Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168251.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_482, 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: 25344
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:3824 original size:27 final size:27
Alignment explanation
Indices: 3736--3824 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
3726 TCTTTTAAGG
3736 AAAATTGATACTTTCAACTTTTCCCTA
1 AAAATTGATACTTTCAACTTTTCCCTA
** * * * *
3763 AAAA-T-ATTTTTTGGAAATTTATTCTTAA
1 AAAATTGATACTTT-CAACTTT-TCCCT-A
3791 GGAAAATTGATACTTTCAACTTTTCCCTA
1 --AAAATTGATACTTTCAACTTTTCCCTA
3820 AAAAT
1 AAAAT
3825 ATTTTTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
25 5 0.12
26 6 0.14
27 12 0.28
28 1 0.02
29 1 0.02
30 7 0.16
31 6 0.14
32 5 0.12
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTCCCTA
Found at i:3881 original size:239 final size:238
Alignment explanation
Indices: 3433--3954 Score: 862
Period size: 239 Copynumber: 2.2 Consensus size: 238
3423 TTTTGTAGGG
*
3433 AAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTTGGAAATTTCGATTTTCAAGGAAA
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTC-ATTTTCAAGGAAA
*
3496 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTTTCAAGGAAAATTGA
65 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTTGATTTTCAAGGAAAATTGA
3561 TACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGAAATTTATTTCTGAGGAAAATTAATACTT
130 TACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGAAATTTATTTCTGAGGAAAATTAATACTT
3626 TCAACTCTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGA
195 TCAACTCTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGA
3670 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTT-ATTTTTCTTTTAA
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTTGGAAATTTCA-TTTTC----AA
*
3734 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAA-TTT-ATTCTT-AAGGAA
60 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTTGATT-TTCAAGGAA
*
3795 AATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTTGAAATTTATTTCTGAGGAAAATTG
124 AATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGAAATTTATTTCTGAGGAAAATTA
* *
3859 ATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
189 ATACTTTCAACTCTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGA
3909 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAA
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAA
3955 TTTTTTATTT
Statistics
Matches: 270, Mismatches: 6, Indels: 17
0.92 0.02 0.06
Matches are distributed among these distances:
237 32 0.12
238 14 0.05
239 118 0.44
240 55 0.20
241 5 0.02
242 10 0.04
243 36 0.13
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (238 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTCATTTTCAAGGAAAA
TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTTGATTTTCAAGGAAAATTGAT
ACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGAAATTTATTTCTGAGGAAAATTAATACTTT
CAACTCTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGA
Found at i:3949 original size:60 final size:59
Alignment explanation
Indices: 3431--3954 Score: 728
Period size: 57 Copynumber: 8.8 Consensus size: 59
3421 TTTTTTGTAG
*
3431 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTT--ATTTCT-AA
*
3491 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTT-GAAATTTTGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAA-TTT-ATTTCT-AA
* *
3551 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTGGAAATTTATTTCTAA
* * *
3611 GGAAAATTAATACTTTCAACTCTTCCCCAAAAATA--TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
*
3668 GAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTTATTTTTCTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTTTGGAAATTTA--TTTC---TA
3733 A
59 A
3734 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGGAAATTTA-TTCTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTC-TAA
* *
3791 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
*
3850 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
3907 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTGGAA
3955 TTTTTTATTT
Statistics
Matches: 426, Mismatches: 18, Indels: 40
0.88 0.04 0.08
Matches are distributed among these distances:
57 144 0.34
59 53 0.12
60 132 0.31
61 37 0.09
62 19 0.04
63 4 0.01
66 37 0.09
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
Found at i:4996 original size:3 final size:3
Alignment explanation
Indices: 4988--5013 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4978 TATATTACAA
4988 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5014 ATATATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5837 original size:2 final size:2
Alignment explanation
Indices: 5832--5910 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
5822 TATATATAAT
5832 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5874 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5911 ACAATCAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7257 original size:21 final size:20
Alignment explanation
Indices: 7228--7275 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
7218 TTTATATAGG
*
7228 TTTGATTTAATTTTATATTAAA
1 TTTG-TTTAATTATATATT-AA
*
7250 TTTGTTTACTTATATATTAA
1 TTTGTTTAATTATATATTAA
7270 TTTGTT
1 TTTGTT
7276 AGTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 12 0.50
22 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (20 bp):
TTTGTTTAATTATATATTAA
Found at i:15752 original size:31 final size:29
Alignment explanation
Indices: 15717--15776 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
15707 AGATATTTTA
15717 ATTTGTATTATTATATCATATAAAATATTAT
1 ATTTGTATTA-TATATCATATAAAA-ATTAT
* *
15748 ATTTGTATTATATTTTATATAAAAATTAT
1 ATTTGTATTATATATCATATAAAAATTAT
15777 GTATTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 5 0.19
30 12 0.44
31 10 0.37
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (29 bp):
ATTTGTATTATATATCATATAAAAATTAT
Found at i:15908 original size:13 final size:13
Alignment explanation
Indices: 15867--15908 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
15857 TTTTAAATTA
15867 TATTTTTTTATAT
1 TATTTTTTTATAT
* *
15880 CATTTATTTATAT
1 TATTTTTTTATAT
*
15893 TATTTTTTTATCT
1 TATTTTTTTATAT
15906 TAT
1 TAT
15909 CATTATATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTTTTTATAT
Found at i:15914 original size:24 final size:23
Alignment explanation
Indices: 15863--15924 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
15853 AAAATTTTAA
*
15863 ATTATATT-TTTTTATATCATTT
1 ATTATATTATTTTTTTATCATTT
15885 ATTTATATTATTTTTTTATC-TTAT
1 A-TTATATTATTTTTTTATCATT-T
*
15909 CATTATATTATATTTT
1 -ATTATATTATTTTTT
15925 AAATTATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 1 0.03
23 9 0.26
24 23 0.68
25 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (23 bp):
ATTATATTATTTTTTTATCATTT
Found at i:18060 original size:72 final size:72
Alignment explanation
Indices: 17919--18067 Score: 185
Period size: 72 Copynumber: 2.1 Consensus size: 72
17909 TGAATATAAA
* * * *
17919 ATTATAAGAAATTAGATATAAGATAATTCATTTTAACATATTTCATCATGTGTAGACAAAAATAA
1 ATTATAAGAAATTAGATATAAGATAAATCATTTTAACAGATCTCATCATATGTAGACAAAAATAA
17984 AAAAAAT
66 AAAAAAT
* * **
17991 ATTATAAGAAATTAGATATTAGATAACAT-ATTTTAATAGATCTCTATCATATGTAGATGAAAAT
1 ATTATAAGAAATTAGATATAAGATAA-ATCATTTTAACAGATCTC-ATCATATGTAGACAAAAAT
*
18055 GAAAAAAAT
64 AAAAAAAAT
18064 -TTAT
1 ATTAT
18068 TATGTGATAG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 41 0.62
73 25 0.38
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (72 bp):
ATTATAAGAAATTAGATATAAGATAAATCATTTTAACAGATCTCATCATATGTAGACAAAAATAA
AAAAAAT
Found at i:18203 original size:35 final size:34
Alignment explanation
Indices: 18125--18216 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 34
18115 TATTATGTTA
* *
18125 AAATATTTAATTTAAA-ATCAATTGATAATAAAT
1 AAATATTTAATTTAAATATAAATTGATAAAAAAT
18158 AAATAAATTTAATTTAAATATAAAATT-ATAAAAAACT
1 AAAT--ATTTAATTTAAATAT-AAATTGATAAAAAA-T
18195 AAATATTT-A-TTAAATATGAAAT
1 AAATATTTAATTTAAATAT-AAAT
18217 AATCTATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
33 16 0.31
34 1 0.02
35 16 0.31
36 9 0.18
37 9 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (34 bp):
AAATATTTAATTTAAATATAAATTGATAAAAAAT
Found at i:20038 original size:13 final size:13
Alignment explanation
Indices: 20002--20052 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
19992 AAATCTATTA
20002 AATATATTAAAAAT
1 AATATA-TAAAAAT
*
20016 --TATATTAAAAT
1 AATATATAAAAAT
20027 AATATATAAAAAT
1 AATATATAAAAAT
* *
20040 AAAATTTAAAAAT
1 AATATATAAAAAT
20053 TGATGAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 6 0.19
12 4 0.13
13 21 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATATATAAAAAT
Found at i:20048 original size:25 final size:25
Alignment explanation
Indices: 20002--20050 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
19992 AAATCTATTA
* *
20002 AATATATTAAAAATTATATTAAAAT
1 AATATATTAAAAATAAAATTAAAAT
20027 AATATA-TAAAAATAAAATTTAAAA
1 AATATATTAAAAATAAAA-TTAAAA
20051 ATTGATGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATATATTAAAAATAAAATTAAAAT
Found at i:21732 original size:20 final size:20
Alignment explanation
Indices: 21695--21732 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21685 ATCTTTAGTG
* *
21695 ATTTATATTTATCTTGCACT
1 ATTTATATTTACCATGCACT
21715 ATTTATATTTACCATGCA
1 ATTTATATTTACCATGCA
21733 TATAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTTATATTTACCATGCACT
Found at i:23384 original size:19 final size:19
Alignment explanation
Indices: 23360--23399 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
23350 CCACCTAAAC
23360 TTTTTTTTCTCC-TATCTT
1 TTTTTTTTCTCCTTATCTT
23378 TTTTTTTTCTCCTTATCTT
1 TTTTTTTTCTCCTTATCTT
23397 TTT
1 TTT
23400 CCTTGTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTTTTCTCCTTATCTT
Found at i:24537 original size:12 final size:13
Alignment explanation
Indices: 24523--24569 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 13
24513 ATCCACGTAA
24523 AATGAAAAATAA-
1 AATGAAAAATAAT
24535 AATGAAAGAATAAT
1 AATGAAA-AATAAT
*
24549 AAT-AATAATAAT
1 AATGAAAAATAAT
24561 AATGCAAAA
1 AATG-AAAA
24570 CAAGTTCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 16 0.55
13 7 0.24
14 6 0.21
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.21
Consensus pattern (13 bp):
AATGAAAAATAAT
Done.