Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168414.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_629, 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: 21163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:4408 original size:13 final size:13
Alignment explanation
Indices: 4387--4438 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
4377 GTTTTGAGGG
* *
4387 TTTAAGGTTTTGT
1 TTTAGGGTTTAGT
*
4400 TTTAGGGTTTGGAGGG
1 TTTAGGGTTT--A-GT
4416 TTTAGGGTTTAGT
1 TTTAGGGTTTAGT
4429 TTTAGGGTTT
1 TTTAGGGTTT
4439 GGAGGGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 20 0.62
14 1 0.03
16 11 0.34
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (13 bp):
TTTAGGGTTTAGT
Found at i:4432 original size:58 final size:58
Alignment explanation
Indices: 4257--4496 Score: 258
Period size: 58 Copynumber: 4.2 Consensus size: 58
4247 AGGCTTCAAA
** * * * *
4257 TTTAGGGTTTGGAAAGTTTAGGGTTTTGATTTTAGGGTTTG-GGGATTAGGATTTAAT
1 TTTAGGGTTTGGAGGGTTTAAGGTTTTGATTTTAAGGTTTGAGGGTTTAGGGTTTAAT
* ** * * *
4314 TTTAGGGTTTGGA-GGTTTAAGGTTTTGATTTCAAGAATT-ACGGTTTGGGGTTTCGAT
1 TTTAGGGTTTGGAGGGTTTAAGGTTTTGATTTTAAGGTTTGAGGGTTTAGGGTTT-AAT
* * *
4371 TTTAGGGTTTTGAGGGTTTAAGGTTTTG-TTTTAGGGTTTGGAGGGTTTAGGGTTTAGT
1 TTTAGGGTTTGGAGGGTTTAAGGTTTTGATTTTAAGGTTT-GAGGGTTTAGGGTTTAAT
4429 TTTAGGGTTTGGAGGGTTT-AGGATTTT-ATTTTAAGGTTTGGAGGGTTTAGGGTTTAAT
1 TTTAGGGTTTGGAGGGTTTAAGG-TTTTGATTTTAAGGTTT-GAGGGTTTAGGGTTTAAT
*
4487 TTTGGGGTTT
1 TTTAGGGTTT
4497 TGATTTTAAG
Statistics
Matches: 152, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
56 29 0.19
57 37 0.24
58 74 0.49
59 12 0.08
ACGTcount: A:0.17, C:0.01, G:0.35, T:0.47
Consensus pattern (58 bp):
TTTAGGGTTTGGAGGGTTTAAGGTTTTGATTTTAAGGTTTGAGGGTTTAGGGTTTAAT
Found at i:4488 original size:29 final size:29
Alignment explanation
Indices: 4257--4496 Score: 211
Period size: 29 Copynumber: 8.3 Consensus size: 29
4247 AGGCTTCAAA
** *
4257 TTTAGGGTTTGGAAAGTTTAGGGTTTTGAT
1 TTTAGGGTTTGGAGGGTTTAGGG-TTTAAT
* *
4287 TTTAGGGTTT-G-GGGATTAGGATTTAAT
1 TTTAGGGTTTGGAGGGTTTAGGGTTTAAT
* *
4314 TTTAGGGTTTGGA-GGTTTAAGGTTTTGAT
1 TTTAGGGTTTGGAGGGTTT-AGGGTTTAAT
* * ** * * *
4343 TTCAAGAATT--ACGGTTTGGGGTTTCGAT
1 TTTAGGGTTTGGAGGGTTTAGGGTTT-AAT
* * **
4371 TTTAGGGTTTTGAGGGTTTAAGGTTTTGT
1 TTTAGGGTTTGGAGGGTTTAGGGTTTAAT
*
4400 TTTAGGGTTTGGAGGGTTTAGGGTTTAGT
1 TTTAGGGTTTGGAGGGTTTAGGGTTTAAT
* *
4429 TTTAGGGTTTGGAGGGTTTAGGATTTTAT
1 TTTAGGGTTTGGAGGGTTTAGGGTTTAAT
*
4458 TTTAAGGTTTGGAGGGTTTAGGGTTTAAT
1 TTTAGGGTTTGGAGGGTTTAGGGTTTAAT
*
4487 TTTGGGGTTT
1 TTTAGGGTTT
4497 TGATTTTAAG
Statistics
Matches: 169, Mismatches: 34, Indels: 15
0.78 0.16 0.07
Matches are distributed among these distances:
27 21 0.12
28 25 0.15
29 102 0.60
30 21 0.12
ACGTcount: A:0.17, C:0.01, G:0.35, T:0.47
Consensus pattern (29 bp):
TTTAGGGTTTGGAGGGTTTAGGGTTTAAT
Found at i:4541 original size:20 final size:21
Alignment explanation
Indices: 4516--4590 Score: 67
Period size: 20 Copynumber: 3.9 Consensus size: 21
4506 GTTTTTGAAA
*
4516 TTTTGGGTTTTGG-TTTTAAC
1 TTTTGGATTTTGGATTTTAAC
4536 TTTTGGATTTTGGATTTT-A-
1 TTTTGGATTTTGGATTTTAAC
*
4555 ----GGATTTATGG-TTTTAAT
1 TTTTGGATTT-TGGATTTTAAC
4572 TTTTGGATTTTGGATTTTA
1 TTTTGGATTTTGGATTTTA
4591 GGGTTTATGA
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
15 10 0.22
16 4 0.09
20 16 0.36
21 15 0.33
ACGTcount: A:0.16, C:0.01, G:0.23, T:0.60
Consensus pattern (21 bp):
TTTTGGATTTTGGATTTTAAC
Found at i:4546 original size:7 final size:7
Alignment explanation
Indices: 4515--4589 Score: 59
Period size: 7 Copynumber: 10.7 Consensus size: 7
4505 AGTTTTTGAA
4515 ATTTTGG
1 ATTTTGG
*
4522 GTTTTGG
1 ATTTTGG
*
4529 -TTTT-A
1 ATTTTGG
4534 ACTTTTGG
1 A-TTTTGG
4542 ATTTTGG
1 ATTTTGG
4549 ATTTTAGG
1 ATTTT-GG
4557 ATTTATGG
1 ATTT-TGG
*
4565 -TTTT-A
1 ATTTTGG
4570 ATTTTTGG
1 A-TTTTGG
4578 ATTTTGG
1 ATTTTGG
4585 ATTTT
1 ATTTT
4590 AGGGTTTATG
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
6 5 0.09
7 39 0.71
8 10 0.18
9 1 0.02
ACGTcount: A:0.16, C:0.01, G:0.23, T:0.60
Consensus pattern (7 bp):
ATTTTGG
Found at i:4567 original size:36 final size:36
Alignment explanation
Indices: 4526--4599 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
4516 TTTTGGGTTT
4526 TGGTTTTAACTTTTGGATTTTGGATTTTAGGATTTA
1 TGGTTTTAACTTTTGGATTTTGGATTTTAGGATTTA
* *
4562 TGGTTTTAATTTTTGGATTTTGGATTTTAGGGTTTA
1 TGGTTTTAACTTTTGGATTTTGGATTTTAGGATTTA
4598 TG
1 TG
4600 AAAAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.18, C:0.01, G:0.24, T:0.57
Consensus pattern (36 bp):
TGGTTTTAACTTTTGGATTTTGGATTTTAGGATTTA
Found at i:4573 original size:21 final size:21
Alignment explanation
Indices: 4536--4590 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
4526 TGGTTTTAAC
*
4536 TTTTGGATTTTGGATTTTAGGA
1 TTTTGGATTTT-AATTTTAGGA
*
4558 TTTATGG-TTTTAATTTTTGGA
1 TTT-TGGATTTTAATTTTAGGA
4579 TTTTGGATTTTA
1 TTTTGGATTTTA
4591 GGGTTTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 3 0.10
21 16 0.55
22 7 0.24
23 3 0.10
ACGTcount: A:0.18, C:0.00, G:0.22, T:0.60
Consensus pattern (21 bp):
TTTTGGATTTTAATTTTAGGA
Found at i:4731 original size:3 final size:3
Alignment explanation
Indices: 4723--4747 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4713 TTATGAAAAT
4723 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
4748 CCTTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5106 original size:11 final size:10
Alignment explanation
Indices: 5078--5104 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5068 AGAAAATTAG
5078 AAAAAAATGA
1 AAAAAAATGA
5088 AAAAAAATGA
1 AAAAAAATGA
5098 AAAAAAA
1 AAAAAAA
5105 ATACTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:5217 original size:12 final size:12
Alignment explanation
Indices: 5202--5240 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
5192 TTGATGATTT
5202 GATCAACGGTTC
1 GATCAACGGTTC
5214 GATCAACGGTTC
1 GATCAACGGTTC
*
5226 GATCAACAGTTC
1 GATCAACGGTTC
5238 GAT
1 GAT
5241 TGAACTGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (12 bp):
GATCAACGGTTC
Found at i:5782 original size:11 final size:11
Alignment explanation
Indices: 5768--5802 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5758 TTTATTTTTA
5768 TTTTTTTGGTT
1 TTTTTTTGGTT
5779 TTTTTTAT-GTT
1 TTTTTT-TGGTT
5790 TTTTTTTGGTT
1 TTTTTTTGGTT
5801 TT
1 TT
5803 CTGGTGGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.05
11 20 0.91
12 1 0.05
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (11 bp):
TTTTTTTGGTT
Found at i:6152 original size:23 final size:22
Alignment explanation
Indices: 6126--6188 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
6116 CTTCTGTTCT
*
6126 TTTTTGTTTCTATTTTTTGTTTG
1 TTTTTGTTTCTATTTATT-TTTG
*
6149 TTTTTGTTTTTATTTATTTTTG
1 TTTTTGTTTCTATTTATTTTTG
*
6171 TTTTTTTTTTCT-TTTATT
1 -TTTTTGTTTCTATTTATT
6189 AATTATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.29
23 25 0.71
ACGTcount: A:0.06, C:0.03, G:0.08, T:0.83
Consensus pattern (22 bp):
TTTTTGTTTCTATTTATTTTTG
Found at i:6158 original size:17 final size:17
Alignment explanation
Indices: 6128--6176 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
6118 TCTGTTCTTT
* * *
6128 TTTGTTTCTATTTTTTG
1 TTTGTTTTTGTTTTTTA
6145 TTTGTTTTTG-TTTTTA
1 TTTGTTTTTGTTTTTTA
*
6161 TTTATTTTTGTTTTTT
1 TTTGTTTTTGTTTTTT
6177 TTTTCTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.06, C:0.02, G:0.10, T:0.82
Consensus pattern (17 bp):
TTTGTTTTTGTTTTTTA
Found at i:6178 original size:26 final size:26
Alignment explanation
Indices: 6139--6202 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
6129 TTGTTTCTAT
* *
6139 TTTTTGTTTGTTTTTGT-TTTTATTTA
1 TTTTTGTTT-TTTTTTTCTTTTATTAA
6165 TTTTTGTTTTTTTTTTCTTTTATTAA
1 TTTTTGTTTTTTTTTTCTTTTATTAA
* *
6191 TTATTATTTTTT
1 TTTTTGTTTTTT
6203 ATAATAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 6 0.18
26 27 0.82
ACGTcount: A:0.11, C:0.02, G:0.06, T:0.81
Consensus pattern (26 bp):
TTTTTGTTTTTTTTTTCTTTTATTAA
Found at i:6185 original size:16 final size:16
Alignment explanation
Indices: 6139--6175 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6129 TTGTTTCTAT
* *
6139 TTTTTGTTTGTTTTTG
1 TTTTTATTTATTTTTG
6155 TTTTTATTTATTTTTG
1 TTTTTATTTATTTTTG
6171 TTTTT
1 TTTTT
6176 TTTTTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.05, C:0.00, G:0.11, T:0.84
Consensus pattern (16 bp):
TTTTTATTTATTTTTG
Found at i:6186 original size:22 final size:23
Alignment explanation
Indices: 6125--6188 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
6115 TCTTCTGTTC
* *
6125 TTTTTTGTTTCTATTTTTTGTTTG
1 TTTTTTTTTTCT-TTTATTGTTTG
*
6149 TTTTTGTTTTT-ATTTATT-TTTG
1 TTTTT-TTTTTCTTTTATTGTTTG
6171 TTTTTTTTTTCTTTTATT
1 TTTTTTTTTTCTTTTATT
6189 AATTATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 5 0.15
22 15 0.44
23 5 0.15
24 5 0.15
25 4 0.12
ACGTcount: A:0.06, C:0.03, G:0.08, T:0.83
Consensus pattern (23 bp):
TTTTTTTTTTCTTTTATTGTTTG
Found at i:10050 original size:39 final size:39
Alignment explanation
Indices: 9992--10066 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
9982 TACGCTAAAT
* *
9992 CAATATTGCCTTGAGCTTTCTAATTGGAGACTAGAGATA
1 CAATATTGCCTTGACCTTTCTAATGGGAGACTAGAGATA
*
10031 CAATATTGCCTTGACCTTTCTAATGGGATACTAGAG
1 CAATATTGCCTTGACCTTTCTAATGGGAGACTAGAG
10067 GGACAATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (39 bp):
CAATATTGCCTTGACCTTTCTAATGGGAGACTAGAGATA
Found at i:14059 original size:21 final size:21
Alignment explanation
Indices: 14033--14072 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
14023 ATTTTATATA
*
14033 TTATTATTAAATTAAATTATT
1 TTATTAATAAATTAAATTATT
14054 TTATTAATAAATTAAATTA
1 TTATTAATAAATTAAATTA
14073 AATGATATTA
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:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTAATAAATTAAATTATT
Found at i:14075 original size:31 final size:32
Alignment explanation
Indices: 14038--14098 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
14028 ATATATTATT
*
14038 ATTAAATTAAATTATTTTATTAAT-AAATTAA
1 ATTAAATGAAATTATTTTATTAATGAAATTAA
*
14069 ATTAAATGATATTATTTTATTAATGAAATT
1 ATTAAATGAAATTATTTTATTAATGAAATT
14099 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
ATTAAATGAAATTATTTTATTAATGAAATTAA
Found at i:14152 original size:27 final size:27
Alignment explanation
Indices: 14096--14152 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
14086 TATTAATGAA
* * *
14096 ATTTTTTTAAAATATTAATTTTTGTAT
1 ATTTTTTTAAAATATTAATATCTATAT
*
14123 ATTTATTTTAAAA-ATTAATATCTATTT
1 ATTT-TTTTAAAATATTAATATCTATAT
14150 ATT
1 ATT
14153 AATAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
ATTTTTTTAAAATATTAATATCTATAT
Done.