Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168227.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_460, 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: 26103
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Found at i:3628 original size:32 final size:32
Alignment explanation
Indices: 3560--3628 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
3550 AAGCCAATAT
* * * *
3560 TAGCTAGCACCAATGAAGTTGTAAGGTTAGTT
1 TAGCTAGCACCAATGAAATTGTAAGCTCAGTC
*
3592 TAGCTAGCATCAATCGAAATT-TAAGCTCAGTC
1 TAGCTAGCACCAAT-GAAATTGTAAGCTCAGTC
3624 TAGCT
1 TAGCT
3629 GACATATAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (32 bp):
TAGCTAGCACCAATGAAATTGTAAGCTCAGTC
Found at i:3687 original size:21 final size:21
Alignment explanation
Indices: 3661--3700 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3651 TGGCATTGAG
3661 AAATCATAAGCCCAAATTAGT
1 AAATCATAAGCCCAAATTAGT
*
3682 AAATCATCAGCCCAAATTA
1 AAATCATAAGCCCAAATTA
3701 CCTTAGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (21 bp):
AAATCATAAGCCCAAATTAGT
Found at i:4058 original size:15 final size:14
Alignment explanation
Indices: 4038--4083 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
4028 CGTTACATAT
4038 ATAAAAATAATAATA
1 ATAAAAATAA-AATA
4053 ATAAAAAGTAAAATA
1 ATAAAAA-TAAAATA
*
4068 TTAAAAATAAAA-A
1 ATAAAAATAAAATA
4081 ATA
1 ATA
4084 CGTATGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 5 0.18
15 17 0.61
16 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (14 bp):
ATAAAAATAAAATA
Found at i:4066 original size:21 final size:21
Alignment explanation
Indices: 4041--4080 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4031 TACATATATA
*
4041 AAAATAATAATAATAAAAAGT
1 AAAATAATAAAAATAAAAAGT
*
4062 AAAATATTAAAAATAAAAA
1 AAAATAATAAAAATAAAAA
4081 ATACGTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAATAATAAAAATAAAAAGT
Found at i:4136 original size:42 final size:42
Alignment explanation
Indices: 4032--4141 Score: 97
Period size: 42 Copynumber: 2.7 Consensus size: 42
4022 GTTGGCCGTT
4032 ACATATATAAAA-ATA-ATAATAATAAAAAGTAAAATATTAAA
1 ACATAT-TAAAACATATATAATAATAAAAAGTAAAATATTAAA
** * * *
4073 A-ATAAAAAATACGTATGTAATAGATATAAAG--AAATATTTAAA
1 ACATATTAAA-ACATATATAATA-ATAAAAAGTAAAATA-TTAAA
4115 ACATATTAAAACATATATAATAA-AAAA
1 ACATATTAAAACATATATAATAATAAAA
4142 TAATATAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
39 3 0.06
40 7 0.13
41 9 0.17
42 21 0.40
43 13 0.25
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.27
Consensus pattern (42 bp):
ACATATTAAAACATATATAATAATAAAAAGTAAAATATTAAA
Found at i:4152 original size:16 final size:18
Alignment explanation
Indices: 4122--4176 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
4112 AAAACATATT
*
4122 AAAACATATATAATAAAA
1 AAAATATATATAATAAAA
*
4140 AATA-ATATA-AATAAAA
1 AAAATATATATAATAAAA
4156 ATAAATATATATAATAAAA
1 A-AAATATATATAATAAAA
4175 AA
1 AA
4177 GTTTAACCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 8 0.25
17 7 0.22
18 9 0.28
19 8 0.25
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATATATATAATAAAA
Found at i:4161 original size:19 final size:19
Alignment explanation
Indices: 4127--4175 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 19
4117 ATATTAAAAC
*
4127 ATATATAATAAAAA-ATA-
1 ATATATAATAAAAATAAAT
4144 ATATA-AATAAAAATAAAT
1 ATATATAATAAAAATAAAT
4162 ATATATAATAAAAA
1 ATATATAATAAAAA
4176 AGTTTAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 5 0.18
19 8 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
ATATATAATAAAAATAAAT
Found at i:22929 original size:15 final size:14
Alignment explanation
Indices: 22904--22934 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
22894 AAAGAAACCT
22904 GAAAAAGAAAAAGA
1 GAAAAAGAAAAAGA
22918 GAAAATAGAAAAAGA
1 GAAAA-AGAAAAAGA
22933 GA
1 GA
22935 TGAGAAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (14 bp):
GAAAAAGAAAAAGA
Done.