Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168427.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_640, 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: 20929
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Found at i:1205 original size:24 final size:24
Alignment explanation
Indices: 1153--1197 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1143 AAGTTATTGA
* *
1153 AATATTAAATTAATATATATTTGT
1 AATATCAAAATAATATATATTTGT
1177 AATATCAAAATAATATA-ATTT
1 AATATCAAAATAATATATATTT
1198 TTATATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
AATATCAAAATAATATATATTTGT
Found at i:6403 original size:13 final size:13
Alignment explanation
Indices: 6387--6419 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
6377 AACAAACTTG
6387 TGGCACAAGAGGC
1 TGGCACAAGAGGC
6400 TGGCACAAGAGGC
1 TGGCACAAGAGGC
6413 TGGCACA
1 TGGCACA
6420 CATGAGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.24, G:0.36, T:0.09
Consensus pattern (13 bp):
TGGCACAAGAGGC
Found at i:9365 original size:11 final size:11
Alignment explanation
Indices: 9351--9375 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9341 AAAAGCTAAG
9351 AAAAAAAGAGA
1 AAAAAAAGAGA
9362 AAAAAAAGAGA
1 AAAAAAAGAGA
9373 AAA
1 AAA
9376 GATAGTTAGT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:10690 original size:11 final size:11
Alignment explanation
Indices: 10674--10704 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
10664 AATCTCATAA
10674 GAGATTTGTTT
1 GAGATTTGTTT
10685 GAGATTTGTTT
1 GAGATTTGTTT
*
10696 AAGATTTGT
1 GAGATTTGT
10705 CAATATTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:11764 original size:11 final size:11
Alignment explanation
Indices: 11748--11804 Score: 87
Period size: 11 Copynumber: 5.2 Consensus size: 11
11738 AATCTCATAA
11748 GAGATTTGTTT
1 GAGATTTGTTT
11759 GAGATTTGTTT
1 GAGATTTGTTT
*
11770 GAGATTTGTTA
1 GAGATTTGTTT
*
11781 GAGATTTATTT
1 GAGATTTGTTT
*
11792 GAGATTTATTT
1 GAGATTTGTTT
11803 GA
1 GA
11805 TATTGCTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:11911 original size:52 final size:52
Alignment explanation
Indices: 11839--11979 Score: 162
Period size: 52 Copynumber: 2.7 Consensus size: 52
11829 TGCAAAAAAA
** * *
11839 AATTCTAAGAGAA-AGTAGATTCTTAATAGGTAAATTTGACTTGCAAGG-GAAG
1 AATTCTAAGAGAAGAG-AGATTCTTAATAGACAAATTTAACTTAC-AGGAGAAG
* * *
11891 AATTCTAAAAGAAGAGAGATTTTTAATAGACAAGTTTAACTTACAGGAGAAG
1 AATTCTAAGAGAAGAGAGATTCTTAATAGACAAATTTAACTTACAGGAGAAG
*
11943 AATTCTAAGAGGAGAGAGATTCTTAAT-GAACAAATTT
1 AATTCTAAGAGAAGAGAGATTCTTAATAG-ACAAATTT
11980 GTATGGTTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
51 4 0.05
52 69 0.92
53 2 0.03
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (52 bp):
AATTCTAAGAGAAGAGAGATTCTTAATAGACAAATTTAACTTACAGGAGAAG
Found at i:14572 original size:44 final size:44
Alignment explanation
Indices: 14507--14594 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
14497 TTTCTATAAA
*
14507 AGAAGCTAATTTAACACGAACAAGGAAAATCAAACACTTACCTG
1 AGAAGCTAATTTAACAAGAACAAGGAAAATCAAACACTTACCTG
*
14551 AGAAGCTGATTTAACAAGAACAAGGAAAATCAAACACTTACCTG
1 AGAAGCTAATTTAACAAGAACAAGGAAAATCAAACACTTACCTG
14595 CTTCAGAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (44 bp):
AGAAGCTAATTTAACAAGAACAAGGAAAATCAAACACTTACCTG
Found at i:18587 original size:24 final size:26
Alignment explanation
Indices: 18551--18601 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
18541 ATGTGATACA
18551 TTAATAAACATG-T-AAAGATACTAT
1 TTAATAAACATGCTAAAAGATACTAT
18575 TTAAGTAAA-ATGTCTAAAAGATACTAT
1 TTAA-TAAACATG-CTAAAAGATACTAT
18602 CAAAAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 7 0.30
25 4 0.17
26 1 0.04
27 11 0.48
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (26 bp):
TTAATAAACATGCTAAAAGATACTAT
Found at i:19321 original size:9 final size:9
Alignment explanation
Indices: 19309--19350 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
19299 AACATTAATT
*
19309 TAATAAAAA
1 TAATAAATA
19318 TAATATAATA
1 TAATA-AATA
19328 TAA-ATAATA
1 TAATA-AATA
19337 TAATAAATA
1 TAATAAATA
19346 TAATA
1 TAATA
19351 TAAATGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAATAAATA
Found at i:19321 original size:14 final size:14
Alignment explanation
Indices: 19304--19353 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
19294 TTAAAAACAT
*
19304 TAATTTAATAAAAA
1 TAATATAATAAAAA
*
19318 TAATATAATATAAA
1 TAATATAATAAAAA
*
19332 TAATATAATAAATA
1 TAATATAATAAAAA
19346 TAATATAA
1 TAATATAA
19354 ATGATAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATATAATAAAAA
Found at i:19325 original size:5 final size:5
Alignment explanation
Indices: 19304--19353 Score: 61
Period size: 5 Copynumber: 10.6 Consensus size: 5
19294 TTAAAAACAT
* *
19304 TAATT TAATA -AAAA TAATA TAATA TAA-A TAATA TAATA -AATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
19351 TAA
1 TAA
19354 ATGATAACTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
4 11 0.28
5 28 0.72
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
TAATA
Found at i:19336 original size:23 final size:24
Alignment explanation
Indices: 19309--19360 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
19299 AACATTAATT
19309 TAATAAAAAT-AATATAATATAAA
1 TAATAAAAATAAATATAATATAAA
*
19332 TAAT-ATAATAAATATAATATAAA
1 TAATAAAAATAAATATAATATAAA
*
19355 TGATAA
1 TAATAA
19361 CTTATAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.16
23 20 0.80
24 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
TAATAAAAATAAATATAATATAAA
Done.