Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014282.1 Kokia drynarioides strain JFW-HI SEQ_129315, 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: 7095
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:955 original size:64 final size:63
Alignment explanation
Indices: 880--1007 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 63
870 TCTGAACCCA
880 AATCTGCGCTTTAATAGAAAAGAGATTAAAAAAGGAGTTTTTTTCATACCTGAGCTGTTGGGG
1 AATCTGCGCTTTAATAGAAAAGAGATTAAAAAAGGAGTTTTTTTCATACCTGAGCTGTTGGGG
*
943 ANATCTGCGCTTTAATAGAAAAGAGATTAAAAAAGGTGTTTTTTTCATACCTGAGCTGTTGGGG
1 A-ATCTGCGCTTTAATAGAAAAGAGATTAAAAAAGGAGTTTTTTTCATACCTGAGCTGTTGGGG
1007 A
1 A
1008 CGGTAGCACG
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 1 0.02
64 62 0.98
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.32
Consensus pattern (63 bp):
AATCTGCGCTTTAATAGAAAAGAGATTAAAAAAGGAGTTTTTTTCATACCTGAGCTGTTGGGG
Found at i:1486 original size:30 final size:30
Alignment explanation
Indices: 1452--1905 Score: 263
Period size: 30 Copynumber: 15.1 Consensus size: 30
1442 ATTAGGTCCT
* * *
1452 TAAACTTTTTAAAAATCATATTTTGACCTC
1 TAAACTTTTTAAAAATTACATTTTAACCTC
* *
1482 TAAACTTCTCT-AAAATTATA-TTTAACCT-
1 TAAACTT-TTTAAAAATTACATTTTAACCTC
1510 TAAACTTTTCT-AAAATTACATTTTAACCTC
1 TAAACTTTT-TAAAAATTACATTTTAACCTC
* ** *
1540 TTAACTTTTCCAAAATTA-AGTTTTAACCAC
1 TAAACTTTTTAAAAATTACA-TTTTAACCTC
** *
1570 TAAACTTTTCCAAAATTACATTTTTACC-C
1 TAAACTTTTTAAAAATTACATTTTAACCTC
* * * *
1599 TTAAACTCTTTAAAAATTATAGTTTATCCT-
1 -TAAACTTTTTAAAAATTACATTTTAACCTC
* *
1629 TAAACTTTTCCAAAAA-TACATTTTAACCCC
1 TAAACTTTT-TAAAAATTACATTTTAACCTC
* * * *
1659 TAAACTTGTATAAAAAATTACATATTGACCCC
1 TAAACTT-T-TTAAAAATTACATTTTAACCTC
** * * * *
1691 TAAACTTTTCCAACATCATATTTTCACC-C
1 TAAACTTTTTAAAAATTACATTTTAACCTC
* * * *
1720 TTAAACTTTTTCAAAATCATATTTTCACCTC
1 -TAAACTTTTTAAAAATTACATTTTAACCTC
* * *
1751 TAAACTTTCCT-AAAATCACATTTTAACCCCC
1 TAAACTTT-TTAAAAATTACATTTTAA-CCTC
* *
1782 TAAACTTTCCT-AAAATCACATTTTAACC-C
1 TAAACTTT-TTAAAAATTACATTTTAACCTC
* * *
1811 TTAAACTTTCTCAAAATAACATTTTAACC-C
1 -TAAACTTTTTAAAAATTACATTTTAACCTC
* *
1841 TAAAACTTTTCT-AAAATTACATTTTTACCCC
1 T-AAACTTTT-TAAAAATTACATTTTAACCTC
* * *
1872 ATACACTTTTTCAAAATTACGTTTTAACC-C
1 -TAAACTTTTTAAAAATTACATTTTAACCTC
1902 TAAA
1 TAAA
1906 TTCTTCGAAA
Statistics
Matches: 352, Mismatches: 47, Indels: 51
0.78 0.10 0.11
Matches are distributed among these distances:
27 1 0.00
28 16 0.05
29 42 0.12
30 207 0.59
31 65 0.18
32 21 0.06
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.39
Consensus pattern (30 bp):
TAAACTTTTTAAAAATTACATTTTAACCTC
Found at i:1591 original size:60 final size:58
Alignment explanation
Indices: 1452--1905 Score: 335
Period size: 60 Copynumber: 7.6 Consensus size: 58
1442 ATTAGGTCCT
** * * * * * * *
1452 TAAACTTTTTAAAAATCATATTTTGACCTCTAAACTTCTCTAAAATTATA-TTTAACCT
1 TAAACTTTTCCAAAATTACATTTTAACC-CTAAACTTTTCCAAAATTACATTTTAACCC
* *
1510 TAAACTTTTCTAAAATTACATTTTAACCTCTTAACTTTTCCAAAATTA-AGTTTTAACCAC
1 TAAACTTTTCCAAAATTACATTTTAACC-CTAAACTTTTCCAAAATTACA-TTTTAACC-C
* * * * * *
1570 TAAACTTTTCCAAAATTACATTTTTACCCTTAAACTCTTT-AAAAATTATAGTTTATCCT
1 TAAACTTTTCCAAAATTACATTTTAACCC-TAAACT-TTTCCAAAATTACATTTTAACCC
* ** * *
1629 TAAACTTTTCCAAAAATACATTTTAACCCCTAAACTTGTATAAAAAATTACATATTGACCCC
1 TAAACTTTTCCAAAATTACATTTTAA-CCCTAAACTT-T-TCCAAAATTACAT-TTTAACCC
* * * * * * * *
1691 TAAACTTTTCCAACATCATATTTTCACCCTTAAACTTTTTCAAAATCATATTTTCACCTC
1 TAAACTTTTCCAAAATTACATTTTAACCC-TAAACTTTTCCAAAATTACATTTTAACC-C
* *
1751 TAAAC-TTTCCTAAAATCACATTTTAACCCCCTAAAC-TTTCCTAAAATCACATTTTAACCC
1 TAAACTTTTCC-AAAATTACATTTTAA--CCCTAAACTTTTCC-AAAATTACATTTTAACCC
* * *
1811 TTAAAC-TTTCTCAAAATAACATTTTAACCCTAAAACTTTTCTAAAATTACATTTTTACCCC
1 -TAAACTTTTC-CAAAATTACATTTTAACCCT-AAACTTTTCCAAAATTACA-TTTTAACCC
* * *
1872 ATACACTTTTTCAAAATTACGTTTTAACCCTAAA
1 -TAAACTTTTCCAAAATTACATTTTAACCCTAAA
1906 TTCTTCGAAA
Statistics
Matches: 323, Mismatches: 50, Indels: 44
0.77 0.12 0.11
Matches are distributed among these distances:
57 1 0.00
58 41 0.13
59 52 0.16
60 95 0.29
61 94 0.29
62 40 0.12
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.39
Consensus pattern (58 bp):
TAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTTCCAAAATTACATTTTAACCC
Found at i:1847 original size:91 final size:89
Alignment explanation
Indices: 1449--1902 Score: 347
Period size: 91 Copynumber: 5.0 Consensus size: 89
1439 TCAATTAGGT
** * * * * * * *
1449 CCTTAAACTTTTTAAAAATCATATTTTGACCTCTAAAC-TTCTCTAAAATT--ATATTTAACCTT
1 CCTTAAACTTTTCCAAAATAACATTTTAACCACTAAACTTTC-CTAAAATTACATTTTTACCCCT
1511 AAACTTTTCTAAAATTACATTTTAAC
65 AAAC-TTTCTAAAATTACATTTTAAC
*
1537 CTCTT-AACTTTTCCAAAATTAA-GTTTTAACCACTAAACTTTTCC-AAAATTACATTTTTACCC
1 C-CTTAAACTTTTCCAAAA-TAACATTTTAACCACTAAAC-TTTCCTAAAATTACATTTTTACCC
* * * *
1599 TTAAACTCTT-TAAAAATTATAGTTT-AT
63 CTAAACT-TTCT-AAAATTACATTTTAAC
* * * *
1626 CCTTAAACTTTTCCAAAA-ATACATTTTAACCCCTAAACTTGT-ATAAAAAATTACATATTGACC
1 CCTTAAACTTTTCCAAAATA-ACATTTTAACCACTAAACTT-TCCT--AAAATTACATTTTTACC
* * * * *
1689 CCTAAACTTTTCCAACATCATATTTTCAC
62 CCTAAAC-TTTCTAAAATTACATTTTAAC
* * * * * * *
1718 CCTTAAACTTTTTCAAAATCATATTTTCACCTCTAAACTTTCCTAAAATCACATTTTAACCCCCT
1 CCTTAAACTTTTCCAAAATAACATTTTAACCACTAAACTTTCCTAAAATTACATTTTTA-CCCCT
*
1783 AAACTTTCCTAAAATCACATTTTAAC
65 AAACTTT-CTAAAATTACATTTTAAC
*
1809 CCTTAAAC-TTTCTCAAAATAACATTTTAACC-CTAAAACTTTTCTAAAATTACATTTTTACCCC
1 CCTTAAACTTTTC-CAAAATAACATTTTAACCACT-AAACTTTCCTAAAATTACATTTTTACCCC
* * *
1872 ATACACTTTTTCAAAATTACGTTTTAAC
64 -TAAACTTTCT-AAAATTACATTTTAAC
1900 CCT
1 CCT
1903 AAATTCTTCG
Statistics
Matches: 294, Mismatches: 46, Indels: 49
0.76 0.12 0.13
Matches are distributed among these distances:
87 1 0.00
88 37 0.13
89 38 0.13
90 55 0.19
91 126 0.43
92 37 0.13
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.39
Consensus pattern (89 bp):
CCTTAAACTTTTCCAAAATAACATTTTAACCACTAAACTTTCCTAAAATTACATTTTTACCCCTA
AACTTTCTAAAATTACATTTTAAC
Found at i:1865 original size:121 final size:116
Alignment explanation
Indices: 1449--1865 Score: 387
Period size: 121 Copynumber: 3.5 Consensus size: 116
1439 TCAATTAGGT
** * * * *
1449 CCTTAAACTTTTTAAAAATCATATTTTGA-CCTCTAAACTTCTCTAAAATTATATTTAACCTTAA
1 CCTTAAACTTTTCCAAAATCACATTTTAACCCT-TAAACTT-TTTAAAATTATATTTTACCTTAA
* * *
1513 ACTTTTCTAAAATTACATTTTAACCTCTTAACTTTTCC-AAAATTA-AGTTTTAAC
64 ACTTTCCTAAAA-TACATTTTAACCCCTAAAC-TTTCCTAAAATTACA-TTTTAAC
* * * *
1567 CAC-TAAACTTTTCCAAAATTACATTTTTACCCTTAAACTCTTTAAAAATTATAGTTTATCCTTA
1 C-CTTAAACTTTTCCAAAATCACATTTTAACCCTTAAACT-TTTTAAAATTATATTTTA-CCTTA
* * * *
1631 AACTTTTCCAAAAATACATTTTAACCCCTAAACTTGT-ATAAAAAATTACATATTGAC
63 AAC-TTTCCTAAAATACATTTTAACCCCTAAACTT-TCCT--AAAATTACATTTTAAC
* * * * *
1688 CCCTAAACTTTTCCAACATCATATTTTCACCCTTAAACTTTTTCAAAATCATATTTTCACCTCTA
1 CCTTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTT-AAAATTATATTTT-ACCT-TA
*
1753 AACTTTCCTAAAATCACATTTTAACCCCCTAAACTTTCCTAAAATCACATTTTAAC
63 AACTTTCCTAAAAT-ACATTTTAA-CCCCTAAACTTTCCTAAAATTACATTTTAAC
* * *
1809 CCTTAAAC-TTTCTCAAAATAACATTTTAACCCTAAAACTTTTCTAAAATTACATTTT
1 CCTTAAACTTTTC-CAAAATCACATTTTAACCCTTAAACTTTT-TAAAATTATATTTT
1866 TACCCCATAC
Statistics
Matches: 244, Mismatches: 36, Indels: 35
0.77 0.11 0.11
Matches are distributed among these distances:
118 43 0.18
119 31 0.13
120 16 0.07
121 124 0.51
122 18 0.07
123 12 0.05
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.40
Consensus pattern (116 bp):
CCTTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTTAAAATTATATTTTACCTTAAAC
TTTCCTAAAATACATTTTAACCCCTAAACTTTCCTAAAATTACATTTTAAC
Found at i:5885 original size:43 final size:43
Alignment explanation
Indices: 5818--5901 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
5808 ATGGCAAATT
*
5818 TCATACACCTAAAGCTGTAGAGGGGCAAATTGAAGTCGCAATC
1 TCATACACCTAAAGCTGTAAAGGGGCAAATTGAAGTCGCAATC
* *
5861 TCATTCACCTAAAGCTGTAAAGGGGCATATTGAAGTCGCAA
1 TCATACACCTAAAGCTGTAAAGGGGCAAATTGAAGTCGCAA
5902 GGACGAATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (43 bp):
TCATACACCTAAAGCTGTAAAGGGGCAAATTGAAGTCGCAATC
Found at i:5991 original size:39 final size:39
Alignment explanation
Indices: 5947--6078 Score: 115
Period size: 39 Copynumber: 3.4 Consensus size: 39
5937 AAAGAACATT
*
5947 CAATCTTTTACCCCAAGCATGGGGTAGATTGAAGCAATC
1 CAATCTTTTACCCCAACCATGGGGTAGATTGAAGCAATC
* *
5986 CAATCTTTTACCCTAACCA-GAAGGTAGATTGAAG-ATCATC
1 CAATCTTTTACCCCAACCATG-GGGTAGATTGAAGCA--ATC
* * * * ** *
6026 AAATCTCTTACCTCGACCATGGGCCAGATTGAAACAATC
1 CAATCTTTTACCCCAACCATGGGGTAGATTGAAGCAATC
* *
6065 CGATATTTTACCCC
1 CAATCTTTTACCCC
6079 TAAAGTTATA
Statistics
Matches: 71, Mismatches: 17, Indels: 10
0.72 0.17 0.10
Matches are distributed among these distances:
38 2 0.03
39 41 0.58
40 26 0.37
41 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (39 bp):
CAATCTTTTACCCCAACCATGGGGTAGATTGAAGCAATC
Done.