Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168311.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_536, 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: 23692
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:632 original size:12 final size:12
Alignment explanation
Indices: 615--655 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
605 ATGGACAGGA
*
615 ATATATATATAT
1 ATATATATATTT
627 ATATATATATTT
1 ATATATATATTT
* *
639 ATTTATTTATTT
1 ATATATATATTT
651 ATATA
1 ATATA
656 CAAGAGTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATATATATATTT
Found at i:4106 original size:2 final size:2
Alignment explanation
Indices: 4099--4146 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
4089 TAATAACAAA
* *
4099 AT AT AT AT AT AT AT AT AT CT AT AC 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 AT AT AT AT AT
*
4141 TT AT AT
1 AT AT AT
4147 TTCCAACAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8761 original size:45 final size:46
Alignment explanation
Indices: 8669--8796 Score: 204
Period size: 45 Copynumber: 2.8 Consensus size: 46
8659 AACAGATCGA
* * * *
8669 TCGGTTCCTTTGATTTTCCATTTCCCTCCTCGGAAGTGATAACTGG
1 TCGGTACCTTTGATTTTGCATATCCCTTCTCGGAAGTGATAACTGG
*
8715 TCGGTACCTTCGATTTTGCATATCCCTTCTC-GAAGTGATAACTGG
1 TCGGTACCTTTGATTTTGCATATCCCTTCTCGGAAGTGATAACTGG
8760 TCGGTACCTTTGATTTTGCATATCCCTTCTCGGAAGT
1 TCGGTACCTTTGATTTTGCATATCCCTTCTCGGAAGT
8797 AATGGTGAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
45 44 0.59
46 31 0.41
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (46 bp):
TCGGTACCTTTGATTTTGCATATCCCTTCTCGGAAGTGATAACTGG
Found at i:9414 original size:12 final size:12
Alignment explanation
Indices: 9369--9423 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
9359 CTGGCTCAGC
9369 GTTTGGGTTAAG
1 GTTTGGGTTAAG
* *
9381 GTTTTGGTTATG
1 GTTTGGGTTAAG
** *
9393 CATTGAGTTAAG
1 GTTTGGGTTAAG
*
9405 GTTTGGGTTAGG
1 GTTTGGGTTAAG
9417 GTTTGGG
1 GTTTGGG
9424 CTAGACATCC
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.15, C:0.02, G:0.40, T:0.44
Consensus pattern (12 bp):
GTTTGGGTTAAG
Found at i:10816 original size:411 final size:410
Alignment explanation
Indices: 10055--10878 Score: 1639
Period size: 411 Copynumber: 2.0 Consensus size: 410
10045 TAATCATGCA
10055 TTTGCCGAAAGGCATTAGATCCTTTTCTCACCCTTTTTTATAAGTATATATTCTTCCAGACGAGA
1 TTTGCCGAAAGGCATTAGATCCTTTTCTCACCCTTTTTTATAAGTATATATTCTTCCAGACGAGA
10120 CTTGGAAAGTTCACCTTAGGATGAGAATCTAATGCTTTCCAATCTCAATTTCAACAAGAATAAAA
66 CTTGGAAAGTTCACCTTAGGATGAGAATCTAATGCTTTCCAATCTCAATTTCAACAAGAATAAAA
10185 AGTTTCGTCCCTACTTTCGACCAGAGCCGCACATTAGAAAATTATAGAATTAATGTAATTTTGTA
131 AGTTTCGTCCCTACTTTCGACCAGAGCCGCACATTAGAAAATTATAGAATTAATGTAATTTTGTA
10250 CAATATCTTTATATTTTCATAGTAGAAGATGTTGTCTGCGCTAAACGACGGCTTTAGTAACAAAT
196 CAATATCTTTATATTTTCATAGTAGAAGATGTTGTCTGCGCTAAACGACGGCTTTAGTAACAAAT
10315 AGTAATTTTTTTAATTTAATTTTCAACAACAATGTTAAAAGGAAGTAGGGAGACTCGAATATGAT
261 AGTAATTTTTTTAATTTAATTTTCAACAACAATGTTAAAAGGAAGTAGGGAGACTCGAATATGAT
10380 TTTTTGAGTAAGGGTTTTTGCATAATTTTCGAAAAGCTATAGGATGGTATCGACATTTTTGCCCC
326 TTTTTGAGTAAGGGTTTTTGCATAATTTTCGAAAAGCTATAGGATGGTATCGACATTTTTGCCCC
10445 ATGTTTAGAAGGCAATATCT
391 ATGTTTAGAAGGCAATATCT
10465 TTTGCCGAAAGGCATTAGATCCTTTTCTCACCCTTTTTTATAAGTATATATTCTTCCAGACGAGA
1 TTTGCCGAAAGGCATTAGATCCTTTTCTCACCCTTTTTTATAAGTATATATTCTTCCAGACGAGA
10530 CTTGGAAAGTTCACCTTAGGATGAGAATCTAATGCTTTCCAATCTCAATTTCAACAAGAATAAAA
66 CTTGGAAAGTTCACCTTAGGATGAGAATCTAATGCTTTCCAATCTCAATTTCAACAAGAAT-AAA
10595 AAGTTTCGTCCCTACTTTCGACCAGAGCCGCACATTAGAAAATTATAGAATTAATGTAATTTTGT
130 AAGTTTCGTCCCTACTTTCGACCAGAGCCGCACATTAGAAAATTATAGAATTAATGTAATTTTGT
10660 ACAATATCTTTATATTTTCATAGTAGAAGATGTTGTCTGCGCTAAACGACGGCTTTAGTAACAAA
195 ACAATATCTTTATATTTTCATAGTAGAAGATGTTGTCTGCGCTAAACGACGGCTTTAGTAACAAA
10725 TAGTAATTTTTTTAATTTAATTTTCAACAACAATGTTAAAAGGAAGTAGGGAGACTCGAATATGA
260 TAGTAATTTTTTTAATTTAATTTTCAACAACAATGTTAAAAGGAAGTAGGGAGACTCGAATATGA
10790 TTTTTTGAGTAAGGGTTTTTGCATAATTTTCGAAAAGCTATAGGATGGTATCGACATTTTTGCCC
325 TTTTTTGAGTAAGGGTTTTTGCATAATTTTCGAAAAGCTATAGGATGGTATCGACATTTTTGCCC
10855 CATGTTTAGAAGGCAATATCT
390 CATGTTTAGAAGGCAATATCT
10876 TTT
1 TTT
10879 TGTTTCCATG
Statistics
Matches: 413, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
410 126 0.31
411 287 0.69
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (410 bp):
TTTGCCGAAAGGCATTAGATCCTTTTCTCACCCTTTTTTATAAGTATATATTCTTCCAGACGAGA
CTTGGAAAGTTCACCTTAGGATGAGAATCTAATGCTTTCCAATCTCAATTTCAACAAGAATAAAA
AGTTTCGTCCCTACTTTCGACCAGAGCCGCACATTAGAAAATTATAGAATTAATGTAATTTTGTA
CAATATCTTTATATTTTCATAGTAGAAGATGTTGTCTGCGCTAAACGACGGCTTTAGTAACAAAT
AGTAATTTTTTTAATTTAATTTTCAACAACAATGTTAAAAGGAAGTAGGGAGACTCGAATATGAT
TTTTTGAGTAAGGGTTTTTGCATAATTTTCGAAAAGCTATAGGATGGTATCGACATTTTTGCCCC
ATGTTTAGAAGGCAATATCT
Found at i:11370 original size:10 final size:10
Alignment explanation
Indices: 11336--11370 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
11326 TTTATCAATG
11336 ATATTTTAGTA
1 ATATTTTA-TA
11347 ATATTTTGATA
1 ATATTTT-ATA
11358 ATATTTTATA
1 ATATTTTATA
11368 ATA
1 ATA
11371 ATGATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.26
11 16 0.70
12 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (10 bp):
ATATTTTATA
Found at i:11453 original size:18 final size:17
Alignment explanation
Indices: 11430--11480 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
11420 GATTTAGAGA
11430 ATATTAGATATTGATTTG
1 ATATTA-ATATTGATTTG
11448 ATATTAAT-TTAGATATTG
1 ATATTAATATT-GAT-TTG
11466 AT-TTAAATATTGATT
1 ATATT-AATATTGATT
11481 ATGTGATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.07
17 8 0.28
18 17 0.59
19 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (17 bp):
ATATTAATATTGATTTG
Found at i:11464 original size:12 final size:12
Alignment explanation
Indices: 11406--11480 Score: 86
Period size: 12 Copynumber: 6.6 Consensus size: 12
11396 AATATTTTAA
11406 ATTGATTT-GAT
1 ATTGATTTAGAT
*
11417 ATTGATTTAGAG
1 ATTGATTTAGAT
*
11429 AAT-A-TTAGAT
1 ATTGATTTAGAT
11439 ATTGATTT-GAT
1 ATTGATTTAGAT
*
11450 ATTAATTTAGAT
1 ATTGATTTAGAT
*
11462 ATTGATTTAAAT
1 ATTGATTTAGAT
11474 ATTGATT
1 ATTGATT
11481 ATGTGATTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
10 7 0.13
11 20 0.38
12 26 0.49
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (12 bp):
ATTGATTTAGAT
Found at i:14315 original size:29 final size:30
Alignment explanation
Indices: 14272--14331 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 30
14262 TTTTTACTTG
14272 AACTACTGAAAATGGTACTATT-TATCTCTT
1 AACTACTGAAAATGGTACTATTCT-TCTCTT
14302 AACTACT-AAAATGGTACTATTCTTCTCTT
1 AACTACTGAAAATGGTACTATTCTTCTCTT
14331 A
1 A
14332 CTTTATGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (30 bp):
AACTACTGAAAATGGTACTATTCTTCTCTT
Done.