Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168388.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_605, 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: 21674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:4445 original size:21 final size:21
Alignment explanation
Indices: 4402--4445 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
4392 AAGAGAATAG
* *
4402 GAATGTGCCAAAATTGAGGAA
1 GAATGTGCCAAAATAGAGCAA
* *
4423 GAATGTGCTAGAATAGAGCAA
1 GAATGTGCCAAAATAGAGCAA
4444 GA
1 GA
4446 GCGTGCAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.18
Consensus pattern (21 bp):
GAATGTGCCAAAATAGAGCAA
Found at i:4917 original size:22 final size:21
Alignment explanation
Indices: 4880--4955 Score: 143
Period size: 21 Copynumber: 3.6 Consensus size: 21
4870 TATTAACATA
4880 AATTTTTTATTTAAAAAATAC
1 AATTTTTTATTTAAAAAATAC
4901 AATTTTTTATTTAAAAAATAC
1 AATTTTTTATTTAAAAAATAC
4922 AATTTTTTATTTAAAAAAATAC
1 AATTTTTTATTT-AAAAAATAC
4944 AATTTTTTATTT
1 AATTTTTTATTT
4956 TGTGATGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 33 0.61
22 21 0.39
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTTTTATTTAAAAAATAC
Found at i:5228 original size:34 final size:34
Alignment explanation
Indices: 5143--5229 Score: 102
Period size: 34 Copynumber: 2.6 Consensus size: 34
5133 GGCGTGTCAA
* *
5143 ATATACAAACGCCGCTAATATAGTGATATTTTTC
1 ATATACAAACGCCGTTAATATAGTGATATTTTCC
** * * *
5177 GGATACAAGCACCGTTAATATAGTGGTATTTTCC
1 ATATACAAACGCCGTTAATATAGTGATATTTTCC
*
5211 ATATACAAACGCTGTTAAT
1 ATATACAAACGCCGTTAAT
5230 GTAGCAGCGT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (34 bp):
ATATACAAACGCCGTTAATATAGTGATATTTTCC
Found at i:9746 original size:18 final size:17
Alignment explanation
Indices: 9718--9759 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
9708 CTAATCAATA
9718 TTCTCCTTTTTAT-TCTT
1 TTCTCCTTTTT-TCTCTT
9735 TTCTCTCTTTTTTCTCTT
1 TTCTC-CTTTTTTCTCTT
9753 TTCTCCT
1 TTCTCCT
9760 GCAAACACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTCCTTTTTTCTCTT
Found at i:17346 original size:33 final size:31
Alignment explanation
Indices: 17293--17398 Score: 90
Period size: 33 Copynumber: 3.3 Consensus size: 31
17283 GACATCTTAA
* *
17293 AAAAAAAAAAGTAATCAAATTATATCCAAACAAT
1 AAAAAATAAA-TAATAAAATTATAT-CAAA-AAT
* *
17327 AAAAAATAAATAATTAAATTATAT-TAAAAT
1 AAAAAATAAATAATAAAATTATATCAAAAAT
*
17357 AATAAATAAA-AATAAAATTATATTCAAATAAT
1 AAAAAATAAATAATAAAATTATA-TCAAA-AAT
*
17389 GAAACAATAA
1 -AAAAAATAA
17399 TAAAGTAGTG
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
29 11 0.18
30 13 0.22
31 4 0.07
32 3 0.05
33 20 0.33
34 9 0.15
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (31 bp):
AAAAAATAAATAATAAAATTATATCAAAAAT
Found at i:17363 original size:26 final size:27
Alignment explanation
Indices: 17326--17388 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
17316 ATCCAAACAA
*
17326 TAAAA-AATAAAT-AATTAAATTATAT
1 TAAAATAATAAATAAATAAAATTATAT
17351 TAAAATAATAAATAAAAATAAAATTATAT
1 TAAAATAATAAAT--AAATAAAATTATAT
*
17380 TCAAATAAT
1 TAAAATAAT
17389 GAAACAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 5 0.16
26 7 0.22
29 20 0.62
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
TAAAATAATAAATAAATAAAATTATAT
Found at i:17385 original size:29 final size:29
Alignment explanation
Indices: 17324--17402 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
17314 ATATCCAAAC
* *
17324 AATAAAAAATAAATAATTAAATTATATTAA
1 AATAATAAATAAA-AATAAAATTATATTAA
*
17354 AATAATAAATAAAAATAAAATTATATTCA
1 AATAATAAATAAAAATAAAATTATATTAA
* *
17383 AATAATGAAACAATAATAAA
1 AATAAT-AAATAAAAATAAA
17403 GTAGTGGTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 20 0.47
30 23 0.53
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (29 bp):
AATAATAAATAAAAATAAAATTATATTAA
Found at i:17899 original size:15 final size:15
Alignment explanation
Indices: 17871--17914 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
17861 AATGAAAGAT
*
17871 TATTAATTTTAATTA
1 TATTAATTTAAATTA
17886 T-TTAAATTTAAATTA
1 TATT-AATTTAAATTA
17901 TGATTAATTTAAAT
1 T-ATTAATTTAAAT
17915 ATAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.08
15 12 0.48
16 9 0.36
17 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TATTAATTTAAATTA
Found at i:18292 original size:160 final size:156
Alignment explanation
Indices: 17985--18389 Score: 526
Period size: 160 Copynumber: 2.6 Consensus size: 156
17975 AAATATATTT
* * * *
17985 TGGGGCTTTTATTTCATTCTGCCAAAGATATCGAAAAGCACCAGCAAAAAAATTTAGGG-TTCTA
1 TGGGGCTTCTATTTCATTATGCCAAAGGTAT-GAAAAGCACCAGCAAAAAAA-ATAGGGCTTCTA
* * * * * *
18049 TTTTATTACGGTGGGCACACCCTGGGGTTTGGGTTGGCACCCTTTATGCTTTAGCTTAGAATAGA
64 TTTCATTACCGTGGGCACACCCTGAGGTTTGGGTTAGCACCCTGTATGCTTTAGCTTAGAATAAA
* *
18114 TAGGAAGAGAAAAGCCCAAGAAACGAAAA
129 CAGGAAAAGAAAAGCCCAAGAAA-GAAAA
* * * *
18143 T-GGGCTTCTATTTCATTTTGCAAAAGGTACTGAAAAGCACTAGCAAAATAAAATGGGGCTTCTA
1 TGGGGCTTCTATTTCATTATGCCAAAGGTA-TGAAAAGCACCAGCAAAA-AAAATAGGGCTTCTA
* * * *
18207 TTTCATTACTGTGGGCATAGCTTGAGGTTTGGGTTAGCAACCTCTGTATGCTTTAGCTTAGAATA
64 TTTCATTACCGTGGGCACACCCTGAGGTTTGGGTTAGC-ACC-CTGTATGCTTTAGCTTAGAATA
18272 AACAGGAAAAGAAAAGCCCAAGAAAGAAAA
127 AACAGGAAAAGAAAAGCCCAAGAAAGAAAA
* *
18302 TGGGGATTCTATTTCATTATACCAAAGGTATTGAAAAGCACCAGCAAAAAAAATAGGGCTTCTAT
1 TGGGGCTTCTATTTCATTATGCCAAAGGTA-TGAAAAGCACCAGCAAAAAAAATAGGGCTTCTAT
18367 TTCATTACCGTGGGCACACCCTG
65 TTCATTACCGTGGGCACACCCTG
18390 GGGCTGGGGG
Statistics
Matches: 212, Mismatches: 29, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
157 44 0.21
158 41 0.19
159 43 0.20
160 84 0.40
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (156 bp):
TGGGGCTTCTATTTCATTATGCCAAAGGTATGAAAAGCACCAGCAAAAAAAATAGGGCTTCTATT
TCATTACCGTGGGCACACCCTGAGGTTTGGGTTAGCACCCTGTATGCTTTAGCTTAGAATAAACA
GGAAAAGAAAAGCCCAAGAAAGAAAA
Found at i:19500 original size:14 final size:14
Alignment explanation
Indices: 19481--19507 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19471 AGTAACAATA
19481 GAATAAAATAAATG
1 GAATAAAATAAATG
19495 GAATAAAATAAAT
1 GAATAAAATAAAT
19508 ATTAGGATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (14 bp):
GAATAAAATAAATG
Found at i:19796 original size:32 final size:32
Alignment explanation
Indices: 19758--19860 Score: 127
Period size: 32 Copynumber: 3.1 Consensus size: 32
19748 TTATTGTCAA
19758 TGATAATATTTTAGAATATTATTGATTTGATT
1 TGATAATATTTTAGAATATTATTGATTTGATT
*
19790 TGATAATATTTTAGAATATTATTAATTTGATT
1 TGATAATATTTTAGAATATTATTGATTTGATT
* * *
19822 TGAGGTTAAT-TTATAGAATATTGTTGATTTTATAT
1 TGA---TAATATTTTAGAATATTATTGATTTGAT-T
19857 TGAT
1 TGAT
19861 TTGGATGATG
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
32 35 0.56
34 19 0.31
35 8 0.13
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (32 bp):
TGATAATATTTTAGAATATTATTGATTTGATT
Done.