Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003240.1 Kokia drynarioides strain JFW-HI SEQ_115888, 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: 9469
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:2547 original size:99 final size:98
Alignment explanation
Indices: 2376--2578 Score: 397
Period size: 99 Copynumber: 2.1 Consensus size: 98
2366 ATTTTTGTAA
2376 ATTAGTCATTATACTTTTATTTCAATAAATTTAGTCTCTATTTTTAATATTTCAAAATTCAGGTC
1 ATTAGTCATTATACTTTTATTTCAATAAATTTAGTCTCTATTTTTAATATTTCAAAATTCAGGTC
2441 CAATTTTTAAAGATTTTTTTTTTTGTTAAAATTT
66 CAATTTTTAAAGA-TTTTTTTTTTGTTAAAATTT
2475 ATTAGTCATTATACTTTTATTTCAATAAATTTAGTCTCTATTTTTAATATTTCAAAATTCAGGTC
1 ATTAGTCATTATACTTTTATTTCAATAAATTTAGTCTCTATTTTTAATATTTCAAAATTCAGGTC
2540 CAATTTTTAAAGATTTTTTTTTTGTTAAAATTT
66 CAATTTTTAAAGATTTTTTTTTTGTTAAAATTT
2573 ATTAGT
1 ATTAGT
2579 GTGACATTTT
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 26 0.25
99 78 0.75
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (98 bp):
ATTAGTCATTATACTTTTATTTCAATAAATTTAGTCTCTATTTTTAATATTTCAAAATTCAGGTC
CAATTTTTAAAGATTTTTTTTTTGTTAAAATTT
Found at i:3614 original size:32 final size:31
Alignment explanation
Indices: 3578--3670 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 31
3568 CTATTGGGGC
3578 TAATTCTACAAGATTGGTTAAATTGGAGGGAT
1 TAATTCT-CAAGATTGGTTAAATTGGAGGGAT
*
3610 TAATTCT---GA------AATTTGGAGGGAT
1 TAATTCTCAAGATTGGTTAAATTGGAGGGAT
*
3632 TAATTTTGCAAGATTGGTTAAATTGGAGGGAT
1 TAATTCT-CAAGATTGGTTAAATTGGAGGGAT
3664 TAATTCT
1 TAATTCT
3671 GAAATTTGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 20
0.66 0.06 0.28
Matches are distributed among these distances:
22 18 0.38
26 2 0.04
28 2 0.04
32 25 0.53
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38
Consensus pattern (31 bp):
TAATTCTCAAGATTGGTTAAATTGGAGGGAT
Found at i:3660 original size:54 final size:54
Alignment explanation
Indices: 3586--3732 Score: 249
Period size: 54 Copynumber: 2.7 Consensus size: 54
3576 GCTAATTCTA
3586 CAAGATTGGTTAAATTGGAGGGATTAATTCTGAAATTTGGAGGGATTAATTTTG
1 CAAGATTGGTTAAATTGGAGGGATTAATTCTGAAATTTGGAGGGATTAATTTTG
3640 CAAGATTGGTTAAATTGGAGGGATTAATTCTGAAATTTGGAGGGATTAATTTTG
1 CAAGATTGGTTAAATTGGAGGGATTAATTCTGAAATTTGGAGGGATTAATTTTG
* * * * *
3694 CAAGATTAGTTAAATTGTAGAGACTAATTTTGAAATTTG
1 CAAGATTGGTTAAATTGGAGGGATTAATTCTGAAATTTG
3733 ACCAAAAGTT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.37
Consensus pattern (54 bp):
CAAGATTGGTTAAATTGGAGGGATTAATTCTGAAATTTGGAGGGATTAATTTTG
Found at i:3972 original size:5 final size:5
Alignment explanation
Indices: 3962--3986 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3952 TTTTAATTAC
3962 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
3987 TATTTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:4915 original size:161 final size:161
Alignment explanation
Indices: 4728--5039 Score: 477
Period size: 161 Copynumber: 1.9 Consensus size: 161
4718 TAATTTCCTC
* *
4728 AACAACATTTTTTATATTTAACCCTTTAGCGTACTATTACTTCATGTG-GACAGTAAGAATCAAC
1 AACAACATTTTTAATATTTAACCCTTTAGCCTACTATTACTTCATGTGAG-CAGTAAGAATCAAC
* *
4792 AAAGGGAGAAAGATGATAAGAAAAGTAC-CGATTTATTCTTGTG-AGATAGAGAATCATCAGACT
65 AAAGAGAGAAAGATGACAAGAAAAGT-CTCGATTTATTCTTGTGTA-ATAGAGAATCATCAGACT
4855 ATAATGATGTAGATGGTTGTAGAGGTTAGAGAGG
128 ATAATGATGTAGATGGTTGTAGAGGTTAGAGAGG
* * *
4889 AACAACATTTTTAATCTTTAACCCTTTAGCCTACTATTACTTCATGTGAGTAGTAGGAATCAACA
1 AACAACATTTTTAATATTTAACCCTTTAGCCTACTATTACTTCATGTGAGCAGTAAGAATCAACA
* * *
4954 AAGAGAGAAAGATGACAAGAAAGGTCTCGATTTATTCTTGTGTAATAGAGAGTCATCGGACTATA
66 AAGAGAGAAAGATGACAAGAAAAGTCTCGATTTATTCTTGTGTAATAGAGAATCATCAGACTATA
*
5019 ATGGTGTAGATGGTTGTAGAG
131 ATGATGTAGATGGTTGTAGAG
5040 AAAGAAGAGT
Statistics
Matches: 137, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
160 1 0.01
161 134 0.98
162 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (161 bp):
AACAACATTTTTAATATTTAACCCTTTAGCCTACTATTACTTCATGTGAGCAGTAAGAATCAACA
AAGAGAGAAAGATGACAAGAAAAGTCTCGATTTATTCTTGTGTAATAGAGAATCATCAGACTATA
ATGATGTAGATGGTTGTAGAGGTTAGAGAGG
Found at i:7585 original size:45 final size:45
Alignment explanation
Indices: 7521--7612 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
7511 AAATGAATTA
*
7521 GAAATATTAATGACTTCTGATTTTAACAGTTACAGAAGATTAAGT
1 GAAATATTAATGACTTCTGATTTTAACAGTAACAGAAGATTAAGT
7566 GAAATATTAATGACTTCTGATTTTAACAGTAACAGAAGATTAAGT
1 GAAATATTAATGACTTCTGATTTTAACAGTAACAGAAGATTAAGT
7611 GA
1 GA
7613 TCCATGATTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (45 bp):
GAAATATTAATGACTTCTGATTTTAACAGTAACAGAAGATTAAGT
Done.