Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011792.1 Kokia drynarioides strain JFW-HI SEQ_126787, 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: 14904
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:509 original size:10 final size:10
Alignment explanation
Indices: 496--533 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
486 AATAATTGGC
496 ATTAATAATT
1 ATTAATAATT
*
506 ATTATTAATT
1 ATTAATAATT
*
516 ATTATTAATT
1 ATTAATAATT
526 A-TAATAAT
1 ATTAATAAT
534 AAGTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 6 0.23
10 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTAATAATT
Found at i:1552 original size:29 final size:28
Alignment explanation
Indices: 1514--1805 Score: 282
Period size: 29 Copynumber: 10.0 Consensus size: 28
1504 GAGGTCCCTA
*
1514 AACTATCCAAAAATTCTATTTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTTTACCC-CG
* * *
1544 AACTTCCAAAAATCCCATTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCCC-G
1573 AACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTA-CCCCG
* *
1602 AACTTCCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCC-G
* *
1632 AACTTCCAAACATTCGATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCC-CG
**
1661 AACTTCCAAAAA-TCTCATTTTTAACCCTAA
1 AACTTCCAAAAATTC-CATTTTT-ACCC-CG
*
1691 AACTTCCAAAAATT-CATTTTTACTCTCG
1 AACTTCCAAAAATTCCATTTTTAC-CCCG
* *
1719 AACTTCTAAAAATCCCATTTTTTACCCCG
1 AACTTCCAAAAATTCCA-TTTTTACCCCG
* *
1748 AAACTTCCAAAAATTCTATTTTTACCCCTA
1 -AACTTCCAAAAATTCCATTTTTACCCC-G
* *
1778 AAATTCCAAAAATGCCATTTTTAACCCC
1 AACTTCCAAAAATTCCATTTTT-ACCCC
1806 AAAAATTCCA
Statistics
Matches: 218, Mismatches: 30, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
28 17 0.08
29 128 0.59
30 72 0.33
31 1 0.00
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:1633 original size:59 final size:59
Alignment explanation
Indices: 1513--1815 Score: 432
Period size: 59 Copynumber: 5.2 Consensus size: 59
1503 CGAGGTCCCT
*
1513 AAACTATCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCA-TTTTAACCCCA
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
*
1572 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * * *
1631 AAACTTCCAAACATTCGATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * * *
1690 AAACTTCCAAAAATT-CATTTTTACTCTCGAACTTCTAAAAATCCCATTTTTTACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * * *
1748 AAACTTCCAAAAATTCTATTTTTACCC-CTAAAATTCCAAAAATGCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATCCCATTTTTAACCCCA
*
1807 AAAATTCCA
1 AAACTTCCA
1816 TTTTTGCCCC
Statistics
Matches: 217, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
58 92 0.42
59 125 0.58
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:1721 original size:117 final size:117
Alignment explanation
Indices: 1513--1815 Score: 441
Period size: 117 Copynumber: 2.6 Consensus size: 117
1503 CGAGGTCCCT
1513 AAACTATCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCA-TTTTAACCCCAAAACT
1 AAACT-TCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAAT-CCATTTTTAACCCCAAAACT
1577 TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
64 TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * *
1631 AAACTTCCAAACATTCGATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCTAAAACTT
1 AAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATC-CATTTTTAACCCCAAAACTT
* * * * *
1696 CCAAAAATT-CATTTTTACTCTCGAACTTCTAAAAATCCCATTTTTTACCCCG
65 CCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * *
1748 AAACTTCCAAAAATTCTATTTTTACCC-CTAAAATTCCAAAAATGCCATTTTTAACCCCAAAAAT
1 AAACTTCCAAAAATTCTATTTTTACCCTC-GAACTTCCAAAAAT-CCATTTTTAACCCCAAAACT
1812 TCCA
64 TCCA
1816 TTTTTGCCCC
Statistics
Matches: 167, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
116 2 0.01
117 134 0.80
118 31 0.19
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.32
Consensus pattern (117 bp):
AAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCATTTTTAACCCCAAAACTTC
CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:1835 original size:21 final size:21
Alignment explanation
Indices: 1783--1829 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1773 CCCTAAAATT
*
1783 CCAAAAATGCCATTTTTAACC
1 CCAAAAATTCCATTTTTAACC
**
1804 CCAAAAATTCCATTTTTGCCC
1 CCAAAAATTCCATTTTTAACC
1825 CCAAA
1 CCAAA
1830 TTTTCCTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.28
Consensus pattern (21 bp):
CCAAAAATTCCATTTTTAACC
Found at i:1855 original size:50 final size:50
Alignment explanation
Indices: 1754--1850 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
1744 CCCGAAACTT
* * *
1754 CCAAAAATTCTATTTTTACCCCTAAAATTCCAAAAATGCCATTTTTAACC
1 CCAAAAATTCCATTTTTACCCCCAAAATTCCAAAAATACCATTTTTAACC
* * *
1804 CCAAAAATTCCATTTTTGCCCCCAAATTTTCCTAAAATTACCATTTT
1 CCAAAAATTCCATTTTTACCCCCAAA-ATTCC-AAAAATACCATTTT
1851 ACCCCCGGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 23 0.59
51 4 0.10
52 12 0.31
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (50 bp):
CCAAAAATTCCATTTTTACCCCCAAAATTCCAAAAATACCATTTTTAACC
Found at i:12537 original size:40 final size:40
Alignment explanation
Indices: 12482--12561 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
12472 TGGGAAATGG
12482 ATGCCCAATTGGGAAGGACCTTATGTGGTAAAGAAAGCTT
1 ATGCCCAATTGGGAAGGACCTTATGTGGTAAAGAAAGCTT
12522 ATGCCCAATTGGGAAGGACCTTATGTGGTAAAGAAAGCTT
1 ATGCCCAATTGGGAAGGACCTTATGTGGTAAAGAAAGCTT
12562 TCTCAGGAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (40 bp):
ATGCCCAATTGGGAAGGACCTTATGTGGTAAAGAAAGCTT
Found at i:13895 original size:205 final size:205
Alignment explanation
Indices: 13543--14011 Score: 830
Period size: 205 Copynumber: 2.3 Consensus size: 205
13533 CATCCACAAA
*
13543 CAGCGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTTGATG
1 CAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTTGATG
*
13608 TGAGCAAACCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAAGG
66 TGAGCAAACCTTCAAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAAGG
*
13673 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGC
131 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
**
13738 GGATTGAAAC
196 AAATTGAAAC
* * *
13748 CAGCGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGATCAAATCAAACCCACGTTTGATG
1 CAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTTGATG
*
13813 TGAGCAAACCTTCAAACCTCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAAGG
66 TGAGCAAACCTTCAAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAAGG
13878 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
131 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
13943 AAATTGAAAC
196 AAATTGAAAC
* * *
13953 AAGTGATGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGC
1 CAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
14012 GAAGTGAACC
Statistics
Matches: 249, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
205 249 1.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (205 bp):
CAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTTGATG
TGAGCAAACCTTCAAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAAAGG
TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
AAATTGAAAC
Found at i:14098 original size:110 final size:111
Alignment explanation
Indices: 13901--14114 Score: 367
Period size: 110 Copynumber: 1.9 Consensus size: 111
13891 GAGATACTGA
* *
13901 GAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAAATTGAAACAAGTGATGCGGTC
1 GAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCAAATTGAAACAAGTGATGCGGTC
*
13966 ATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGC
66 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* **
14012 GAAGTGAACCAAATTTGTCTT-CTAATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTC
1 GAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCAAATTGAAACAAGTGATGCGGTC
14076 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA
66 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA
14115 GTGAGCAAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 78 0.80
111 19 0.20
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (111 bp):
GAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCAAATTGAAACAAGTGATGCGGTC
ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
Found at i:14667 original size:6 final size:6
Alignment explanation
Indices: 14656--14722 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
14646 ATTTGTTATA
* * *
14656 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT TATTTT CAAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT
*
14703 AAAATT --ATTAT AAATTT AAA
1 AAATTT AAATT-T AAATTT AAA
14723 ATAAATAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
4 2 0.04
5 10 0.21
6 29 0.60
7 7 0.15
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:14680 original size:41 final size:41
Alignment explanation
Indices: 14642--14722 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
14632 TATTTTAAGA
* * *
14642 TTAAATTTGTTATAAAATTTAAATTTATTTTAAATTTAAAT
1 TTAAATTTATTATAAAATTTAAAATTATTATAAATTTAAAT
* * *
14683 TTAATTTTATTTTCAAATTTAAAATTATTATAAATTTAAA
1 TTAAATTTATTATAAAATTTAAAATTATTATAAATTTAAA
14723 ATAAATAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (41 bp):
TTAAATTTATTATAAAATTTAAAATTATTATAAATTTAAAT
Found at i:14686 original size:23 final size:24
Alignment explanation
Indices: 14656--14705 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
14646 ATTTGTTATA
14656 AAATTTAAATTTATTTT-AAATTT
1 AAATTTAAATTTATTTTCAAATTT
*
14679 AAATTTAATTTTATTTTCAAATTT
1 AAATTTAAATTTATTTTCAAATTT
14703 AAA
1 AAA
14706 ATTATTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
AAATTTAAATTTATTTTCAAATTT
Found at i:14689 original size:18 final size:17
Alignment explanation
Indices: 14624--14691 Score: 84
Period size: 17 Copynumber: 3.9 Consensus size: 17
14614 CCAAATTCAT
14624 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
14642 -TTAAATTTGTTATAAAA
1 TTTAAATTTATT-TTAAA
14659 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
14676 TTTAAATTTAATTTTA
1 TTTAAATTT-ATTTTA
14692 TTTTCAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
17 24 0.56
18 19 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:14700 original size:18 final size:18
Alignment explanation
Indices: 14624--14704 Score: 73
Period size: 17 Copynumber: 4.6 Consensus size: 18
14614 CCAAATTCAT
14624 TTTAAATTT-ATTTTAAGA
1 TTTAAATTTAATTTTAA-A
* *
14642 -TTAAATTT-GTTATAAAA
1 TTTAAATTTAATT-TTAAA
14659 TTTAAATTT-ATTTTAAA
1 TTTAAATTTAATTTTAAA
*
14676 TTTAAATTTAATTTT-AT
1 TTTAAATTTAATTTTAAA
14693 TTTCAAATTTAA
1 TTT-AAATTTAA
14705 AATTATTATA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
17 28 0.52
18 26 0.48
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAAATTTAATTTTAAA
Found at i:14719 original size:17 final size:17
Alignment explanation
Indices: 14678--14724 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
14668 ATTTTAAATT
** *
14678 TAAATTTAATTTTATTT
1 TAAATTTAAAATTATTA
14695 TCAAATTTAAAATTATTA
1 T-AAATTTAAAATTATTA
14713 TAAATTTAAAAT
1 TAAATTTAAAAT
14725 AAATAAAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAATTTAAAATTATTA
Done.