Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168196.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_432, 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: 27056
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:2169 original size:122 final size:122
Alignment explanation
Indices: 1952--2195 Score: 434
Period size: 122 Copynumber: 2.0 Consensus size: 122
1942 CGATCAATTC
* *
1952 AATGCCGCCTGCAAAGGTTACTCCTCTGCTGTCGTTCAACGCTGCTTCGCCTTTCGTCCTGGCGA
1 AATGCCGCCTGCAAAGGTTACTCCTCTGCTCTCGTTCAACGCTGCTTCGCCTTTCGTCCTAGCGA
2017 TTCTCAAGTGAGTTCTCAAAATTAGGGTTTTTCTGTACTTAAATTTAATCAAATGCT
66 TTCTCAAGTGAGTTCTCAAAATTAGGGTTTTTCTGTACTTAAATTTAATCAAATGCT
*
2074 AATGCCGCCTGCAAAGGTTACTCCTCTGCTCTCGTTCAACGCTGCTTCGCCTTTTGTCCTAGCGA
1 AATGCCGCCTGCAAAGGTTACTCCTCTGCTCTCGTTCAACGCTGCTTCGCCTTTCGTCCTAGCGA
* * *
2139 TTCTCAAGTGAGTTCTCAGAATTAGGGTTTTTCTTTACTTAAATTTAATCAGATGCT
66 TTCTCAAGTGAGTTCTCAAAATTAGGGTTTTTCTGTACTTAAATTTAATCAAATGCT
2196 GACATGCTGC
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
122 116 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (122 bp):
AATGCCGCCTGCAAAGGTTACTCCTCTGCTCTCGTTCAACGCTGCTTCGCCTTTCGTCCTAGCGA
TTCTCAAGTGAGTTCTCAAAATTAGGGTTTTTCTGTACTTAAATTTAATCAAATGCT
Found at i:5017 original size:23 final size:20
Alignment explanation
Indices: 4991--5034 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 20
4981 AAAAATGTAT
4991 ATATTTTAAAATTTAATATTATA
1 ATATTTT-AAATTT-AT-TTATA
5014 ATATTTTAAATTTATTTATA
1 ATATTTTAAATTTATTTATA
5034 A
1 A
5035 ATGAGATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 6 0.29
23 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTTTAAATTTATTTATA
Found at i:5751 original size:12 final size:12
Alignment explanation
Indices: 5736--5761 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5726 AGCAATAATA
5736 ATTATAATAAAC
1 ATTATAATAAAC
5748 ATTATAATAAAC
1 ATTATAATAAAC
5760 AT
1 AT
5762 AACCTTGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (12 bp):
ATTATAATAAAC
Found at i:7448 original size:21 final size:20
Alignment explanation
Indices: 7416--7455 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
7406 TAGTTCCTAT
7416 AATAAGAATAAATTAATAAA
1 AATAAGAATAAATTAATAAA
*
7436 AATAGAGATTAAATTAATAA
1 AATA-AGAATAAATTAATAA
7456 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (20 bp):
AATAAGAATAAATTAATAAA
Found at i:11341 original size:26 final size:26
Alignment explanation
Indices: 11291--11341 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
11281 AAAAATTACA
* *
11291 AAATAATATTATTAATTTATTATAAT
1 AAATAATATTATTAATATATAATAAT
* *
11317 AAATAATTTTATTACTATATAATAA
1 AAATAATATTATTAATATATAATAA
11342 ATTAATAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATAATATTATTAATATATAATAAT
Found at i:18492 original size:68 final size:68
Alignment explanation
Indices: 18370--18507 Score: 177
Period size: 68 Copynumber: 2.0 Consensus size: 68
18360 TTGCTGGGGG
*
18370 GGAGATTGTTGGCAAATTGGAGATTGGCCGTATCCATCAACTCTATGTACTCGAACACCAGTATT
1 GGAGATTGTTGGCAAATTGGAGATTGACCGTATCCATCAACTCTATGTACTCGAACACCAGTATT
18435 AAA
66 AAA
* * * * * * * * **
18438 GGAGATTGTTGGTAGATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATT
1 GGAGATTGTTGGCAAATTGGAGATTGACCGTATCCATCAACTCTATGTACTCGAACACCAGTATT
18503 AAA
66 AAA
18506 GG
1 GG
18508 TTTGACTTGA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (68 bp):
GGAGATTGTTGGCAAATTGGAGATTGACCGTATCCATCAACTCTATGTACTCGAACACCAGTATT
AAA
Found at i:18570 original size:42 final size:42
Alignment explanation
Indices: 18511--18593 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
18501 TTAAAGGTTT
*
18511 GACTTGAATGCTGCGAGTATATAATAATATGTAAAAATGGAC
1 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGAC
18553 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGA
1 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGA
18594 TTTGAGGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (42 bp):
GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGAC
Found at i:18704 original size:140 final size:140
Alignment explanation
Indices: 18452--18733 Score: 564
Period size: 140 Copynumber: 2.0 Consensus size: 140
18442 ATTGTTGGTA
18452 GATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATTAAAGGTTTGACTTG
1 GATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATTAAAGGTTTGACTTG
18517 AATGCTGCGAGTATATAATAATATGTAAAAATGGACGACTTGAATGCTGCGAGTATATAATAATA
66 AATGCTGCGAGTATATAATAATATGTAAAAATGGACGACTTGAATGCTGCGAGTATATAATAATA
18582 TGCAAAAATG
131 TGCAAAAATG
18592 GATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATTAAAGGTTTGACTTG
1 GATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATTAAAGGTTTGACTTG
18657 AATGCTGCGAGTATATAATAATATGTAAAAATGGACGACTTGAATGCTGCGAGTATATAATAATA
66 AATGCTGCGAGTATATAATAATATGTAAAAATGGACGACTTGAATGCTGCGAGTATATAATAATA
18722 TGCAAAAATG
131 TGCAAAAATG
18732 GA
1 GA
18734 ATACCTAAGT
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (140 bp):
GATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATTAAAGGTTTGACTTG
AATGCTGCGAGTATATAATAATATGTAAAAATGGACGACTTGAATGCTGCGAGTATATAATAATA
TGCAAAAATG
Found at i:18710 original size:42 final size:42
Alignment explanation
Indices: 18651--18733 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
18641 TTAAAGGTTT
*
18651 GACTTGAATGCTGCGAGTATATAATAATATGTAAAAATGGAC
1 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGAC
18693 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGA
1 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGA
18734 ATACCTAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (42 bp):
GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGAC
Found at i:18975 original size:19 final size:19
Alignment explanation
Indices: 18942--18988 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
18932 CACATGTGAG
*
18942 TAAAGAATC-TCACATCAT
1 TAAAAAATCTTCACATCAT
18960 TAAAAAATCTTCACATCAT
1 TAAAAAATCTTCACATCAT
18979 TAAAAAATCT
1 TAAAAAATCT
18989 AAATGAGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAAATCTTCACATCAT
Done.