Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012021.1 Kokia drynarioides strain JFW-HI SEQ_127019, 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: 19269
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:3423 original size:6 final size:6
Alignment explanation
Indices: 3412--3452 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
3402 ATATTTGCAT
*
3412 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA
3453 TTTAATTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:6384 original size:17 final size:17
Alignment explanation
Indices: 6364--6397 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6354 TTTTACATAA
*
6364 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
6381 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
6398 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:6835 original size:16 final size:16
Alignment explanation
Indices: 6790--6829 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
6780 CGTATCAGCA
*
6790 TATTTTTTAAA-AATT
1 TATTATTTAAATAATT
6805 TATTATTTAAATAATT
1 TATTATTTAAATAATT
*
6821 TTTTATTTA
1 TATTATTTA
6830 TTTAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATTTAAATAATT
Found at i:10050 original size:16 final size:15
Alignment explanation
Indices: 10029--10058 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
10019 AATTATTTAA
10029 TTAAAAATATTAAATT
1 TTAAAAA-ATTAAATT
10045 TTAAAAAATTAAAT
1 TTAAAAAATTAAAT
10059 ATTCATTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAAAATTAAATT
Found at i:14170 original size:22 final size:24
Alignment explanation
Indices: 14124--14172 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 24
14114 ATGTGTTTAT
14124 TTTTAAATTTATAAAAACAATATA
1 TTTTAAATTTATAAAAACAATATA
14148 TTTTATAATTT-T-AAAA-AATATA
1 TTTTA-AATTTATAAAAACAATATA
14170 TTT
1 TTT
14173 GACAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.38
23 4 0.17
24 6 0.25
25 5 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTTAAATTTATAAAAACAATATA
Found at i:14179 original size:22 final size:23
Alignment explanation
Indices: 14137--14179 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
14127 TAAATTTATA
* *
14137 AAAACAATATATTTTATAATTTT
1 AAAACAATATATTTGACAATTTT
14160 AAAA-AATATATTTGACAATT
1 AAAACAATATATTTGACAATT
14180 AAATGAGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAACAATATATTTGACAATTTT
Found at i:15844 original size:2 final size:2
Alignment explanation
Indices: 15837--15864 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15827 TATACTTTAA
15837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15865 GAAAAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15943 original size:17 final size:17
Alignment explanation
Indices: 15915--15977 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
15905 GGCCTATTGG
*
15915 AAATTGAATTTATTTTA
1 AAATTAAATTTATTTTA
*
15932 AAATTAAGTTTATTTTA
1 AAATTAAATTTATTTTA
*
15949 AATTTAAATTTA-TTTA
1 AAATTAAATTTATTTTA
15965 AAATTTAAATTTA
1 AAA-TTAAATTTA
15978 AAATGTCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
16 6 0.15
17 34 0.85
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
AAATTAAATTTATTTTA
Found at i:15954 original size:23 final size:23
Alignment explanation
Indices: 15928--15981 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
15918 TTGAATTTAT
*
15928 TTTAAAATTAAGTTT-ATTTTAAA
1 TTTAAAATTAA-TTTAAATTTAAA
*
15951 TTT-AAATTTATTTAAAATTTAAA
1 TTTAAAATTAATTT-AAATTTAAA
15974 TTTAAAAT
1 TTTAAAAT
15982 GTCTAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 3 0.12
22 6 0.23
23 13 0.50
24 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAAAATTAATTTAAATTTAAA
Found at i:16039 original size:15 final size:15
Alignment explanation
Indices: 16015--16085 Score: 99
Period size: 15 Copynumber: 4.7 Consensus size: 15
16005 GTACAGATCT
*
16015 AAATGACCCAATTAC
1 AAATGGCCCAATTAC
16030 AAATGGCCCAATT-C
1 AAATGGCCCAATTAC
*
16044 TAAACGGCCCAATTAC
1 -AAATGGCCCAATTAC
*
16060 AGATGGCCCAATTAC
1 AAATGGCCCAATTAC
16075 AAATGGCCCAA
1 AAATGGCCCAA
16086 GATTCCAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
14 1 0.02
15 47 0.96
16 1 0.02
ACGTcount: A:0.39, C:0.28, G:0.14, T:0.18
Consensus pattern (15 bp):
AAATGGCCCAATTAC
Found at i:16680 original size:3 final size:3
Alignment explanation
Indices: 16674--16701 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16664 AATATTTTAT
16674 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
16702 GAGTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:17869 original size:30 final size:29
Alignment explanation
Indices: 17833--18050 Score: 241
Period size: 30 Copynumber: 7.4 Consensus size: 29
17823 TTTATCCCCC
*
17833 ACTTCCAAAAATCCCATTTTTGACCCCAAA
1 ACTTCCAAAAATCCCATTTTT-ACCCCGAA
*
17863 ACTTCCAAAAATTACCA-TTTTACCCCCG-A
1 ACTTCCAAAAA-TCCCATTTTTA-CCCCGAA
*
17892 ACTTCCAAAAATCCCATTTTTAACCTCGAA
1 ACTTCCAAAAATCCCATTTTT-ACCCCGAA
*
17922 ACTTCCAAAAATTACCA-TTTTACCCCG-A
1 ACTTCCAAAAA-TCCCATTTTTACCCCGAA
* *
17950 ACTTCTAAAAATCCCATTTTTGACCTCGAA
1 ACTTCCAAAAATCCCATTTTT-ACCCCGAA
* *
17980 ATTTCCAAAAATTACCA-TTTTACCCTCG-A
1 ACTTCCAAAAA-TCCCATTTTTACCC-CGAA
18009 ACTTCCAAAAATCCCATTTTTGACCCCGAA
1 ACTTCCAAAAATCCCATTTTT-ACCCCGAA
18039 ACTTCCAAAAAT
1 ACTTCCAAAAAT
18051 TAACATTTTT
Statistics
Matches: 159, Mismatches: 15, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
27 4 0.03
28 23 0.14
29 51 0.32
30 69 0.43
31 12 0.08
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (29 bp):
ACTTCCAAAAATCCCATTTTTACCCCGAA
Found at i:17976 original size:58 final size:59
Alignment explanation
Indices: 17809--18059 Score: 400
Period size: 59 Copynumber: 4.3 Consensus size: 59
17799 CCTTATACTC
*
17809 CCAAAAATTACCATTTTATCCCCC--ACTTCCAAAAATCCCATTTTTGACCCCAAAACTT
1 CCAAAAATTACCATTTTA-CCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
* *
17867 CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAACTT
1 CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
* * *
17926 CCAAAAATTACCATTTTA-CCCCGAACTTCTAAAAATCCCATTTTTGACCTCGAAATTT
1 CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
*
17984 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
1 CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
*
18043 CCAAAAATTAACATTTT
1 CCAAAAATTACCATTTT
18060 TAATCCCGAA
Statistics
Matches: 179, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
57 5 0.03
58 73 0.41
59 101 0.56
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
Found at i:18015 original size:117 final size:117
Alignment explanation
Indices: 17809--18176 Score: 408
Period size: 117 Copynumber: 3.1 Consensus size: 117
17799 CCTTATACTC
*
17809 CCAAAAATTACCATTTTATCCCCCACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAA
1 CCAAAAATTACCATTTTATCCCCAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAA
*
17874 TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAACTT
66 TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAACTT
* * * *
17926 CCAAAAATTACCATTTTA-CCCCGAACTTCTAAAAATCCCATTTTTGACCTCGAAATTTCCAAAA
1 CCAAAAATTACCATTTTATCCCC-AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAA
* *
17990 ATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
65 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAACTT
* * * * * * *
18043 CCAAAAATTAACATTTTTAATCCCGAA-TGTCCGAAGA-CTCCATTCTCGACCTCAAAAC-TCTC
1 CCAAAAATTACCA-TTTT-ATCCCCAACT-TCCAAAAATC-CCATTTTTGACCCCAAAACTTC-C
* * * * * ** *
18105 -AAAGTTACCCTTTTACCCCCGAA-TGT-CTAAAATTCCATTCTTAACCCTAAAATTT
61 AAAAATTACCATTTTACCCCCGAACT-TCCAAAAATCCCATTTTTAACCCCGAAACTT
*
18160 CCCAAAATTACCATTTT
1 CCAAAAATTACCATTTT
18177 GCCCCGTGCA
Statistics
Matches: 214, Mismatches: 29, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
116 8 0.04
117 150 0.70
118 29 0.14
119 24 0.11
120 3 0.01
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (117 bp):
CCAAAAATTACCATTTTATCCCCAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAA
TTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAACTT
Found at i:18171 original size:58 final size:59
Alignment explanation
Indices: 17809--18181 Score: 388
Period size: 59 Copynumber: 6.4 Consensus size: 59
17799 CCTTATACTC
*
17809 CCAAAAATTACCATTTTATCCCCC--ACTTCCAAAAATCCCATTTTTGACCCCAAAACTT
1 CCAAAAATTACCATTTTA-CCCCCGAACTTCCAAAAATCCCATTTTTGACCTCAAAACTT
* *
17867 CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAAACTT
1 CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCAAAACTT
* * *
17926 CCAAAAATTACCATTTTA-CCCCGAACTTCTAAAAATCCCATTTTTGACCTCGAAATTT
1 CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCAAAACTT
* * *
17984 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
1 CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCAAAACTT
* ** * * * *
18043 CCAAAAATTAACATTTTTAATCCCGAA-TGTCCGAAGA-CTCCATTCTCGACCTCAAAAC-T
1 CCAAAAATTACCA-TTTTACCCCCGAACT-TCCAAAAATC-CCATTTTTGACCTCAAAACTT
* * * * * * *
18102 CTC-AAAGTTACCCTTTTACCCCCGAA-TGT-CTAAAATTCCATTCTTAACC-CTAAAATTT
1 C-CAAAAATTACCATTTTACCCCCGAACT-TCCAAAAATCCCATTTTTGACCTC-AAAACTT
* *
18160 CCCAAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
18182 GTGCATCCGA
Statistics
Matches: 270, Mismatches: 34, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
56 1 0.00
57 24 0.09
58 105 0.39
59 108 0.40
60 32 0.12
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCAAAACTT
Found at i:18533 original size:96 final size:96
Alignment explanation
Indices: 18416--18607 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
18406 CTTTAAAAAA
* * *
18416 AATCGAGGCAGTATTCTTTTAT-TTCGAGTTTTGAAAATTTGTGCCTTAA-TTCACTAGGCGCAA
1 AATCGAGGCAGTATTCTTTTATCTTCGA-TTCTGAAAAATTGCGCCTTAACTT-ACTAGGCGCAA
**
18479 TTTTTCTTCAAATCGAAATAATCGAATACCCTT
64 CCTTTCTTCAAATCGAAATAATCGAATACCCTT
*
18512 AATCGAGGCAATGT-TTC-TTTATCTTCGATTCTGAAAAATTGCGCCTTAACTTACTAGGTGCAA
1 AATCGAGGC-A-GTATTCTTTTATCTTCGATTCTGAAAAATTGCGCCTTAACTTACTAGGCGCAA
* * *
18575 CCTTTCTTTAAATCGAGATAATCGAATATCCTT
64 CCTTTCTTCAAATCGAAATAATCGAATACCCTT
18608 TCTGCAAATT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
96 70 0.84
97 11 0.13
98 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAGTATTCTTTTATCTTCGATTCTGAAAAATTGCGCCTTAACTTACTAGGCGCAACC
TTTCTTCAAATCGAAATAATCGAATACCCTT
Done.