Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003490.1 Kokia drynarioides strain JFW-HI SEQ_116309, 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: 4470
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Found at i:1400 original size:37 final size:37
Alignment explanation
Indices: 1314--1414 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 37
1304 ACAAAACACG
*
1314 GAGAGCAGCA-TAAAGATTCTCTGCAAAGAAAAGATA
1 GAGAGCAACAGTAAAGATTCTCTGCAAAGAAAAGATA
* ** *
1350 GAGATCAACAGTAAAGATTCTCTGCAAAGAATGGATG
1 GAGAGCAACAGTAAAGATTCTCTGCAAAGAAAAGATA
* * * *
1387 GAGAGGAATAGTAAAAATTTTCTGCAAA
1 GAGAGCAACAGTAAAGATTCTCTGCAAA
1415 ATTTTTGTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 8 0.15
37 46 0.85
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.21
Consensus pattern (37 bp):
GAGAGCAACAGTAAAGATTCTCTGCAAAGAAAAGATA
Found at i:1773 original size:15 final size:16
Alignment explanation
Indices: 1744--1775 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1734 AAACCAAATC
1744 AAATTTAAGTTTTCAA
1 AAATTTAAGTTTTCAA
1760 AAATTTAA-TTTTCAA
1 AAATTTAAGTTTTCAA
1775 A
1 A
1776 TTATTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATTTAAGTTTTCAA
Found at i:1906 original size:6 final size:6
Alignment explanation
Indices: 1895--1972 Score: 67
Period size: 6 Copynumber: 13.7 Consensus size: 6
1885 GGCCCAACAG
* * * *
1895 AATTTA AATTT- ATTTTA AGTTTA AATTT- ACTTAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
1940 -A-TTA TAATTTA AGTTTA AATTTA AATTTA AATT
1 AATTTA -AATTTA AATTTA AATTTA AATTTA AATT
1973 AATGTCCAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 7 0.12
6 44 0.77
7 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:1919 original size:17 final size:17
Alignment explanation
Indices: 1895--1972 Score: 86
Period size: 17 Copynumber: 4.6 Consensus size: 17
1885 GGCCCAACAG
1895 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* * *
1912 AGTTTAAATTTACTTAA
1 AATTTAAATTTATTTTA
*
1929 AATTTAAATTTATTAT-
1 AATTTAAATTTATTTTA
* *
1945 AATTTAAGTTTAAATTTA
1 AATTTAAATTT-ATTTTA
1963 AATTTAAATT
1 AATTTAAATT
1973 AATGTCCAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
16 10 0.21
17 29 0.60
18 9 0.19
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:1938 original size:34 final size:34
Alignment explanation
Indices: 1895--1972 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
1885 GGCCCAACAG
* *
1895 AATTTAAATTTATTTTAAGTTTAAATTT-ACTTAA
1 AATTTAAATTTATTATAA-TTTAAATTTAAATTAA
* *
1929 AATTTAAATTTATTATAATTTAAGTTTAAATTTA
1 AATTTAAATTTATTATAATTTAAATTTAAATTAA
1963 AATTTAAATT
1 AATTTAAATT
1973 AATGTCCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 8 0.21
34 31 0.79
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
AATTTAAATTTATTATAATTTAAATTTAAATTAA
Found at i:3876 original size:30 final size:29
Alignment explanation
Indices: 3779--4029 Score: 122
Period size: 29 Copynumber: 8.6 Consensus size: 29
3769 CCCTAAACTG
* * *
3779 TCCAAAAATTCCATTTTTGATCCTAAAATT
1 TCCAAAAATTCTATTTTT-ACCCCAAAATT
*** * * *
3809 TTTGAAAATTATA-TTTTACCCTCGAACTT
1 TCCAAAAATTCTATTTTTACCC-CAAAATT
3838 T-CAAAAATTCTATTTTTGACCCCAAAATT
1 TCCAAAAATTCTATTTTT-ACCCCAAAATT
* * *
3867 TCAAAAAATTAT-TTTTTAGCCCC-AAACT
1 TCCAAAAATTCTATTTTTA-CCCCAAAATT
* *
3895 TCCAAAAATTCTATTTTTAACCTCGAAATT
1 TCCAAAAATTCTATTTTT-ACCCCAAAATT
* **
3925 TCCAAAAATTAC-ATTTTTA-CCCACGAACC
1 TCCAAAAATT-CTATTTTTACCCCA-AAATT
* * ***
3954 TCCAAAATTTCCATTTTTGACCCCAAGCCT
1 TCCAAAAATTCTATTTTT-ACCCCAAAATT
* ** *
3984 T-CAAAAATTACCA-TTTTACCCCTGAATG
1 TCCAAAAATT-CTATTTTTACCCCAAAATT
*
4012 TCCAAAAATTCCATTTTT
1 TCCAAAAATTCTATTTTT
4030 TATCTCGATT
Statistics
Matches: 167, Mismatches: 38, Indels: 33
0.70 0.16 0.14
Matches are distributed among these distances:
28 38 0.23
29 77 0.46
30 47 0.28
31 5 0.03
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (29 bp):
TCCAAAAATTCTATTTTTACCCCAAAATT
Found at i:3989 original size:58 final size:55
Alignment explanation
Indices: 3774--4088 Score: 220
Period size: 58 Copynumber: 5.4 Consensus size: 55
3764 GAGGTCCCTA
** ** *
3774 AACTGTCCAAAAATTCCATTTTTGATCCTAAAATTTTTGAAAATTATATTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTTTGA-CCCCAAA-TTTCAAAAATTACATTTTACCC-CG
* * ** *
3833 AACTTTCAAAAATTCTATTTTTGACCCCAAAATTTCAAAAAATTATTTTTTAGCCCCA
1 AACTTCCAAAAATTCCATTTTTGACCCC-AAATTTC-AAAAATTACATTTTA-CCCCG
* * *
3891 AACTTCCAAAAATTCTATTTTTAACCTCGAAATTTCCAAAAATTACATTTTTACCCACG
1 AACTTCCAAAAATTCCATTTTTGACC-CCAAATTT-CAAAAATTACA-TTTTACCC-CG
* * **
3950 AACCTCCAAAATTTCCATTTTTGACCCCAAGCCTTCAAAAATTACCATTTTACCCCTG
1 AACTTCCAAAAATTCCATTTTTGACCCCAA-ATTTCAAAAATTA-CATTTTACCCC-G
* * * * *
4008 AA-TGTCCAAAAATTCCATTTTTTATCTCGATTTTCCTAAAAATTACCATTTTATCCCCG
1 AACT-TCCAAAAATTCCATTTTTGACCCCAAATTT-C-AAAAATTA-CATTTTA-CCCCG
* *
4067 GA-TGTCCAAAAATTCCGTTTTT
1 AACT-TCCAAAAATTCCATTTTT
4089 TATCCCGATT
Statistics
Matches: 211, Mismatches: 31, Indels: 28
0.78 0.11 0.10
Matches are distributed among these distances:
57 8 0.04
58 121 0.57
59 78 0.37
60 4 0.02
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.37
Consensus pattern (55 bp):
AACTTCCAAAAATTCCATTTTTGACCCCAAATTTCAAAAATTACATTTTACCCCG
Found at i:4017 original size:29 final size:28
Alignment explanation
Indices: 3925--4080 Score: 97
Period size: 29 Copynumber: 5.4 Consensus size: 28
3915 CCTCGAAATT
**
3925 TCCAAAAATTA-CATTTTTACCCACGAACC
1 TCCAAAAATTACCA-TTTTACCC-CGAATG
*
3954 TCC-AAAATTTCCATTTTTGACCCC-AA-G
1 TCCAAAAATTACCA-TTTT-ACCCCGAATG
*
3981 CCTTCAAAAATTACCATTTTACCCCTGAATG
1 --TCCAAAAATTACCATTTTACCCC-GAATG
* * * *
4012 TCCAAAAATT-CCATTTTTTATCTCGATTT
1 TCCAAAAATTACCA--TTTTACCCCGAATG
*
4041 TCCTAAAAATTACCATTTTATCCCCGGATG
1 TCC-AAAAATTACCATTTTA-CCCCGAATG
4071 TCCAAAAATT
1 TCCAAAAATT
4081 CCGTTTTTTA
Statistics
Matches: 100, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
28 16 0.16
29 44 0.44
30 36 0.36
31 4 0.04
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.35
Consensus pattern (28 bp):
TCCAAAAATTACCATTTTACCCCGAATG
Found at i:4049 original size:30 final size:29
Alignment explanation
Indices: 4012--4100 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 29
4002 CCCCTGAATG
*
4012 TCCAAAAATTCCATTTTTTATCTCGATTT
1 TCCAAAAATTCCATTTTTTATCCCGATTT
*
4041 TCCTAAAAATTACCA--TTTTATCCCCGGA-TG
1 TCC-AAAAATT-CCATTTTTTAT-CCC-GATTT
*
4071 TCCAAAAATTCCGTTTTTTATCCCGATTT
1 TCCAAAAATTCCATTTTTTATCCCGATTT
4100 T
1 T
4101 TTTAAAAGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
28 4 0.08
29 21 0.43
30 19 0.39
31 5 0.10
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.43
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTTATCCCGATTT
Found at i:4060 original size:59 final size:59
Alignment explanation
Indices: 3986--4177 Score: 226
Period size: 59 Copynumber: 3.3 Consensus size: 59
3976 CCAAGCCTTC
3986 AAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTTATCTCGATTTTCCT
1 AAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTTATCTCGATTTTCCT
* * * **
4045 AAAAATTACCATTTTATCCCC-GGATGTCCAAAAATTCCGTTTTTTATCCCGATTTTTTT
1 AAAAATTACCATTTTA-CCCCTGAATGTCCAAAAATTCCATTTTTTATCTCGATTTTCCT
* * * * * * * *
4104 AAAAGTTACCGTTTTACCCCTGAGTGTCTATAAATTCCATTTTTAACCTCGAACTTTCC-
1 AAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTTATCTCG-ATTTTCCT
*
4163 CAAAATTACCATTTT
1 AAAAATTACCATTTT
4178 TCCTCAAAGT
Statistics
Matches: 109, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
58 4 0.04
59 97 0.89
60 8 0.07
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.40
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTTATCTCGATTTTCCT
Found at i:4088 original size:29 final size:27
Alignment explanation
Indices: 3985--4094 Score: 71
Period size: 30 Copynumber: 3.7 Consensus size: 27
3975 CCCAAGCCTT
*
3985 CAAAAATTACCATTTTA-CCCCTGAATGTC
1 CAAAAATT-CCTTTTTATCCCC-G-ATGTC
* *
4014 CAAAAATTCCATTTTTTAT-CTCGATTTTC
1 CAAAAATTCC--TTTTTATCCCCGA-TGTC
*
4043 CTAAAAATTACCATTTTATCCCCGGATGTC
1 C-AAAAATT-CCTTTTTATCCCC-GATGTC
4073 CAAAAATTCCGTTTTTTATCCC
1 CAAAAATTCC--TTTTTATCCC
4095 GATTTTTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
28 5 0.08
29 26 0.41
30 29 0.45
31 4 0.06
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.38
Consensus pattern (27 bp):
CAAAAATTCCTTTTTATCCCCGATGTC
Done.