Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168176.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_414, 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: 27878
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Found at i:155 original size:34 final size:32
Alignment explanation
Indices: 107--239 Score: 154
Period size: 34 Copynumber: 4.2 Consensus size: 32
97 CCGATTTAGT
107 CAACACTGACAACTTCAAAACTATTAAGCGGTATA
1 CAAC-CTGACAACTTCAAAACTA-TAAG-GGTATA
142 CAACCTGACAACTTCAAAACTAT-A--G--T-
1 CAACCTGACAACTTCAAAACTATAAGGGTATA
168 CAACACTGACAACTTCAAAACTATTAAGCGGTATA
1 CAAC-CTGACAACTTCAAAACTA-TAAG-GGTATA
*
203 CAACCTGACAACTTCAAAACTA-CAGGGTATA
1 CAACCTGACAACTTCAAAACTATAAGGGTATA
234 CAACCT
1 CAACCT
240 AACTCCGATT
Statistics
Matches: 88, Mismatches: 1, Indels: 22
0.79 0.01 0.20
Matches are distributed among these distances:
26 4 0.05
27 19 0.22
28 1 0.01
29 2 0.02
31 12 0.14
32 4 0.05
33 1 0.01
34 37 0.42
35 8 0.09
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (32 bp):
CAACCTGACAACTTCAAAACTATAAGGGTATA
Found at i:198 original size:61 final size:61
Alignment explanation
Indices: 103--224 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
93 AACTCCGATT
103 TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTGACAACTTCAAAACTA
1 TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTGACAACTTCAAAACTA
164 TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTGACAACTTCAAAACTA
1 TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTGACAACTTCAAAACTA
225 CAGGGTATAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.43, C:0.25, G:0.10, T:0.23
Consensus pattern (61 bp):
TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTGACAACTTCAAAACTA
Found at i:264 original size:86 final size:88
Alignment explanation
Indices: 164--385 Score: 346
Period size: 86 Copynumber: 2.5 Consensus size: 88
154 TTCAAAACTA
164 TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTGACAACTTCAAAACTACAGG
1 TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTGACAACTTCAAAACTACAGG
*
229 GTATACAA-C-CTAACTCCGATT
66 GTATACAATCACAAACTCCGATT
250 TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTGACAACTTCAAAACTACAGG
1 TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTGACAACTTCAAAACTACAGG
315 GTATACAACTTCAAAACAAACTCCGATT
66 GTATACAA--TC---ACAAACTCCGATT
*
343 TAGTCAACACTGACAACTTCAAAACTA--CAG-GGTATACAACCTG
1 TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTG
386 GTATGCTAGA
Statistics
Matches: 127, Mismatches: 2, Indels: 10
0.91 0.01 0.07
Matches are distributed among these distances:
86 73 0.57
89 1 0.01
90 13 0.10
91 2 0.02
93 38 0.30
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.23
Consensus pattern (88 bp):
TAGTCAACACTGACAACTTCAAAACTATTAAGCGGTATACAACCTGACAACTTCAAAACTACAGG
GTATACAATCACAAACTCCGATT
Found at i:8943 original size:13 final size:12
Alignment explanation
Indices: 8921--8950 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
8911 AGTGTTTCTC
8921 TTTTTGTTTTAA
1 TTTTTGTTTTAA
8933 TTTTATGTTTTAA
1 TTTT-TGTTTTAA
8946 TTTTT
1 TTTTT
8951 ATCTTGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTGTTTTAA
Found at i:12264 original size:2 final size:2
Alignment explanation
Indices: 12257--12288 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12247 AGCCAGTTTC
12257 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12289 TAACACTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19965 original size:4 final size:4
Alignment explanation
Indices: 19956--20008 Score: 60
Period size: 4 Copynumber: 13.8 Consensus size: 4
19946 ATTAACTGAA
19956 TAAT TAAT T-AT TATAT TATAT T-A- TAAT T-AT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TA-AT TA-AT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
20002 TAAT TAA
1 TAAT TAA
20009 ACTATAACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 1 0.02
3 8 0.18
4 27 0.61
5 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TAAT
Found at i:19972 original size:38 final size:39
Alignment explanation
Indices: 19930--20027 Score: 103
Period size: 38 Copynumber: 2.5 Consensus size: 39
19920 TCATAATGAA
19930 ATATTATATCTATATAATTAACTGAA-TAATTAATT-ATT
1 ATATTATATCTATATAATTAA-TGAATTAATTAATTAATT
* *
19968 ATATTATAT-TATAATTATTAATTAATTAATTAATTAATT
1 ATATTATATCTAT-ATAATTAATGAATTAATTAATTAATT
* * * *
20007 AAACTATAACTAAATAATTAA
1 ATATTATATCTATATAATTAA
20028 ATTCAAGATT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
37 6 0.12
38 25 0.51
39 16 0.33
40 2 0.04
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (39 bp):
ATATTATATCTATATAATTAATGAATTAATTAATTAATT
Found at i:19982 original size:23 final size:20
Alignment explanation
Indices: 19955--20008 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
19945 AATTAACTGA
19955 ATAATTAATTATTATATT-AT
1 ATAATTAATTATTA-ATTAAT
*
19975 ATTA-TAATTATTAATTAAT
1 ATAATTAATTATTAATTAAT
19994 -TAATTAATTAATTAA
1 ATAATTAATT-ATTAA
20009 ACTATAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 5 0.17
19 16 0.55
20 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTAATTATTAATTAAT
Found at i:20744 original size:21 final size:21
Alignment explanation
Indices: 20719--20759 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20709 TGTTTTTACT
* *
20719 AATGTTAATTTATTTTAAATG
1 AATGTTAATTCATTTAAAATG
*
20740 AATGTTTATTCATTTAAAAT
1 AATGTTAATTCATTTAAAAT
20760 AAATTAACTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
AATGTTAATTCATTTAAAATG
Found at i:22523 original size:11 final size:11
Alignment explanation
Indices: 22507--22531 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22497 TTATTTGTCC
22507 TCTCACAATCG
1 TCTCACAATCG
22518 TCTCACAATCG
1 TCTCACAATCG
22529 TCT
1 TCT
22532 ACACCATGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.36, G:0.08, T:0.32
Consensus pattern (11 bp):
TCTCACAATCG
Found at i:23133 original size:1 final size:1
Alignment explanation
Indices: 23127--23151 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
23117 GGCAAATGCG
23127 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
23152 CTAAATTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:23742 original size:21 final size:21
Alignment explanation
Indices: 23698--23755 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
23688 GATATTTATG
* *
23698 AATAAAATT-ATTTTTATATA
1 AATATAATTAATTTTAATATA
23718 AATATAATTAATGTTTAATAT-
1 AATATAATTAAT-TTTAATATA
*
23739 AATATAATTTATTTTAA
1 AATATAATTAATTTTAA
23756 ACACATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 13 0.39
21 13 0.39
22 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AATATAATTAATTTTAATATA
Found at i:25547 original size:19 final size:19
Alignment explanation
Indices: 25523--25565 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
25513 CCAAATCAAA
*
25523 TTATATATTTTCTT-AGTTT
1 TTATATATTTT-TTAAATTT
25542 TTATATATTTTTTAAATTT
1 TTATATATTTTTTAAATTT
25561 TTATA
1 TTATA
25566 AATAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATATATTTTTTAAATTT
Done.