Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008312.1 Kokia drynarioides strain JFW-HI SEQ_122977, 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: 43295
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:3178 original size:96 final size:96
Alignment explanation
Indices: 3004--3195 Score: 241
Period size: 96 Copynumber: 2.0 Consensus size: 96
2994 ATTTTGGGAA
* ** * *
3004 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTAGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA
3069 GAATCAAAGAT-AAAGAAATATTGA-CTCGATT
66 GAATCAAAGATAAAAG-AATATT-ACCTCGATT
*
3100 AAGGGTATTCGATTATCTAGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTAGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATA-TTTC
*
3164 -GAAACTCGAA-ATAAAAGAATATTACCTCGATT
65 AG-AA-TCAAAGATAAAAGAATATTACCTCGATT
3196 TTAAAGTCTT
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
95 3 0.04
96 73 0.87
97 8 0.10
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTAGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA
GAATCAAAGATAAAAGAATATTACCTCGATT
Found at i:3574 original size:30 final size:30
Alignment explanation
Indices: 3445--3722 Score: 191
Period size: 29 Copynumber: 9.5 Consensus size: 30
3435 ATATGGTGTT
* * *
3445 AAAAATGGAATTTTT-AGA-TATTCGGGGTA
1 AAAAATGGAATTTTTGAAAGT-TTCGAGGTC
*
3474 AAAAATGGAATTTTTG-GAGTTTCGAGGTC
1 AAAAATGGAATTTTTGAAAGTTTCGAGGTC
* * * *
3503 AAAAATAGAGTTTTTGGACA--TTCGAGG-G
1 AAAAATGGAATTTTT-GAAAGTTTCGAGGTC
*
3531 AAAAATGGTAATTTTTGAAACTTTCGAGGTC
1 AAAAATGG-AATTTTTGAAAGTTTCGAGGTC
* * * * *
3562 TAAAATAGAATTTTTTAAAGTTTGGGGGT-
1 AAAAATGGAATTTTTGAAAGTTTCGAGGTC
* * * *
3591 GAAAATGGATTTTTTGAAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGAAAGTTTCGAGGTC
* * * *
3621 -AAAATGGAATTTTTGGAAGTTTTGGGGTA
1 AAAAATGGAATTTTTGAAAGTTTCGAGGTC
* *
3650 AAAAATGGAATTTTTGGAAGTTT-TAGGGTC
1 AAAAATGGAATTTTTGAAAGTTTCGA-GGTC
* * *
3680 AAAAATGGATTTTTTGGATGTTT-GAGGGT-
1 AAAAATGGAATTTTTGAAAGTTTCGA-GGTC
3709 AAAAATGGAATTTT
1 AAAAATGGAATTTT
3723 CGAACAATTT
Statistics
Matches: 207, Mismatches: 31, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
28 10 0.05
29 113 0.55
30 77 0.37
31 7 0.03
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (30 bp):
AAAAATGGAATTTTTGAAAGTTTCGAGGTC
Found at i:3734 original size:59 final size:58
Alignment explanation
Indices: 3469--3736 Score: 215
Period size: 59 Copynumber: 4.5 Consensus size: 58
3459 TAGATATTCG
* * * * * *
3469 GGGTAAAAAATGGAATTTTTG-GAGTTTCGAGGTCAAAAATAGAGTTTTTGGACA-TTCGA
1 GGGT-AAAAATGGAATTTTTGAAATTTTAG-GGTCAAAAATGGATTTTTTGGA-AGTTTGA
* * * * * *
3528 GGG-AAAAATGGTAATTTTTGAAACTTTCGAGGTCTAAAATAGAATTTTTT-AAAGTTTGG
1 GGGTAAAAATGG-AATTTTTGAAATTTTAG-GGTCAAAAAT-GGATTTTTTGGAAGTTTGA
* * * *
3587 GGGTGAAAATGGATTTTTTGAAAGTTTTGGGGTC-AAAATGGAATTTTTGGAAGTTTTG-
1 GGGTAAAAATGGAATTTTTGAAA-TTTTAGGGTCAAAAATGGATTTTTTGGAAG-TTTGA
* *
3645 GGGTAAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGATTTTTTGGATGTTTGA
1 GGGT-AAAAATGGAATTTTT-GAAATTTTAGGGTCAAAAATGGATTTTTTGGAAGTTTGA
* *
3705 GGGTAAAAATGGAATTTTCGAACAATTTAGGG
1 GGGTAAAAATGGAATTTTTGAA-ATTTTAGGG
3737 ACCTTCAAGG
Statistics
Matches: 171, Mismatches: 25, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
57 15 0.09
58 24 0.14
59 91 0.53
60 41 0.24
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (58 bp):
GGGTAAAAATGGAATTTTTGAAATTTTAGGGTCAAAAATGGATTTTTTGGAAGTTTGA
Found at i:5536 original size:17 final size:17
Alignment explanation
Indices: 5498--5572 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
5488 TAATTGAACT
* *
5498 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAAATAAA
* *
5516 TTTAAATTTAAGATTAA
1 TTTAAATTTAAAATAAA
*
5533 TTTAAATTTAAAATGAA
1 TTTAAATTTAAAATAAA
*
5550 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
5567 TTTAAA
1 TTTAAA
5573 AAAAAGAGGC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
17 40 0.83
18 8 0.17
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:5563 original size:7 final size:6
Alignment explanation
Indices: 5498--5572 Score: 52
Period size: 6 Copynumber: 13.0 Consensus size: 6
5488 TAATTGAACT
*
5498 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
* * * *
5545 -ATGAA TCTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5573 AAAAAGAGGC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
4 1 0.02
5 13 0.24
6 37 0.69
7 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:6521 original size:29 final size:29
Alignment explanation
Indices: 6484--6701 Score: 178
Period size: 29 Copynumber: 7.4 Consensus size: 29
6474 ACTATCTAAG
*
6484 AATTACATTTTTACCCCCTAACTTCCAAA
1 AATTCCATTTTTACCCCCTAACTTCCAAA
**
6513 AATTCCATTTTTTGACCCCAAAACTTCCAAA
1 AATTCCA-TTTTT-ACCCCCTAACTTCCAAA
* * *
6544 AATTACAGTTTTA-CCCCTAAGTTCCAAAA
1 AATTCCATTTTTACCCCCTAACTTCC-AAA
* *
6573 AATT-CA-TTTTAGACCTCTAAACTTCCAAA
1 AATTCCATTTTTA-CCCCCT-AACTTCCAAA
6602 AATT--ATATTTTA-CCCCTAAACTTCCAAA
1 AATTCCAT-TTTTACCCCCT-AACTTCCAAA
* **
6630 AATTCCATTTGTAACCCCGAAACTTCCAAA
1 AATTCCATTT-TTACCCCCTAACTTCCAAA
** * * *
6660 AATTGTATTTTTACCCTCAAACCTCCAAA
1 AATTCCATTTTTACCCCCTAACTTCCAAA
6689 AATTCCATTTTTA
1 AATTCCATTTTTA
6702 ACCCTAAAAC
Statistics
Matches: 155, Mismatches: 22, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
27 5 0.03
28 31 0.20
29 53 0.34
30 42 0.27
31 24 0.15
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AATTCCATTTTTACCCCCTAACTTCCAAA
Found at i:6573 original size:59 final size:58
Alignment explanation
Indices: 6484--6825 Score: 295
Period size: 59 Copynumber: 5.8 Consensus size: 58
6474 ACTATCTAAG
*
6484 AATTACATTTTTACCCCCTAACTTCCAAAAATTCCATTTTTTGACCCCAAAACTTCCAAA
1 AATTACATTTTTA-CCCCTAACTTCCAAAAATTCCA-TTTTTAACCCCAAAACTTCCAAA
* * * *
6544 AATTACAGTTTTACCCCTAAGTTCCAAAAAATT-CA-TTTTAGACCTCTAAACTTCCAAA
1 AATTACATTTTTACCCCTAACTTCC-AAAAATTCCATTTTTA-ACCCCAAAACTTCCAAA
* * *
6602 AATTATA-TTTTACCCCTAAACTTCCAAAAATTCCATTTGTAACCCCGAAACTTCCAAA
1 AATTACATTTTTACCCCT-AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAA
** * * * * *
6660 AATTGTATTTTTACCCTCAAACCTCCAAAAATTCCATTTTTAACCCTAAAACTTCTAGA
1 AATTACATTTTTACCC-CTAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAA
* * * * * * *
6719 AATTACCTTTTTACCACC-AAATGTCTAAAAACTCTATTTTTTACCTCAAAAC--CCTTAAA
1 AATTACATTTTTACC-CCTAACT-TCCAAAAATTCCATTTTTAACCCCAAAACTTCC--AAA
* *
6778 AATTACCA-TTTTACCCTCGAA-TATCCAAAAATTCCATTTTTATCCCCA
1 AATTA-CATTTTTACCC-CTAACT-TCCAAAAATTCCATTTTTAACCCCA
6826 TTTTCTAAAA
Statistics
Matches: 229, Mismatches: 39, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
57 22 0.10
58 53 0.23
59 130 0.57
60 24 0.10
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
AATTACATTTTTACCCCTAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAA
Found at i:6601 original size:30 final size:28
Alignment explanation
Indices: 6468--6733 Score: 198
Period size: 30 Copynumber: 9.0 Consensus size: 28
6458 CCTTGGAGGT
* * *
6468 CCCTAAACTATCTAAGAATTACATTTTTACC
1 CCCTAAACT-TCCAAAAATTCCA-TTTTA-C
6499 CCCT-AACTTCCAAAAATTCCATTTTTTGAC
1 CCCTAAACTTCCAAAAATTCCA--TTTT-AC
* *
6529 CCCAAAACTTCCAAAAATTACAGTTTTAC
1 CCCTAAACTTCCAAAAATTCCA-TTTTAC
*
6558 CCCT-AAGTTCCAAAAAATT-CATTTTAGAC
1 CCCTAAACTTCC-AAAAATTCCATTTT--AC
* **
6587 CTCTAAACTTCCAAAAATTATATTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTAC
6615 CCCTAAACTTCCAAAAATTCCATTTGTAAC
1 CCCTAAACTTCCAAAAATTCCATTT-T-AC
* **
6645 CCCGAAACTTCCAAAAATTGTATTTTTA-
1 CCCTAAACTTCCAAAAATTCCA-TTTTAC
* *
6673 CCCTCAAACCTCCAAAAATTCCATTTTTAA
1 CCCT-AAACTTCCAAAAATTCCA-TTTTAC
* * *
6703 CCCTAAAACTTCTAGAAATTACCTTTTTAC
1 CCCT-AAACTTCCAAAAATT-CCATTTTAC
6733 C
1 C
6734 ACCAAATGTC
Statistics
Matches: 194, Mismatches: 27, Indels: 29
0.78 0.11 0.12
Matches are distributed among these distances:
27 4 0.02
28 35 0.18
29 57 0.29
30 72 0.37
31 26 0.13
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTCCATTTTAC
Found at i:6627 original size:58 final size:58
Alignment explanation
Indices: 6492--6723 Score: 256
Period size: 58 Copynumber: 3.9 Consensus size: 58
6482 AGAATTACAT
* *
6492 TTTTACCCCCTAACTTCCAAAAATTCCATTTTTTGACCCCAAAACTTCCAAAAATTACAG
1 TTTTA-CCCCTAACTTCCAAAAATTCCA-TTTTAGACCCCAAAACTTCCAAAAATTATAG
* * *
6552 TTTTACCCCTAAGTTCCAAAAAATT-CATTTTAGACCTCTAAACTTCCAAAAATTATA-
1 TTTTACCCCTAACTTCC-AAAAATTCCATTTTAGACCCCAAAACTTCCAAAAATTATAG
* * *
6609 TTTTACCCCTAAACTTCCAAAAATTCCATTTGTA-ACCCCGAAACTTCCAAAAATTGTAT
1 TTTTACCCCT-AACTTCCAAAAATTCCATTT-TAGACCCCAAAACTTCCAAAAATTATAG
* * * * *
6668 TTTTACCCTCAAACCTCCAAAAATTCCATTTTTA-ACCCTAAAACTTCTAGAAATTA
1 TTTTACCC-CTAACTTCCAAAAATTCCA-TTTTAGACCCCAAAACTTCCAAAAATTA
6724 CCTTTTTACC
Statistics
Matches: 149, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
57 17 0.11
58 58 0.39
59 58 0.39
60 16 0.11
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (58 bp):
TTTTACCCCTAACTTCCAAAAATTCCATTTTAGACCCCAAAACTTCCAAAAATTATAG
Found at i:6816 original size:28 final size:29
Alignment explanation
Indices: 6775--6951 Score: 98
Period size: 28 Copynumber: 6.2 Consensus size: 29
6765 CAAAACCCTT
6775 AAAAATTACCATTTTACCCTCGAATATCC
1 AAAAATTACCATTTTACCCTCGAATATCC
* * *
6804 AAAAATT-CCATTTTTATCCC-C-ATTTTCT
1 AAAAATTACCA-TTTTA-CCCTCGAATATCC
* *
6832 AAAAATTACCGTTTTACCCTCGAATGT-C
1 AAAAATTACCATTTTACCCTCGAATATCC
* * ** *
6860 TAAAATT-CCATTTTAAACCATAAAATTTCC
1 AAAAATTACCATTTT--ACCCTCGAATATCC
* * * *
6890 CAAAATTACTATTTTGCCCTC-AAGAATCC
1 AAAAATTACCATTTTACCCTCGAA-TATCC
* * * *
6919 -AAAATTACCATTTTGCCCCCGAGTATCT
1 AAAAATTACCATTTTACCCTCGAATATCC
6947 AAAAA
1 AAAAA
6952 GTCTAATTTT
Statistics
Matches: 111, Mismatches: 25, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
27 9 0.08
28 49 0.44
29 37 0.33
30 10 0.09
31 6 0.05
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCGAATATCC
Found at i:35278 original size:57 final size:57
Alignment explanation
Indices: 35190--35304 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
35180 AATCTAGTCT
35190 CATAGCTCCCATAGGAGAATCCCACAATCAACCTCAATCGTCCCAAAGTTTAAATCA
1 CATAGCTCCCATAGGAGAATCCCACAATCAACCTCAATCGTCCCAAAGTTTAAATCA
*
35247 CATAGCTCCCATAGGTGAATCCCACAATCAACCTCAATCGTCCCAAAGTTTAAATCA
1 CATAGCTCCCATAGGAGAATCCCACAATCAACCTCAATCGTCCCAAAGTTTAAATCA
35304 C
1 C
35305 TTAAACAGGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.36, C:0.32, G:0.10, T:0.22
Consensus pattern (57 bp):
CATAGCTCCCATAGGAGAATCCCACAATCAACCTCAATCGTCCCAAAGTTTAAATCA
Done.