Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004069.1 Kokia drynarioides strain JFW-HI SEQ_117227, 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: 6016
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Found at i:4299 original size:49 final size:48
Alignment explanation
Indices: 4242--4606 Score: 290
Period size: 49 Copynumber: 7.5 Consensus size: 48
4232 ATCGAGAAAC
* *
4242 AAGGGAAAGATCTAAGTCGCAATGGCGGATCTAGTACCATGAAGACATG
1 AAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACC-TGAAGACATG
* * **
4291 AAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACC-GCAAAGACACA
1 AAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCTG--AAGACATG
* * * * *
4340 AAGGGAAGGGTTTAAGTCGCAACGGC-GAACCTAGTACCTCAGAGACATG
1 AAGGGAAAGATCTAAGTCGCAACGGCGGATCC-AGTACCTGA-AGACATG
* *
4389 AAGGGAAAGATCTAAG-CTGCAATGGCGGATCCAATA-CTGCAAAGACATG
1 AAGGGAAAGATCTAAGTC-GCAACGGCGGATCCAGTACCTG--AAGACATG
* * * * * *
4438 AAGGGAAATATTTAATTCGCAACGGCGAATCCAATACCATGAAGACGTG
1 AAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACC-TGAAGACATG
* * * * * * *
4487 AGGGGAAGGGTTTAAGTCGCAACGG-GGAACCTTGTACCTCAGAGACATG
1 AAGGGAAAGATCTAAGTCGCAACGGCGGATCC-AGTACCTGA-AGACATG
* * **
4536 AAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCGTGAAGACACA
1 AAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACC-TGAAGACATG
* * *
4585 AAGGGAAGGGTTTAAGTCGCAA
1 AAGGGAAAGATCTAAGTCGCAA
4607 TGACGAACCT
Statistics
Matches: 248, Mismatches: 52, Indels: 32
0.75 0.16 0.10
Matches are distributed among these distances:
47 1 0.00
48 14 0.06
49 217 0.88
50 14 0.06
51 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.16
Consensus pattern (48 bp):
AAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCTGAAGACATG
Found at i:4599 original size:147 final size:147
Alignment explanation
Indices: 4242--4606 Score: 460
Period size: 147 Copynumber: 2.5 Consensus size: 147
4232 ATCGAGAAAC
* * * *
4242 AAGGGAAAGATCTAAGTCGCAATGGCGGATCTAGTACCATGAAGACATGAAGGGAAAGATCTAAG
1 AAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGTGAAGACATGAAGGGAAAGATTTAAG
* * * * *
4307 CCGCAATGGCGGATCCAGTACCGCAAAGACACAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCT
66 TCGCAACGGCGAATCCAATACCACAAAGACACAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCT
4372 AGTACCTCAGAGACATG
131 AGTACCTCAGAGACATG
* * * ** * *
4389 AAGGGAAAGATCTAAGCTGCAATGGCGGATCCAATACTGCAAAGACATGAAGGGAAATATTTAAT
1 AAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGTGAAGACATGAAGGGAAAGATTTAAG
** *** * *
4454 TCGCAACGGCGAATCCAATACCATGAAGACGTGAGGGGAAGGGTTTAAGTCGCAACGGGGAACCT
66 TCGCAACGGCGAATCCAATACCACAAAGACACAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCT
*
4519 TGTACCTCAGAGACATG
131 AGTACCTCAGAGACATG
* * ** * *
4536 AAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCGTGAAGACACAAAGGGAAGGGTTTAAG
1 AAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGTGAAGACATGAAGGGAAAGATTTAAG
4601 TCGCAA
66 TCGCAA
4607 TGACGAACCT
Statistics
Matches: 181, Mismatches: 37, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
147 181 1.00
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.16
Consensus pattern (147 bp):
AAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCGTGAAGACATGAAGGGAAAGATTTAAG
TCGCAACGGCGAATCCAATACCACAAAGACACAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCT
AGTACCTCAGAGACATG
Found at i:4622 original size:49 final size:49
Alignment explanation
Indices: 4489--4623 Score: 130
Period size: 49 Copynumber: 2.8 Consensus size: 49
4479 AAGACGTGAG
** **
4489 GGGAAGGGTTTAAGTCGCAACGGGGAACCTTGTACCTCAGAGACATGAA
1 GGGAAGGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAGACACAAA
* * * * * * *
4538 GGGAAAGATCTAAGCCGCAACGACGGATCC-AGTACCGTGA-AGACACAAA
1 GGGAAGGGTTTAAGTCGCAACGAC-GAACCTTGTACC-TCAGAGACACAAA
*
4587 GGGAAGGGTTTAAGTCGCAATGACGAACCTTGTACCT
1 GGGAAGGGTTTAAGTCGCAACGACGAACCTTGTACCT
4624 TAAAAACCTA
Statistics
Matches: 65, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
48 5 0.08
49 54 0.83
50 6 0.09
ACGTcount: A:0.33, C:0.21, G:0.30, T:0.17
Consensus pattern (49 bp):
GGGAAGGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAGACACAAA
Found at i:5329 original size:17 final size:17
Alignment explanation
Indices: 5309--5390 Score: 94
Period size: 17 Copynumber: 4.7 Consensus size: 17
5299 TTCATTTTGG
*
5309 GTTTAAATTTAGTTTAA
1 GTTTAAATTTAATTTAA
**
5326 GTTTAAACTTTTCTTTTAA
1 GTTTAAA--TTTAATTTAA
*
5345 GTTTAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
5362 GTTTAAATTTAATTTGAA
1 GTTTAAATTTAATTT-AA
5380 -TTTAAATTTAA
1 GTTTAAATTTAA
5391 AATTAATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
17 39 0.70
18 2 0.04
19 15 0.27
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:5372 original size:23 final size:24
Alignment explanation
Indices: 5340--5396 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
5330 AAACTTTTCT
* *
5340 TTTAAGTTTAAATTT-AAATTAAG
1 TTTAAATTTAAATTTGAAATTAAA
*
5363 TTTAAATTT-AATTTGAATTTAAA
1 TTTAAATTTAAATTTGAAATTAAA
*
5386 TTTAAAATTAA
1 TTTAAATTTAA
5397 TAAAGGCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 5 0.18
23 22 0.79
24 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (24 bp):
TTTAAATTTAAATTTGAAATTAAA
Found at i:5373 original size:12 final size:12
Alignment explanation
Indices: 5340--5396 Score: 64
Period size: 11 Copynumber: 4.9 Consensus size: 12
5330 AAACTTTTCT
*
5340 TTTAAGTTTAAA
1 TTTAAATTTAAA
*
5352 TTTAAA-TTAAG
1 TTTAAATTTAAA
5363 TTTAAATTT-AA
1 TTTAAATTTAAA
*
5374 TTTGAATTTAAA
1 TTTAAATTTAAA
*
5386 TTTAAAATTAA
1 TTTAAATTTAA
5397 TAAAGGCCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 19 0.51
12 18 0.49
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:5391 original size:6 final size:6
Alignment explanation
Indices: 5340--5396 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
5330 AAACTTTTCT
* * *
5340 TTTAAG TTTAAA TTTAAA -TTAAG TTTAAA TTT-AA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
5386 TTTAAA ATTAA
1 TTTAAA TTTAA
5397 TAAAGGCCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
5 9 0.20
6 35 0.80
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (6 bp):
TTTAAA
Done.