Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168118.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_362, 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: 31379
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:14710 original size:89 final size:87
Alignment explanation
Indices: 14561--14732 Score: 254
Period size: 89 Copynumber: 2.0 Consensus size: 87
14551 AAATTAAGTA
* *
14561 TTAAACTTCAAAGATTAATTATATTTGATACTTGAATTAGAGAAAAATTCTTTGAAACTTAAATT
1 TTAAACTTCAAAGATTAATTACATTTGATACATGAATTAGAGAAAAATTCTTTGAAACTTAAATT
14626 TGAAAACTTACAATCTTATGTG
66 TGAAAACTTACAATCTTATGTG
* * **
14648 TTAAACTTCAAAGATTAATTACACATTTGATACATGAATTAGAGCAAAATTTTTTGGTACTTAAA
1 TTAAACTTCAAAGATTAATT--ACATTTGATACATGAATTAGAGAAAAATTCTTTGAAACTTAAA
* *
14713 TTTGAAAAGTTGCAATCTTA
64 TTTGAAAACTTACAATCTTA
14733 ATACTACTTG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
87 20 0.27
89 55 0.73
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (87 bp):
TTAAACTTCAAAGATTAATTACATTTGATACATGAATTAGAGAAAAATTCTTTGAAACTTAAATT
TGAAAACTTACAATCTTATGTG
Found at i:16826 original size:144 final size:144
Alignment explanation
Indices: 16586--17127 Score: 982
Period size: 144 Copynumber: 3.8 Consensus size: 144
16576 TGTTCTCAAG
*
16586 TAAAACAAGTTCTGTAAGAGATACAAGCATCCCCATCTCTTGAGGTATTGACCCGGAAAGCTTAT
1 TAAAATAAGTTCTGTAAGAGATACAAGCATCCCCATCTCTTGAGGTATTGACCCGGAAAGCTTAT
16651 TTTCAGGAAGGTAAAGACTAGACAATTTGGTTAAGTTTCCTATGGGAGCGGGGATTGAACCAGAG
66 TTTCAGGAAGGTAAAGACTAGACAATTTGGTTAAGTTTCCTATGGGAGCGGGGATTGAACCAGAG
16716 AAATTGTTATCCGA
131 AAATTGTTATCCGA
*
16730 TAAAATAAGTTCTGTAAGAGATACAAGCATCCCTATCTCTTGAGGTATTGACCCGGAAAGCTTAT
1 TAAAATAAGTTCTGTAAGAGATACAAGCATCCCCATCTCTTGAGGTATTGACCCGGAAAGCTTAT
16795 TTTCAGGAAGGTAAAGACTAGACAATTTGGTTAAGTTTCCTATGGGAGCGGGGATTGAACCAGAG
66 TTTCAGGAAGGTAAAGACTAGACAATTTGGTTAAGTTTCCTATGGGAGCGGGGATTGAACCAGAG
16860 AAATTGTTATCCGA
131 AAATTGTTATCCGA
16874 TAAAATAAGTTCTGTAAGAGATACAAGCATCCCCATCTCTTGAGGTATTGACCCGGAAAGCTTAT
1 TAAAATAAGTTCTGTAAGAGATACAAGCATCCCCATCTCTTGAGGTATTGACCCGGAAAGCTTAT
16939 TTTCAGGAAGGTAAAGACTAGACAATTTGGTTAAGTTTCCTATGGGAGCGGGGATTGAACCAGAG
66 TTTCAGGAAGGTAAAGACTAGACAATTTGGTTAAGTTTCCTATGGGAGCGGGGATTGAACCAGAG
17004 AAATTGTTATCCGA
131 AAATTGTTATCCGA
* *
17018 TAAAATAAGTTCTGTAAGAGATACAAGCATCCCTATCTCTTGAGGTATTGACCCGCAAAGCTTAT
1 TAAAATAAGTTCTGTAAGAGATACAAGCATCCCCATCTCTTGAGGTATTGACCCGGAAAGCTTAT
* *
17083 TTTCA--AAGAGTTTAAGACTTA-ACAAATTGGTTAAGTTTCCTATGG
66 TTTCAGGAAG-G-TAAAGAC-TAGACAATTTGGTTAAGTTTCCTATGG
17128 AATTAGGGAT
Statistics
Matches: 388, Mismatches: 7, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
142 3 0.01
143 1 0.00
144 382 0.98
145 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (144 bp):
TAAAATAAGTTCTGTAAGAGATACAAGCATCCCCATCTCTTGAGGTATTGACCCGGAAAGCTTAT
TTTCAGGAAGGTAAAGACTAGACAATTTGGTTAAGTTTCCTATGGGAGCGGGGATTGAACCAGAG
AAATTGTTATCCGA
Found at i:19656 original size:19 final size:19
Alignment explanation
Indices: 19632--19678 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
19622 TAAAAAATTT
19632 AAATTATTTAA-TATTTATA
1 AAATTATTTAATTA-TTATA
* *
19651 AAATTATTAAATTATTATT
1 AAATTATTTAATTATTATA
19670 AAATTATTT
1 AAATTATTT
19679 TATGTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTATTTAATTATTATA
Found at i:19667 original size:11 final size:11
Alignment explanation
Indices: 19653--19677 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19643 TATTTATAAA
19653 ATTATTAAATT
1 ATTATTAAATT
19664 ATTATTAAATT
1 ATTATTAAATT
19675 ATT
1 ATT
19678 TTATGTCAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:20884 original size:17 final size:17
Alignment explanation
Indices: 20866--20898 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20856 AAAATATTAT
*
20866 TTTTA-ATTAAACCTTA
1 TTTTACATTAAAACTTA
20882 TTTTACATTAAAACTTA
1 TTTTACATTAAAACTTA
20899 ATAAAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTACATTAAAACTTA
Found at i:21016 original size:19 final size:19
Alignment explanation
Indices: 20994--21032 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
20984 TTTTAATTAG
20994 ATATAATTGATTAATTAAA
1 ATATAATTGATTAATTAAA
* **
21013 ATATTATTTTTTAATTAAA
1 ATATAATTGATTAATTAAA
21032 A
1 A
21033 AATCTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
ATATAATTGATTAATTAAA
Found at i:21595 original size:17 final size:17
Alignment explanation
Indices: 21575--21614 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
21565 TTGTTTTTTT
21575 TTATTTCTATTTTATCA
1 TTATTTCTATTTTATCA
* * *
21592 TTATTTTTATTTTTTTA
1 TTATTTCTATTTTATCA
21609 TTATTT
1 TTATTT
21615 AAATTAACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (17 bp):
TTATTTCTATTTTATCA
Found at i:24759 original size:13 final size:15
Alignment explanation
Indices: 24741--24798 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 15
24731 ATTCATCTCT
24741 TTTTATTT-AT-TTA
1 TTTTATTTAATATTA
24754 TTTTATTTAATATTA
1 TTTTATTTAATATTA
*
24769 TTTTAAATTTAATAAATA
1 TTTT--ATTTAAT-ATTA
24787 TTTTTATTTAAT
1 -TTTTATTTAAT
24799 TATTTTGTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 8 0.21
14 2 0.05
15 7 0.18
17 14 0.37
18 3 0.08
19 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTATTTAATATTA
Found at i:25447 original size:21 final size:19
Alignment explanation
Indices: 25421--25459 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
25411 ATGTATTTTA
25421 TAATAATATATTTACAAAAAT
1 TAATAA-ATATTTA-AAAAAT
*
25442 TAATAAATTTTTAAAAAA
1 TAATAAATATTTAAAAAA
25460 CTTTATCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATAAATATTTAAAAAAT
Done.