Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168394.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_610, 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: 21604
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Found at i:3600 original size:57 final size:57
Alignment explanation
Indices: 3536--3796 Score: 384
Period size: 57 Copynumber: 4.6 Consensus size: 57
3526 TTTTGTGCAG
3536 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAA
* * * *
3593 GAAAAATTGATACTTTCAAATTTTCCTCAAAAATC-GTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAA
** * *
3649 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTAGAAAGTTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAA
* *
3706 GAAAAATTGATACTTTCAACTTTTTCTCAAAAACTTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAC-CTTTTTTGAAAATTTATTTTTAA
3764 -AGAAAATTGATACTTTCAACTTTT-CTCCAAAAA
1 GA-AAAATTGATACTTTCAACTTTTCCT-CAAAAA
3797 TATTTTTTTT
Statistics
Matches: 185, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
56 52 0.28
57 85 0.46
58 48 0.26
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAA
Found at i:3672 original size:113 final size:114
Alignment explanation
Indices: 3536--3803 Score: 398
Period size: 113 Copynumber: 2.4 Consensus size: 114
3526 TTTTGTGCAG
* *
3536 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAAGAAAAATT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTAGAAAATTTATTTTTAAGAAAAATT
3601 GATACTTTCAAATTTTCCTCAAAAA-TCGTTTTAAAAATTTATTTTTAA
66 GATACTTTCAAATTTTCCTCAAAAACTCGTTTTAAAAATTTATTTTTAA
* *
3649 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTAGAAAGTTTATTTTTAAGAAAAATT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTAGAAAATTTATTTTTAAGAAAAATT
* * ** *
3714 GATACTTTCAACTTTTTCTCAAAAACTTTTTTTTGAAAATTTATTTTTAA
66 GATACTTTCAAATTTTCCTCAAAAAC-TCGTTTTAAAAATTTATTTTTAA
*
3764 -AGAAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTT
1 GA-AAAATTGATACTTTCAACTTTTCCT-CAAAAACATTTTT
3804 TTTGGATTTT
Statistics
Matches: 142, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
113 84 0.59
114 3 0.02
115 55 0.39
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (114 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTAGAAAATTTATTTTTAAGAAAAATT
GATACTTTCAAATTTTCCTCAAAAACTCGTTTTAAAAATTTATTTTTAA
Found at i:3868 original size:6 final size:6
Alignment explanation
Indices: 3822--3919 Score: 62
Period size: 6 Copynumber: 16.5 Consensus size: 6
3812 TTATTTAAAG
* *
3822 AAAAT- AAAATA ATAAA-A CAAAATA AAAGTGA AAATAAA AAAATA AAAA-A
1 AAAATA AAAATA A-AAATA -AAAATA AAAAT-A AAA-ATA AAAATA AAAATA
* * * * *
3871 TAAAGA AAAGT- AAAACA AAAATA AAAAT- AAAATA AAGATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
3917 AAA
1 AAA
3920 GAATATTAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
5 17 0.24
6 41 0.58
7 13 0.18
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:3901 original size:17 final size:16
Alignment explanation
Indices: 3822--3919 Score: 74
Period size: 17 Copynumber: 5.9 Consensus size: 16
3812 TTATTTAAAG
*
3822 AAAATAAAATAATAAAAC
1 AAAAT-AAA-AATAAAAA
* *
3840 AAAATAAAAGT-GAAA
1 AAAATAAAAATAAAAA
*
3855 ATAA-AAAAATAAAAA
1 AAAATAAAAATAAAAA
* *
3870 ATAAAGAAAAGTAAAACA
1 A-AAATAAAAATAAAA-A
3888 AAAATAAAAATAAAATA
1 AAAATAAAAATAAAA-A
*
3905 AAGATAAAAATAAAA
1 AAAATAAAAATAAAA
3920 GAATATTAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
14 5 0.08
15 9 0.14
16 4 0.06
17 39 0.61
18 7 0.11
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (16 bp):
AAAATAAAAATAAAAA
Found at i:3952 original size:5 final size:5
Alignment explanation
Indices: 3822--3933 Score: 61
Period size: 5 Copynumber: 21.6 Consensus size: 5
3812 TTATTTAAAG
* *
3822 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAA- AAATAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAA-AT
* *
3867 AAAAT AAAGA- AAAGT AAAACA AAAAT AAAAAT AAAAT AAAGAT AAAAAT
1 AAAAT AAA-AT AAAAT AAAA-T AAAAT -AAAAT AAAAT AAA-AT -AAAAT
* * *
3916 AAAAG AATAT TAAAT AAA
1 AAAAT AAAAT AAAAT AAA
3934 CTTAATCTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
3 3 0.04
4 3 0.04
5 50 0.61
6 19 0.23
7 7 0.09
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:4811 original size:13 final size:14
Alignment explanation
Indices: 4793--4860 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 14
4783 TTTTCAGTCG
*
4793 AATAAATAAAA-AA
1 AATAAAAAAAATAA
*
4806 AATAAAAAAAATCA
1 AATAAAAAAAATAA
4820 AATAAAAATATTAATGAA
1 AATAAAAA-A--AAT-AA
* *
4838 AATAAATAAGAT-A
1 AATAAAAAAAATAA
4851 AATAAAAAAA
1 AATAAAAAAA
4861 TTAACAGATA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
13 19 0.44
14 9 0.21
15 3 0.07
17 4 0.09
18 8 0.19
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (14 bp):
AATAAAAAAAATAA
Found at i:4814 original size:8 final size:9
Alignment explanation
Indices: 4796--4829 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
4786 TCAGTCGAAT
4796 AAATAAAAA
1 AAATAAAAA
4805 AAATAAAAA
1 AAATAAAAA
4814 AAATCAAATAA
1 AAAT-AAA-AA
4825 AAATA
1 AAATA
4830 TTAATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.57
10 4 0.17
11 6 0.26
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (9 bp):
AAATAAAAA
Found at i:4857 original size:31 final size:32
Alignment explanation
Indices: 4804--4864 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
4794 ATAAATAAAA
*
4804 AAAATAAAAAAAATCAAATAAAAATATTAATG
1 AAAATAAAAAAAATCAAATAAAAAAATTAATG
* *
4836 AAAATAAATAAGAT-AAATAAAAAAATTAA
1 AAAATAAAAAAAATCAAATAAAAAAATTAA
4865 CAGATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (32 bp):
AAAATAAAAAAAATCAAATAAAAAAATTAATG
Found at i:4923 original size:3 final size:3
Alignment explanation
Indices: 4915--5047 Score: 51
Period size: 3 Copynumber: 43.7 Consensus size: 3
4905 AATATTAACA
* * * * *
4915 AAT AAT AAT AAT AAT AAT AAG GAT -AT ATAT ATT AAT AAAT AGT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AAT AAT
* * * *
4961 AAT AAAT AAAT AAAT AAT AAAT ACAT AA- GAT AAA AAT AA- AAG AAA
1 AAT -AAT -AAT -AAT AAT -AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * * *
5006 AAT -AT AAA AAC AAT AAT AAT AAT AAA AAT AAA AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5048 AAATGTAAAA
Statistics
Matches: 100, Mismatches: 20, Indels: 20
0.71 0.14 0.14
Matches are distributed among these distances:
2 9 0.09
3 68 0.68
4 23 0.23
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:4980 original size:15 final size:15
Alignment explanation
Indices: 4960--5048 Score: 58
Period size: 15 Copynumber: 5.7 Consensus size: 15
4950 TAAATAGTAG
4960 TAATAAATAAATAAA
1 TAATAAATAAATAAA
*
4975 TAATAAATACATAAGA
1 TAATAAATAAATAA-A
*
4991 TAA-AAATAAAAGAAA
1 TAATAAAT-AAATAAA
* *
5006 AATATAAAAACAAT-AA
1 TA-ATAAATA-AATAAA
*
5022 TAATAATAAAAATAAA
1 TAATAA-ATAAATAAA
5038 -AATAAAATAAA
1 TAAT-AAATAAA
5049 AATGTAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
15 33 0.57
16 20 0.34
17 5 0.09
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (15 bp):
TAATAAATAAATAAA
Found at i:5013 original size:43 final size:43
Alignment explanation
Indices: 4973--5077 Score: 126
Period size: 43 Copynumber: 2.4 Consensus size: 43
4963 TAAATAAATA
*
4973 AATAATAAATACAT-AAGATAAAAATAAAAGAAAAATATAAAAAC
1 AATAAT-AATA-ATAAAAATAAAAATAAAAGAAAAATATAAAAAC
* *
5017 AATAATAATAATAAAAATAAAAATAAAATAAAAATGTAAAATAC
1 AATAATAATAATAAAAATAAAAATAAAAGAAAAATATAAAA-AC
*
5061 AAAAATAA-AA-AAAAATA
1 AATAATAATAATAAAAATA
5078 GACTTACCTA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
42 9 0.16
43 31 0.56
44 15 0.27
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (43 bp):
AATAATAATAATAAAAATAAAAATAAAAGAAAAATATAAAAAC
Found at i:5046 original size:26 final size:25
Alignment explanation
Indices: 4993--5077 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 25
4983 ACATAAGATA
* *
4993 AAAAT-AAAAGAAAAATATAAAAAC
1 AAAATAAAAATAAAAATATAAAAAT
*
5017 AATAATAATAAT-AAAA-ATAAAAAT
1 AA-AATAAAAATAAAAATATAAAAAT
* *
5041 AAAATAAAAATGTAAAATACAAAAAT
1 AAAATAAAAAT-AAAAATATAAAAAT
5067 AAAA-AAAAATA
1 AAAATAAAAATA
5078 GACTTACCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
23 8 0.16
24 11 0.22
25 17 0.34
26 14 0.28
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAATAAAAATAAAAATATAAAAAT
Found at i:5050 original size:6 final size:6
Alignment explanation
Indices: 4968--5075 Score: 71
Period size: 6 Copynumber: 17.3 Consensus size: 6
4958 AGTAATAAAT
* *
4968 AAATAA ATAATAA ATACAT-A AGATAA AAATAA AAGA-AA AATATAA AAACAA
1 AAATAA A-AATAA A-A-ATAA AAATAA AAATAA AA-ATAA AA-ATAA AAATAA
* * *
5019 TAATAA TAATAA AAATAA AAAT-A AAATAA AAATGTAA AATACAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA--TAA AA-ATAA AAATAA
5069 AAA-AA AA
1 AAATAA AA
5076 TAGACTTACC
Statistics
Matches: 84, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
5 11 0.13
6 46 0.55
7 19 0.23
8 7 0.08
9 1 0.01
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:5370 original size:41 final size:41
Alignment explanation
Indices: 5242--5410 Score: 232
Period size: 42 Copynumber: 4.1 Consensus size: 41
5232 TTGATCAAAA
5242 CTCCTCTAAAT-AGAGGCTCAACGACTTTGAAAAAATAAATGG
1 CTCCTCT-AATCAGAGGCTCAACGACTTTG-AAAAATAAATGG
*
5284 CTCCTCTAATCAGAGGCTCAATGACTTTAGAAAAATAAATGG
1 CTCCTCTAATCAGAGGCTCAACGACTTT-GAAAAATAAATGG
* *
5326 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAATTG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATGG
* * * * *
5367 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATGG
5408 CTC
1 CTC
5411 ATTAACAATC
Statistics
Matches: 118, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
41 55 0.47
42 62 0.53
43 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (41 bp):
CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATGG
Found at i:6454 original size:17 final size:17
Alignment explanation
Indices: 6420--6455 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6410 TCCCTTTTCA
**
6420 TTCACTTTTTTTTTTTT
1 TTCACTTTTTTTCCTTT
6437 TTCACTTTTTTTCCTTT
1 TTCACTTTTTTTCCTTT
6454 TT
1 TT
6456 TTTAAGCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (17 bp):
TTCACTTTTTTTCCTTT
Found at i:16271 original size:21 final size:22
Alignment explanation
Indices: 16230--16272 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16220 TCAACAAAAC
* *
16230 AAAATAAATAAAAACATAATTT
1 AAAAAAAATAAAAACACAATTT
16252 AAAAAAAATAAAAA-ACAATTT
1 AAAAAAAATAAAAACACAATTT
16273 TAAACAGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAAAATAAAAACACAATTT
Found at i:16893 original size:32 final size:33
Alignment explanation
Indices: 16849--16933 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 33
16839 AAATTGAGTT
**
16849 TTATCCTATTATAAGTAATAAAGCAAATGGGCC
1 TTATCCTATTATAAAAAATAAAGCAAATGGGCC
* **
16882 TTATCC-ATTATAAAAAATAAAGCAGATGGATC
1 TTATCCTATTATAAAAAATAAAGCAAATGGGCC
* *
16914 TTATCTTATTATAATAAATA
1 TTATCCTATTATAAAAAATA
16934 TATATATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.34
Consensus pattern (33 bp):
TTATCCTATTATAAAAAATAAAGCAAATGGGCC
Found at i:21567 original size:18 final size:19
Alignment explanation
Indices: 21527--21573 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
21517 TTAATATATC
*
21527 TTATTTATAATTTTTTCATT
1 TTATTT-TAATTTTTTCAAT
*
21547 TTATTTTAGTTTTTT-AAT
1 TTATTTTAATTTTTTCAAT
21565 TTATTTTAA
1 TTATTTTAA
21574 AGTAATTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.42
19 8 0.33
20 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
TTATTTTAATTTTTTCAAT
Done.