Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013149.1 Kokia drynarioides strain JFW-HI SEQ_128168, 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: 2932
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Found at i:310 original size:43 final size:43
Alignment explanation
Indices: 263--578 Score: 194
Period size: 43 Copynumber: 7.4 Consensus size: 43
253 ACTAAAGATT
* *
263 ATGTTTTTTAGCGACGTTTGTTGAAAAAGCGTCGTTAAAAACC
1 ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC
* * * * * ** * *
306 ATG-TTCTTAGGGGCGTTTATGGTAGAAA-CACCATTAAAGATC
1 ATGTTTTTTAGCGGCGTTTGTTG-AAAAAGCGTCGTTAAAGACC
* * * ** *
348 ATGTTCTTTAGTGACGTTTG-TGATAAAATTGTCGATAAAGACC
1 ATGTTTTTTAGCGGCGTTTGTTGA-AAAAGCGTCGTTAAAGACC
* * * * *
391 ATGTTTTTTAACGGTGTTTG-TGAGAAAAGCGTAGCTAAAAACC
1 ATGTTTTTTAGCGGCGTTTGTTGA-AAAAGCGTCGTTAAAGACC
* * * * * *
434 ATGTTCTTTAGCGGTGTTTGTGGAAAAAGCGCCATTAAAGATC
1 ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC
* ** *
477 ATG-TTTTTAGCGGCGTTTATACAAAAAGCGTCGTTAAATACC
1 ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC
** ** ** * *
519 ACATTTTTTAGTTGCGTTT-TTGGGAAAGCGTCGTTAAGGACT
1 ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC
*
561 ACGTTTTTTAGCGGCGTT
1 ATGTTTTTTAGCGGCGTT
579 ATTGGGAAGC
Statistics
Matches: 200, Mismatches: 67, Indels: 13
0.71 0.24 0.05
Matches are distributed among these distances:
41 1 0.00
42 92 0.46
43 105 0.52
44 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (43 bp):
ATGTTTTTTAGCGGCGTTTGTTGAAAAAGCGTCGTTAAAGACC
Found at i:526 original size:128 final size:128
Alignment explanation
Indices: 278--528 Score: 285
Period size: 128 Copynumber: 2.0 Consensus size: 128
268 TTTTAGCGAC
* * * *
278 GTTTGTTGAAAAAGCGTCGTTAAAAACCATGTTCTTAGGGGCGTTTATGGTAGAAACACCATTAA
1 GTTTGTTGAAAAAGCGTAGCTAAAAACCATGTTCTTAGCGGCGTTTATGGTAAAAACACCATTAA
* * * ** **
343 AGATCATGTTCTTTAGTGACGTTTGTGATAAAATTGTCGATAAAGACCATGTTTTTTAACGGT
66 AGATCATGTTCTTTAGCGACGTTTATGAAAAAAGCGTCGATAAAGACCACATTTTTTAACGGT
* * *
406 GTTTG-TGAGAAAAGCGTAGCTAAAAACCATGTTCTTTAGCGGTGTTTGTGG-AAAAAGCGCCAT
1 GTTTGTTGA-AAAAGCGTAGCTAAAAACCATGTTC-TTAGCGGCGTTTATGGTAAAAA-CACCAT
* * *
469 TAAAGATCATGTT-TTTAGCGGCGTTTAT-ACAAAAAGCGTCGTTAAATACCACATTTTTTA
63 TAAAGATCATGTTCTTTAGCGACGTTTATGA-AAAAAGCGTCGATAAAGACCACATTTTTTA
529 GTTGCGTTTT
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
127 4 0.04
128 67 0.66
129 31 0.30
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (128 bp):
GTTTGTTGAAAAAGCGTAGCTAAAAACCATGTTCTTAGCGGCGTTTATGGTAAAAACACCATTAA
AGATCATGTTCTTTAGCGACGTTTATGAAAAAAGCGTCGATAAAGACCACATTTTTTAACGGT
Found at i:589 original size:41 final size:42
Alignment explanation
Indices: 501--616 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 42
491 GTTTATACAA
* ** *
501 AAAGCGTCGTTAAATACCACATTTTTTAGTTGCGTTTTTGGG
1 AAAGCGTCGTTAAAGACCACATTTTTTAGCGGCGTTATTGGG
* * *
543 AAAGCGTCGTTAAGGACTACGTTTTTTAGCGGCGTTATTGGG
1 AAAGCGTCGTTAAAGACCACATTTTTTAGCGGCGTTATTGGG
* * * *
585 -AAGCGCCGCTAAAGACCATATTTTATAGCGGC
1 AAAGCGTCGTTAAAGACCACATTTTTTAGCGGC
617 ATTTTTTTCT
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 25 0.42
42 35 0.58
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
AAAGCGTCGTTAAAGACCACATTTTTTAGCGGCGTTATTGGG
Found at i:1728 original size:43 final size:43
Alignment explanation
Indices: 1632--1740 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 43
1622 ATCTGTTAAT
* *
1632 TTTAGCGGCGTTTGTGGGAAAAATGTCGCTAAAGAACATTATC
1 TTTAGCGGCGTTTGTGGGAAAAACGTCACTAAAGAACATTATC
* ** * **
1675 TATAATGGCGTTTGTGGGAAAAACGTCATTAAAGATTA-TACTC
1 TTTAGCGGCGTTTGTGGGAAAAACGTCACTAAAGAACATTA-TC
*
1718 TTTAGCGGCGTTTGTGAGAAAAA
1 TTTAGCGGCGTTTGTGGGAAAAA
1741 TGACATTTGT
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 2 0.04
43 51 0.96
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAACGTCACTAAAGAACATTATC
Found at i:1812 original size:43 final size:43
Alignment explanation
Indices: 1746--2089 Score: 225
Period size: 43 Copynumber: 8.1 Consensus size: 43
1736 AAAAATGACA
* * ** *
1746 TTTGTGGGAAAAGTC-TCGCTAAAGATTATGTTTTTTAGCGACG
1 TTTGTGGAAAAAG-CGTCGTTAAAGACCATGTTCTTTAGCGACG
* *
1789 TTTGTGGAAAAAGCGTCGTTAAAGACCATATTCTTTAGCGGCG
1 TTTGTGGAAAAAGCGTCGTTAAAGACCATGTTCTTTAGCGACG
* * * * * *
1832 TTTATGGTAGAAGCGTCATTAAAGACCATGTTTTTTAGTGACG
1 TTTGTGGAAAAAGCGTCGTTAAAGACCATGTTCTTTAGCGACG
** * * * *
1875 TTTGT-GATAAAAGTATCGATAAAGATCATGTTCTTTAACGATG
1 TTTGTGGA-AAAAGCGTCGTTAAAGACCATGTTCTTTAGCGACG
* **
1918 TTTGTGAGAAAAA-CGTCGTTAAAAACCATGTTCTTTAGCGGGG
1 TTTGTG-GAAAAAGCGTCGTTAAAGACCATGTTCTTTAGCGACG
* * * * * *
1961 TTTGTGGAAAAAGCGCCATTAAAGATCATGTT-TTTAACGGCT
1 TTTGTGGAAAAAGCGTCGTTAAAGACCATGTTCTTTAGCGACG
* ** * * * *
2003 TTTATACAAAAAGCGTCGCTAAATACCACGTTTTTTAGCTG-CG
1 TTTGTGGAAAAAGCGTCGTTAAAGACCATGTTCTTTAGC-GACG
* * * * * * *
2046 TTTTTGG-GAAAGC-CCGTTAAGGACCACGTTTTTTAGCGGCG
1 TTTGTGGAAAAAGCGTCGTTAAAGACCATGTTCTTTAGCGACG
2087 TTT
1 TTT
2090 TTGGGAAGCG
Statistics
Matches: 232, Mismatches: 61, Indels: 18
0.75 0.20 0.06
Matches are distributed among these distances:
40 1 0.00
41 25 0.11
42 43 0.19
43 156 0.67
44 5 0.02
45 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (43 bp):
TTTGTGGAAAAAGCGTCGTTAAAGACCATGTTCTTTAGCGACG
Found at i:1981 original size:129 final size:129
Alignment explanation
Indices: 1754--1995 Score: 342
Period size: 129 Copynumber: 1.9 Consensus size: 129
1744 CATTTGTGGG
* * * * * *
1754 AAAAGTCTCGCTAAAGATTATGTTTTTTAGCGACGTTTGTGGAAAAAGCGTCGTTAAAGACCATA
1 AAAAGTATCGATAAAGATCATGTTCTTTAACGACGTTTGTGGAAAAAGCGTCGTTAAAAACCATA
* * *
1819 TTCTTTAGCGGCGTTTATGGTAGAAGCGTCATTAAAGACCATGTTTTTTAGTGACGTTTGTGAT
66 TTCTTTAGCGGCGTTTATGGAAAAAGCGCCATTAAAGACCATGTTTTTTAGTGACGTTTGTGAT
*
1883 AAAAGTATCGATAAAGATCATGTTCTTTAACGATGTTTGTGAGAAAAA-CGTCGTTAAAAACCAT
1 AAAAGTATCGATAAAGATCATGTTCTTTAACGACGTTTGTG-GAAAAAGCGTCGTTAAAAACCAT
* * * *
1947 GTTCTTTAGCGGGGTTTGTGGAAAAAGCGCCATTAAAGATCATGTTTTT
65 ATTCTTTAGCGGCGTTTATGGAAAAAGCGCCATTAAAGACCATGTTTTT
1996 AACGGCTTTT
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
129 92 0.94
130 6 0.06
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (129 bp):
AAAAGTATCGATAAAGATCATGTTCTTTAACGACGTTTGTGGAAAAAGCGTCGTTAAAAACCATA
TTCTTTAGCGGCGTTTATGGAAAAAGCGCCATTAAAGACCATGTTTTTTAGTGACGTTTGTGAT
Found at i:2112 original size:41 final size:41
Alignment explanation
Indices: 2019--2132 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 41
2009 CAAAAAGCGT
* *
2019 CGCTAAATACCACGTTTTTTAGCTGCGTTTTTGGGAAAGCC
1 CGCTAAAGACCACGTTTTTTAGCGGCGTTTTTGGGAAAGCC
* *
2060 CGTTAAGGACCACGTTTTTTAGCGGCGTTTTTGGG-AAGCGC
1 CGCTAAAGACCACGTTTTTTAGCGGCGTTTTTGGGAAAGC-C
* * * *
2101 TGCTAAAGACCATGTTTTATAGCGGTGTTTTT
1 CGCTAAAGACCACGTTTTTTAGCGGCGTTTTT
2133 TCTCATAAAC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
40 4 0.06
41 58 0.94
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (41 bp):
CGCTAAAGACCACGTTTTTTAGCGGCGTTTTTGGGAAAGCC
Done.