Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008284.1 Kokia drynarioides strain JFW-HI SEQ_122949, 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: 16814
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:6423 original size:30 final size:29
Alignment explanation
Indices: 6218--6702 Score: 266
Period size: 29 Copynumber: 16.6 Consensus size: 29
6208 GAAAATTTGT
* *
6218 GGTCGAAAATGTGACTTTT-AGAAATTTGAG
1 GGTC-AAAATGTGA-TTTTGAGAAGTTCGAG
* *
6248 GGT-AAAATGGTAATTTTTG-GATGTTCGAG
1 GGTCAAAAT-GTGA-TTTTGAGAAGTTCGAG
* * * *
6277 GGT-AAAATGCTAATTTTTAGATGTT-TAG
1 GGTCAAAATG-TGATTTTGAGAAGTTCGAG
* ** * *
6305 GGGCAAAAATGCAATTTTAGAAAAGTT-TAG
1 GGTC-AAAATGTGATTTT-GAGAAGTTCGAG
* *
6335 GGTGAAAATGTGATTTTG-G-AGTTCAAG
1 GGTCAAAATGTGATTTTGAGAAGTTCGAG
* *
6362 GGTCGAAATGTGATTTTGAAAAGTTCGAG
1 GGTCAAAATGTGATTTTGAGAAGTTCGAG
*
6391 GGTCAAAATGTGATTCTTGAGAAGTTCAAG
1 GGTCAAAATGTGATT-TTGAGAAGTTCGAG
* * * * *
6421 GGTTAAAATGTAATTTTTATAAAGTTTGA-
1 GGTCAAAATGTGATTTTGA-GAAGTTCGAG
* * *
6450 GGTCAAAATGTAATTTTGGAAAAGCTCGA-
1 GGTCAAAATGTGATTTT-GAGAAGTTCGAG
* *
6479 GGTTAAAATG-GTATTTTTTG-GATGTTCGAG
1 GGTCAAAATGTG-A--TTTTGAGAAGTTCGAG
* * *
6509 GG-CAAAAATGTAATTTTAGAAAAGTTTG-G
1 GGTC-AAAATGTGATTTT-GAGAAGTTCGAG
* * * *
6538 TGTGAAAATGTGATTTTGAAAAAGTT-TAGG
1 GGTCAAAATGTGATTTTG-AGAAGTTCGA-G
*
6568 GGTCAAAATGTAATTTTTG-GAAAGTTCGAG
1 GGTCAAAATGTGA-TTTTGAG-AAGTTCGAG
* * *
6598 GGTCAAAATGTTATTTTGAGAAGCTCGGG
1 GGTCAAAATGTGATTTTGAGAAGTTCGAG
6627 GGTCAAAATGTGATTTTTGAGAAGTTCGAG
1 GGTCAAAATGTGA-TTTTGAGAAGTTCGAG
* * * *
6657 GGTGAAAATATAATTTTTGTGAAGTTCGA-
1 GGTCAAAATGTGA-TTTTGAGAAGTTCGAG
*
6686 GGTCAAAATGTAATTTT
1 GGTCAAAATGTGATTTT
6703 TTAAACAAAA
Statistics
Matches: 359, Mismatches: 66, Indels: 62
0.74 0.14 0.13
Matches are distributed among these distances:
26 4 0.01
27 18 0.05
28 24 0.07
29 168 0.47
30 135 0.38
31 10 0.03
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (29 bp):
GGTCAAAATGTGATTTTGAGAAGTTCGAG
Found at i:6437 original size:59 final size:58
Alignment explanation
Indices: 6218--6702 Score: 300
Period size: 59 Copynumber: 8.3 Consensus size: 58
6208 GAAAATTTGT
* * * * *
6218 GGTCGAAAATGTGACTTTT-AGAAATTTGAGGGT-AAAATGGTAATTTTTG-GATGTTCGAG
1 GGTC-AAAATGT-AATTTTGAGAAGTTCGAGGGTCAAAAT-GTAA-TTTTGAAAAGTTCGAG
* * * * * *
6277 GGT-AAAATGCTAATTTTTAGATGTT-TAGGGGCAAAAATGCAATTTTAGAAAAGTT-TAG
1 GGTCAAAATG-TAATTTTGAGAAGTTCGAGGGTC-AAAATGTAATTTT-GAAAAGTTCGAG
* * * * *
6335 GGTGAAAATGTGATTTTG-G-AGTTCAAGGGTCGAAATGTGATTTTGAAAAGTTCGAG
1 GGTCAAAATGTAATTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTGAAAAGTTCGAG
* * * * *
6391 GGTCAAAATGTGATTCTTGAGAAGTTCAAGGGTTAAAATGTAATTTTTATAAAGTTTGA-
1 GGTCAAAATGTAATT-TTGAGAAGTTCGAGGGTCAAAATGTAATTTTGA-AAAGTTCGAG
* * * * * *
6450 GGTCAAAATGTAATTTTGGAAAAGCTCGA-GGTTAAAATGGTATTTTTTG-GATGTTCGAG
1 GGTCAAAATGTAATTTT-GAGAAGTTCGAGGGTCAAAAT-GTA-ATTTTGAAAAGTTCGAG
* * * * * *
6509 GG-CAAAAATGTAATTTTAGAAAAGTTTG-GTGTGAAAATGTGATTTTGAAAAAGTT-TAGG
1 GGTC-AAAATGTAATTTT-GAGAAGTTCGAGGGTCAAAATGTAATTTTG-AAAAGTTCGA-G
* * * *
6568 GGTCAAAATGTAATTTTTG-GAAAGTTCGAGGGTCAAAATGTTATTTTGAGAAGCTCGGG
1 GGTCAAAATGTAA-TTTTGAG-AAGTTCGAGGGTCAAAATGTAATTTTGAAAAGTTCGAG
* * * **
6627 GGTCAAAATGTGATTTTTGAGAAGTTCGAGGGTGAAAATATAATTTTTGTGAAGTTCGA-
1 GGTCAAAATGT-AATTTTGAGAAGTTCGAGGGTCAAAATGTAA-TTTTGAAAAGTTCGAG
6686 GGTCAAAATGTAATTTT
1 GGTCAAAATGTAATTTT
6703 TTAAACAAAA
Statistics
Matches: 336, Mismatches: 60, Indels: 61
0.74 0.13 0.13
Matches are distributed among these distances:
55 8 0.02
56 29 0.09
57 33 0.10
58 48 0.14
59 171 0.51
60 47 0.14
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (58 bp):
GGTCAAAATGTAATTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTGAAAAGTTCGAG
Found at i:7847 original size:27 final size:27
Alignment explanation
Indices: 7809--7864 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
7799 CAAATTATTT
7809 TATTATTATTATTTATTAT-CTATTTAA
1 TATTATTATTATTTATTATGC-ATTTAA
7836 TATTA-TATTTATTTATTATGCATTTAA
1 TATTATTA-TTATTTATTATGCATTTAA
7863 TA
1 TA
7865 ACATTTAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 2 0.07
27 24 0.89
28 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (27 bp):
TATTATTATTATTTATTATGCATTTAA
Found at i:8477 original size:11 final size:11
Alignment explanation
Indices: 8463--8530 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
8453 TTTTAATTTT
8463 TTTAAATTAAA
1 TTTAAATTAAA
*
8474 TTTAGAA-TGAA
1 TTTA-AATTAAA
8485 TTTAAATTCAAA
1 TTTAAATT-AAA
*
8497 -ATAAATTTAAA
1 TTTAAA-TTAAA
*
8508 TTTAAACTAAAA
1 TTTAAA-TTAAA
*
8520 TTAAAATTAAA
1 TTTAAATTAAA
8531 ATTCAAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
10 2 0.05
11 23 0.52
12 19 0.43
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:8491 original size:17 final size:17
Alignment explanation
Indices: 8465--8532 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
8455 TTAATTTTTT
*
8465 TAAA-TTAAATTTAGAA
1 TAAATTTAAATTTAAAA
* *
8481 TGAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
8498 TAAATTTAAATTTAAAC
1 TAAATTTAAATTTAAAA
* *
8515 TAAAATTAAAATTAAAA
1 TAAATTTAAATTTAAAA
8532 T
1 T
8533 TCAAAAATGG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
16 3 0.07
17 39 0.93
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:8513 original size:23 final size:23
Alignment explanation
Indices: 8483--8530 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
8473 ATTTAGAATG
* *
8483 AATTTAAATTCAAAA-TAAATTTA
1 AATTTAAACT-AAAATTAAAATTA
8506 AATTTAAACTAAAATTAAAATTA
1 AATTTAAACTAAAATTAAAATTA
8529 AA
1 AA
8531 ATTCAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
AATTTAAACTAAAATTAAAATTA
Found at i:9072 original size:39 final size:39
Alignment explanation
Indices: 9021--9267 Score: 250
Period size: 39 Copynumber: 6.3 Consensus size: 39
9011 TCTTAGGTTT
* *
9021 GGGTAAGAGATTGGTTGATGGTGATCTGCCCTAGGCTCG
1 GGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGCTCG
* *
9060 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG
1 GGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGCTCG
* * * *
9099 GGGTAAAAGATCGGATG-T-CTGCAATCTGCCTCAGGCTCG
1 GGGTAAGAGATTGGATGATGGTG--ATCTGCCCCAGGCTCG
* * *
9138 GGGTAAGAGATTGGTTGATGGTGATCTGCCCCGGGCTCA
1 GGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGCTCG
* * * * *
9177 GGGTAAAAGATCGGATG-T-CTACAATTTGCCCCAGGCTCG
1 GGGTAAGAGATTGGATGATGGT--GATCTGCCCCAGGCTCG
* *
9216 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG
1 GGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGCTCG
* *
9255 AGGTAAAAGATTG
1 GGGTAAGAGATTG
9268 AATGTCTGTA
Statistics
Matches: 167, Mismatches: 33, Indels: 16
0.77 0.15 0.07
Matches are distributed among these distances:
37 3 0.02
38 2 0.01
39 157 0.94
40 2 0.01
41 3 0.02
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (39 bp):
GGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGCTCG
Found at i:9285 original size:39 final size:39
Alignment explanation
Indices: 9044--9309 Score: 178
Period size: 39 Copynumber: 6.8 Consensus size: 39
9034 GTTGATGGTG
* * * * * *
9044 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGAT-GGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATG-TCTGTA
* *
9083 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGTCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGTCTGTA
* * * * * *
9122 ATCTGCCTCAGGCTCGGGGTAAGAGATTGGTTGAT-GGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATG-TCTGTA
** * * **
9161 ATCTGCCCCGGGCTCAGGGTAAAAGATCGGATGTCTACA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGTCTGTA
* * * * * *
9200 ATTTGCCCCAGGCTCGGGGTAAGAGATTGGCTGAT-GGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATG-TCTGTA
* *
9239 ATCTGCCCCAAGCTCGAGGTAAAAGATTGAATGTCTGTA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGTCTGTA
* * ** * *
9278 ATTTGCCCTAAGCTTTGGTTAAGAGATTGGAT
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGAT
9310 CTTCAATCTG
Statistics
Matches: 170, Mismatches: 52, Indels: 10
0.73 0.22 0.04
Matches are distributed among these distances:
38 3 0.02
39 165 0.97
40 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.26
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGTCTGTA
Found at i:9301 original size:78 final size:78
Alignment explanation
Indices: 9047--9307 Score: 364
Period size: 78 Copynumber: 3.3 Consensus size: 78
9037 GATGGTGATC
*
9047 TGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCG
1 TGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCG
*
9112 GATGTCTGCAATC
66 GATGTCTGCAATT
* **
9125 TG-CCTCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCGGGCTC-AGGGTAAAAGAT
1 TGCCCT-AGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGA-GGTAAAAGAT
*
9188 CGGATGTCTACAATT
64 CGGATGTCTGCAATT
* *
9203 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATTG
1 TGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCG
* *
9268 AATGTCTGTAATT
66 GATGTCTGCAATT
* ** *
9281 TGCCCTAAGCTTTGGTTAAGAGATTGG
1 TGCCCTAGGCTCGGGGTAAGAGATTGG
9308 ATCTTCAATC
Statistics
Matches: 160, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
77 3 0.02
78 154 0.96
79 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.26
Consensus pattern (78 bp):
TGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCG
GATGTCTGCAATT
Done.