4920 CCGCTAAAGGTCAGAGCAATAAAGAC-C--A-GAGC-AGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
* ** * * *
4956 CCGCTAAAGGTTAGAGCAATA---AAGATCA-GAGC-AGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
* *
4992 CCGCTAAATGTTAGAGCAATAGCGGCGCTTATGGGCAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
*
5033 CCGCTAAAGGTCA-ATGCAATAGCGGCGCTTATGGGAAAGCG
1 CCGCTAAAGGTCAGA-GCAATAGCGGCGCTTATGGGCAAGCG
* * *
5074 CTGCTAAAGGTCAGAGCAATAG-GACGCTTATGAGCAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
* * * *
5114 CCGCTACAGATCAGAGCAATAGCGGCGCTTAAGGGCAAGTG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
**
5155 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTAT-GAAAATGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAA-GCG
*
5196 CCGCTAAAAGTCAGAGCAATAG
1 CCGCTAAAGGTCAGAGCAATAG
5218 TGGAGCTTTC
Statistics
Matches: 247, Mismatches: 38, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
33 1 0.00
36 53 0.21
37 2 0.01
38 1 0.00
39 3 0.01
40 52 0.21
41 134 0.54
42 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.30, T:0.15
Consensus pattern (41 bp):
CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
Found at i:5119 original size:81 final size:82
Alignment explanation
Indices: 4880--5217 Score: 317
Period size: 81 Copynumber: 4.3 Consensus size: 82
4870 TACATAAACA
* * * * * **
4880 CCGCAAAAGGT-AGAGCAATAGCAGTGCTTATGGGGAAGCGCCGCTAAAGGTCAGAGCAATAAAG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTAAGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCG
*
4944 AC-C--A-GAGC-AGCG
66 GCGCTTATGAGCAAGCG
* ** * * * * * *
4956 CCGCTAAAGGTTAGAGCAATA---AAG-ATCAGAG-CAGCGCCGCTAAATGTTAGAGCAATAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTAAGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCG
*
5016 GCGCTTATGGGCAAGCG
66 GCGCTTATGAGCAAGCG
* *
5033 CCGCTAAAGGTCA-ATGCAATAGCGGCGCTTATGGGAAAGCGCTGCTAAAGGTCAGAGCAATAG-
1 CCGCTAAAGGTCAGA-GCAATAGCGGCGCTTAAGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGC
*
5096 GACGCTTATGAGCAAGCG
65 GGCGCTTATGAGCAAGCG
* * * *
5114 CCGCTACAGATCAGAGCAATAGCGGCGCTTAAGGGCAAGTGCCGCTAAAGGTCAGAGCAATAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTAAGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCG
*
5179 GCGCTTATGA-AAATGCG
66 GCGCTTATGAGCAA-GCG
*
5196 CCGCTAAAAGTCAGAGCAATAG
1 CCGCTAAAGGTCAGAGCAATAG
5218 TGGAGCTTTC
Statistics
Matches: 209, Mismatches: 38, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
72 25 0.12
73 4 0.02
74 1 0.00
75 1 0.00
76 14 0.07
77 31 0.15
80 1 0.00
81 76 0.36
82 56 0.27
ACGTcount: A:0.33, C:0.22, G:0.30, T:0.15
Consensus pattern (82 bp):
CCGCTAAAGGTCAGAGCAATAGCGGCGCTTAAGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCG
GCGCTTATGAGCAAGCG
Done.