Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014541.1 Kokia drynarioides strain JFW-HI SEQ_129580, 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: 4173
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Found at i:1705 original size:17 final size:18
Alignment explanation
Indices: 1682--1791 Score: 122
Period size: 17 Copynumber: 6.3 Consensus size: 18
1672 CCAAACTCAT
1682 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
* *
1700 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGA
*
1717 TTTAAATTTAGTTTAA-A
1 TTTAAATTTATTTTAAGA
*
1734 TTTAAATTTAATTTAAG-
1 TTTAAATTTATTTTAAGA
1751 TTTAAATTTATTTTCAA-A
1 TTTAAATTTATTTT-AAGA
* *
1769 TTTAAAATTATTATAA-A
1 TTTAAATTTATTTTAAGA
1786 TTTAAA
1 TTTAAA
1792 ATAAATAAAG
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
17 53 0.66
18 27 0.34
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:1725 original size:6 final size:6
Alignment explanation
Indices: 1714--1791 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
1704 ATTTGTTTTA
* *
1714 AAATTT AAATTT -AGTTT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
1760 -ATTTT CAAATTT AAAATT --ATTAT AAATTT AAA
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAA
1792 ATAAATAAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
4 2 0.04
5 14 0.25
6 34 0.60
7 7 0.12
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:1731 original size:11 final size:11
Alignment explanation
Indices: 1717--1772 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
1707 TGTTTTAAAA
1717 TTTAAATTTAG
1 TTTAAATTTAG
*
1728 TTTAAATTTAAA
1 TTTAAATTT-AG
1740 TTT-AATTTAAG
1 TTTAAATTT-AG
*
1751 TTTAAATTTAT
1 TTTAAATTTAG
1762 TTTCAAATTTA
1 TTT-AAATTTA
1773 AAATTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 23 0.59
12 16 0.41
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAG
Found at i:1744 original size:23 final size:23
Alignment explanation
Indices: 1714--1760 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
1704 ATTTGTTTTA
1714 AAATTTAAATTT-AGTTTAAATTT
1 AAATTT-AATTTAAGTTTAAATTT
1737 AAATTTAATTTAAGTTTAAATTT
1 AAATTTAATTTAAGTTTAAATTT
1760 A
1 A
1761 TTTTCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
AAATTTAATTTAAGTTTAAATTT
Found at i:1749 original size:52 final size:52
Alignment explanation
Indices: 1682--1791 Score: 159
Period size: 52 Copynumber: 2.1 Consensus size: 52
1672 CCAAACTCAT
* * *
1682 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTTAAATTTAGTT-TAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTA-TTATAAA
* *
1734 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
1786 TTTAAA
1 TTTAAA
1792 ATAAATAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
51 2 0.04
52 50 0.96
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
Found at i:1770 original size:35 final size:33
Alignment explanation
Indices: 1682--1791 Score: 123
Period size: 35 Copynumber: 3.2 Consensus size: 33
1672 CCAAACTCAT
*
1682 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTT-ATTT-AAA
* *
1717 TTTAAATTTAGTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATTTAAATTT-ATTTAAA
*
1751 TTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTATTTT-AAATTTAAATTTATT-TAAA
1786 TTTAAA
1 TTTAAA
1792 ATAAATAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
34 19 0.29
35 46 0.71
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (33 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAAA
Found at i:2511 original size:3 final size:3
Alignment explanation
Indices: 2503--2602 Score: 137
Period size: 3 Copynumber: 33.0 Consensus size: 3
2493 ATAATGACAT
2503 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** **
2551 TAA TAA TAA AAA TAA AAA TAAA TAA TTG TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
2597 TAA TAA
1 TAA TAA
2603 ATATTAAATA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
3 84 0.97
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3647 original size:29 final size:29
Alignment explanation
Indices: 3615--4074 Score: 284
Period size: 29 Copynumber: 15.8 Consensus size: 29
3605 AAACTGTCTG
*
3615 AAAATTACATTTTTGCCCTCGAACTTCCA
1 AAAATTCCATTTTTGCCCTCGAACTTCCA
** *
3644 AAAATTCCATTTCCGACCC-CAAAACTTCCA
1 AAAATTCCATTTTTG-CCCTC-GAACTTCCA
* * *
3674 AAAA-TCCTATTTTTACCCTTGAACTTCTA
1 AAAATTCC-ATTTTTGCCCTCGAACTTCCA
*
3703 AAAATTCCA-TTTTGACCCTCAAACTTCCA
1 AAAATTCCATTTTTG-CCCTCGAACTTCCA
** *
3732 AAAATTCCATTTTTAACCTCGAAACTTCCC
1 AAAATTCCATTTTTGCCCTCG-AACTTCCA
* * *
3762 AAAATTCCATTTTTACCCCCAAACTTCC-
1 AAAATTCCATTTTTGCCCTCGAACTTCCA
*
3790 AAAATTCCATTTTTGACCC-CAAAACTTCC-
1 AAAATTCCATTTTTG-CCCTC-GAACTTCCA
* * *
3819 AAAATTCCATTTTTACCCTCGATCTTCTA
1 AAAATTCCATTTTTGCCCTCGAACTTCCA
* *
3848 AAAATTCCA-TTTTGACCC-CAAAACTT-AA
1 AAAATTCCATTTTTG-CCCTC-GAACTTCCA
* * * * *
3876 GAAAATTACAATTTTACCCTCGAACCTCTA
1 -AAAATTCCATTTTTGCCCTCGAACTTCCA
* *
3906 AAATTTCCATTTTTGACCC-CGAAACTTTCA
1 AAAATTCCATTTTTG-CCCTCG-AACTTCCA
*
3936 AAAATTACCA-TTTTGCCGTCGAA-TGTCCA
1 AAAATT-CCATTTTTGCCCTCGAACT-TCCA
* * *
3965 AAAACTCTATTTTTGACCTCGAAAC-TCCA
1 AAAATTCCATTTTTGCCCTCG-AACTTCCA
* * *
3994 AAAATTCCA-TTTTCCCCCCGAA-TGTCTA
1 AAAATTCCATTTTTGCCCTCGAACT-TCCA
* ** *
4022 AAAATTTCATCTTTTAACCTCGAACTTCCCC
1 AAAATTCCAT-TTTTGCCCTCGAACTT-CCA
* * *
4053 AAAATTACAATTTTACCCTCGA
1 AAAATTCCATTTTTGCCCTCGA
4075 GTATCCAAAG
Statistics
Matches: 335, Mismatches: 64, Indels: 63
0.73 0.14 0.14
Matches are distributed among these distances:
27 2 0.01
28 55 0.16
29 164 0.49
30 101 0.30
31 13 0.04
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAATTCCATTTTTGCCCTCGAACTTCCA
Found at i:3746 original size:58 final size:58
Alignment explanation
Indices: 3615--4072 Score: 318
Period size: 59 Copynumber: 7.8 Consensus size: 58
3605 AAACTGTCTG
* * *
3615 AAAATTACATTTTTGCCCTCGAACTTCCAAAAATTCCATTTCCGACCC-CAAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTT-TGACCCTC-AAACTTCCA
* *
3674 AAAA-TCCTATTTTTACCCTTGAACTTCTAAAAATTCCATTTTGACCCTCAAACTTCCA
1 AAAATTCC-ATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCCTCAAACTTCCA
* * * *
3732 AAAATTCCATTTTTAACCTCGAAACTTCCCAAAATTCCATTTTTACCCCCAAACTTCC-
1 AAAATTCCATTTTTACCCTCG-AACTTCCAAAAATTCCATTTTGACCCTCAAACTTCCA
* * * * *
3790 AAAATTCCATTTTTGACCC-CAAAACTTCC-AAAATTCCATTTTTACCCTCGATCTTCTA
1 AAAATTCCATTTTT-ACCCTC-GAACTTCCAAAAATTCCATTTTGACCCTCAAACTTCCA
* * * * * * *
3848 AAAATTCCATTTTGACCC-CAAAACTT-AAGAAAATTACAATTTT-ACCCTCGAACCTCTA
1 AAAATTCCATTTTTACCCTC-GAACTTCCA-AAAATT-CCATTTTGACCCTCAAACTTCCA
* * * *
3906 AAATTTCCATTTTTGACCC-CGAAACTTTCAAAAATTACCATTTTG-CCGTCGAA-TGTCCA
1 AAAATTCCATTTTT-ACCCTCG-AACTTCCAAAAATT-CCATTTTGACCCTCAAACT-TCCA
* * * * * *
3965 AAAACTCTATTTTTGA-CCTCGAAAC-TCCAAAAATTCCATTTT-CCCCCCGAA-TGTCTA
1 AAAATTCCATTTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTGACCCTCAAACT-TCCA
* * * *
4022 AAAATTTCATCTTTTAACCTCGAACTTCCCCAAAATTACAATTTT-ACCCTC
1 AAAATTCCAT-TTTTACCCTCGAACTT-CCAAAAATT-CCATTTTGACCCTC
4073 GAGTATCCAA
Statistics
Matches: 333, Mismatches: 44, Indels: 43
0.79 0.10 0.10
Matches are distributed among these distances:
57 65 0.20
58 118 0.35
59 139 0.42
60 11 0.03
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (58 bp):
AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCCTCAAACTTCCA
Found at i:3766 original size:88 final size:89
Alignment explanation
Indices: 3605--4006 Score: 335
Period size: 88 Copynumber: 4.6 Consensus size: 89
3595 GAAGGTCCCT
* * * *** * *
3605 AAACTGTCTGAAAATTACATTTTTG-CCCTCGAACTTCCAAAAATTCCATTTCCGACCCCAAAAC
1 AAACT-TCTAAAAATTCCATTTTTGACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGAAAC
**
3669 TTCCAAAAA-TCCTATTTTTACCCTT
65 TTCCAAAAATTCC-ATTTTTACCCCC
*
3694 GAACTTCTAAAAATTCCA-TTTTGACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACT
1 AAACTTCTAAAAATTCCATTTTTGACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACT
*
3758 TCCCAAAATTCCATTTTTACCCCC
66 TCCAAAAATTCCATTTTTACCCCC
* * *
3782 AAACTTC-CAAAATTCCATTTTTGACCC-CAAAACTTCC-AAAATTCCATTTTTACCCTCG-ATC
1 AAACTTCTAAAAATTCCATTTTTGACCCTC-AAACTTCCAAAAATTCCATTTTTAACCTCGAAAC
* * *
3843 TTCTAAAAATTCCATTTTGACCCCA
65 TTCCAAAAATTCCATTTTTACCCCC
* * * * * * * * *
3868 AAACTT-AAGAAAATTACAATTTT-ACCCTCGAACCTCTAAAATTTCCATTTTTGACCCCGAAAC
1 AAACTTCTA-AAAATTCCATTTTTGACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGAAAC
* * **
3931 TTTCAAAAATTACCA-TTTTGCCGTC
65 TTCCAAAAATT-CCATTTTTACCCCC
* * * *
3956 GAA-TGTCCAAAAACTCTATTTTTGA-CCTCGAAAC-TCCAAAAATTCCATTTT
1 AAACT-TCTAAAAATTCCATTTTTGACCCTC-AAACTTCCAAAAATTCCATTTT
4007 CCCCCCGAAT
Statistics
Matches: 252, Mismatches: 47, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
86 38 0.15
87 66 0.26
88 133 0.53
89 15 0.06
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (89 bp):
AAACTTCTAAAAATTCCATTTTTGACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACT
TCCAAAAATTCCATTTTTACCCCC
Done.