Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168373.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_592, 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: 22005
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Found at i:5000 original size:18 final size:18
Alignment explanation
Indices: 4988--5084 Score: 110
Period size: 18 Copynumber: 5.6 Consensus size: 18
4978 TATCCACTAT
*
4988 AAATGTATCATCCACGTC
1 AAATGTATCATCCACCTC
* *
5006 AAGTGTATCATCTACCTC
1 AAATGTATCATCCACCTC
*
5024 AAATGTATCATTCACCTC
1 AAATGTATCATCCACCTC
5042 AAATGTATCAT---CCTC
1 AAATGTATCATCCACCTC
* *
5057 AAATATATCCTCCACCTC
1 AAATGTATCATCCACCTC
*
5075 AAATGCATCA
1 AAATGTATCA
5085 AGAACAAGGG
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
15 13 0.20
18 52 0.80
ACGTcount: A:0.34, C:0.29, G:0.07, T:0.30
Consensus pattern (18 bp):
AAATGTATCATCCACCTC
Found at i:5073 original size:33 final size:35
Alignment explanation
Indices: 4988--5084 Score: 117
Period size: 33 Copynumber: 2.8 Consensus size: 35
4978 TATCCACTAT
* *
4988 AAATGTATCATCCACGTCAAGTGTATCATCTACCTC
1 AAATGTATCATCCACCTCAAATGTATCA-CTACCTC
*
5024 AAATGTATCATTCACCTCAAATGTATCA-T-CCTC
1 AAATGTATCATCCACCTCAAATGTATCACTACCTC
* * *
5057 AAATATATCCTCCACCTCAAATGCATCA
1 AAATGTATCATCCACCTCAAATGTATCA
5085 AGAACAAGGG
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 28 0.52
34 1 0.02
36 25 0.46
ACGTcount: A:0.34, C:0.29, G:0.07, T:0.30
Consensus pattern (35 bp):
AAATGTATCATCCACCTCAAATGTATCACTACCTC
Found at i:7126 original size:21 final size:21
Alignment explanation
Indices: 7084--7126 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
7074 CTGAACAAAT
* *
7084 AAAATATAAAAGAAAGACATA
1 AAAATAGAAAAGAAAAACATA
* *
7105 AAAATAGAAAATAAAAATATA
1 AAAATAGAAAAGAAAAACATA
7126 A
1 A
7127 CTAAATATGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAATAGAAAAGAAAAACATA
Found at i:7209 original size:13 final size:13
Alignment explanation
Indices: 7193--7219 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7183 GTTTTTTCAT
7193 ATAATAATAAAAC
1 ATAATAATAAAAC
7206 ATAATAATAAAAC
1 ATAATAATAAAAC
7219 A
1 A
7220 AATGTTAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAATAATAAAAC
Found at i:11749 original size:24 final size:24
Alignment explanation
Indices: 11698--11759 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
11688 AGAATATAGT
* * *
11698 TGAAGAAGTAAAGACTGCAGCCCT
1 TGAAGCAGTAAAGACTGCAACCCG
* *
11722 TGAAGCAGTAAAGATTGCAATCCG
1 TGAAGCAGTAAAGACTGCAACCCG
11746 TGAAGCTA-TAAAGA
1 TGAAGC-AGTAAAGA
11760 GTGTAGTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.19
Consensus pattern (24 bp):
TGAAGCAGTAAAGACTGCAACCCG
Found at i:13222 original size:27 final size:26
Alignment explanation
Indices: 13174--13241 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
13164 AGAGGTGGTA
* *
13174 GCAGAAAAGTGGAAAAAGAACAATACG
1 GCAGAAAAGTGGAAAGACAACAATA-G
*
13201 GCAGAAAAGTGGAAAGCCAACAATAG
1 GCAGAAAAGTGGAAAGACAACAATAG
**
13227 GC-GAACGGTGGAAAG
1 GCAGAAAAGTGGAAAG
13242 GAGGATTCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
25 11 0.31
26 3 0.08
27 22 0.61
ACGTcount: A:0.49, C:0.13, G:0.31, T:0.07
Consensus pattern (26 bp):
GCAGAAAAGTGGAAAGACAACAATAG
Found at i:18544 original size:21 final size:21
Alignment explanation
Indices: 18482--18545 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
18472 ATTAGTTTGA
* * *
18482 TTTTAGAGAGAGAGAATGAAA
1 TTTTAGAGAGAAAGGATGAAT
18503 TTTTAGAGAGAAAGGATGAAT
1 TTTTAGAGAGAAAGGATGAAT
18524 TTTTAGAGAGAAAGGATGAAT
1 TTTTAGAGAGAAAGGATGAAT
18545 T
1 T
18546 GAGATGAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (21 bp):
TTTTAGAGAGAAAGGATGAAT
Found at i:20630 original size:16 final size:18
Alignment explanation
Indices: 20600--20632 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
20590 TCCATTTTTT
20600 ATATATAAATCAATTATA
1 ATATATAAATCAATTATA
20618 ATATA-AAAT-AATTAT
1 ATATATAAATCAATTAT
20633 TATTCTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATATAAATCAATTATA
Done.