Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168400.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_616, 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: 21457
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Found at i:2159 original size:2 final size:2
Alignment explanation
Indices: 2152--2190 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2142 ATATACGGGA
2152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2191 AAACATCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4705 original size:18 final size:19
Alignment explanation
Indices: 4671--4715 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
4661 TCATCATATT
4671 ATTTAATTTAATAATTTTA
1 ATTTAATTTAATAATTTTA
*
4690 ATTTAA-TTACTAATTTT-
1 ATTTAATTTAATAATTTTA
4707 A-TTAATTTA
1 ATTTAATTTA
4716 TTCGTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 10 0.42
19 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTAATTTAATAATTTTA
Found at i:5039 original size:24 final size:25
Alignment explanation
Indices: 5007--5071 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
4997 TTTTTTTACT
5007 TTTTTTTAAAAAATTAAAATTTA-A
1 TTTTTTTAAAAAATTAAAATTTATA
* *
5031 TTTTTTTAAAAAAATCAATATTTATA
1 TTTTTTT-AAAAAATTAAAATTTATA
*
5057 ATTTTTTAAAAAATT
1 TTTTTTTAAAAAATT
5072 TTCATATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.20
25 21 0.60
26 7 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTTTTTAAAAAATTAAAATTTATA
Found at i:5078 original size:27 final size:24
Alignment explanation
Indices: 5008--5085 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 24
4998 TTTTTTACTT
* * *
5008 TTTTTTAAAAAATTAAAATTTAAT
1 TTTTTTAAAAAATTCATATTTAAA
*
5032 TTTTTTAAAAAAATCAATATTTATAA
1 TTTTTTAAAAAATTC-ATATTTA-AA
5058 TTTTTTAAAAAATTTTCATA-TTAAA
1 TTTTTTAAAAAA--TTCATATTTAAA
5083 TTT
1 TTT
5086 AATATTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
24 13 0.29
25 11 0.24
26 16 0.36
27 3 0.07
28 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTTTAAAAAATTCATATTTAAA
Found at i:5125 original size:24 final size:22
Alignment explanation
Indices: 5106--5167 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
5096 AGATATTTAC
5106 ATTTTTTTTAAAAATCATATATT
1 ATTTTTTTTAAAAATCATAT-TT
*
5129 -TTTTAATTTTTAAAATCATATTTT
1 ATTTT--TTTTAAAAATCATA-TTT
*
5153 ATTTTTTTAAAAAAT
1 ATTTTTTTTAAAAAT
5168 TCAATATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 15 0.47
25 5 0.16
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTTTTTAAAAATCATATTT
Found at i:5738 original size:18 final size:18
Alignment explanation
Indices: 5711--5758 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5701 AATATTTTTT
* *
5711 TTAAATAAAATGTTAAAAT
1 TTAAA-AAAATGTAAAAAC
* *
5730 TTTAAAAAATATAAAAAC
1 TTAAAAAAATGTAAAAAC
5748 TTAAAAAAATG
1 TTAAAAAAATG
5759 AAGTCTAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (18 bp):
TTAAAAAAATGTAAAAAC
Found at i:5957 original size:22 final size:21
Alignment explanation
Indices: 5909--5968 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
5899 TAACAAATTT
* *
5909 AAAAATTTATTTTTCAAAAAAA
1 AAAAATATAATTTT-AAAAAAA
* *
5931 TAAAATCTAATTTTAAAAAATA
1 AAAAATATAATTTTAAAAAA-A
5953 AAAAATATAAATTTTA
1 AAAAATAT-AATTTTA
5969 TTATTAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 6 0.19
22 18 0.58
23 7 0.23
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATATAATTTTAAAAAAA
Found at i:6235 original size:15 final size:15
Alignment explanation
Indices: 6212--6253 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
6202 AAAATAATAC
6212 AAAAATTAAATTTAT
1 AAAAATTAAATTTAT
**
6227 ATGAATTAAA-TTAT
1 AAAAATTAAATTTAT
6241 AAAAATTAAATTT
1 AAAAATTAAATTT
6254 CAAATTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAAAATTAAATTTAT
Found at i:10648 original size:15 final size:17
Alignment explanation
Indices: 10638--10679 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
10628 TATTTATTTA
10638 TATATATTTTATATAAT
1 TATATATTTTATATAAT
*
10655 TATATA-TTTAAAT-AT
1 TATATATTTTATATAAT
10670 T-TATATTTTA
1 TATATATTTTA
10680 AAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.17
15 7 0.30
16 6 0.26
17 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATATTTTATATAAT
Found at i:10657 original size:8 final size:8
Alignment explanation
Indices: 10628--10679 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
10618 ATTTTTTAAT
*
10628 TATTTATT
1 TATTTATA
*
10636 TATATATA
1 TATTTATA
10644 T-TTTATA
1 TATTTATA
*
10651 TAATTATA
1 TATTTATA
*
10659 TATTTAAA
1 TATTTATA
10667 TATTTATA
1 TATTTATA
10675 T-TTTA
1 TATTTA
10680 AAAATAATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
7 10 0.28
8 26 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTATA
Found at i:10681 original size:15 final size:15
Alignment explanation
Indices: 10640--10690 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 15
10630 TTTATTTATA
*
10640 TATATTTTATATAAT
1 TATATTTTAAATAAT
*
10655 TATATATTTAAATATT
1 TATAT-TTTAAATAAT
10671 TATATTTTAAA-AAT
1 TATATTTTAAATAAT
*
10685 AATATT
1 TATATT
10691 ATATTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 7 0.23
15 11 0.35
16 13 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTTTAAATAAT
Found at i:10937 original size:41 final size:41
Alignment explanation
Indices: 10880--10962 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
10870 TTCTAGTAGA
* *
10880 ATTGAACATTTTCATCTCAAATAGGAGGCTCTATAGTCTAT
1 ATTGAACATTTTCATCTCAAATAGCAGGCTCTATAATCTAT
10921 ATTGAACATTTTCATCTCAAATAGCAGGCTCTATAATCTAT
1 ATTGAACATTTTCATCTCAAATAGCAGGCTCTATAATCTAT
10962 A
1 A
10963 GGGAACTTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (41 bp):
ATTGAACATTTTCATCTCAAATAGCAGGCTCTATAATCTAT
Found at i:11632 original size:2 final size:2
Alignment explanation
Indices: 11614--11647 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
11604 GAGGTAATGA
*
11614 AT AT AA AT AT AT CAT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT A
11648 ATTCATGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Done.