Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168214.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_449, 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: 26528
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Found at i:360 original size:21 final size:21
Alignment explanation
Indices: 335--394 Score: 120
Period size: 21 Copynumber: 2.9 Consensus size: 21
325 TATTATTAAG
335 AAAATTATTTTTAATTATACA
1 AAAATTATTTTTAATTATACA
356 AAAATTATTTTTAATTATACA
1 AAAATTATTTTTAATTATACA
377 AAAATTATTTTTAATTAT
1 AAAATTATTTTTAATTAT
395 TTATTTATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAATTATTTTTAATTATACA
Found at i:402 original size:8 final size:8
Alignment explanation
Indices: 402--438 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
392 TATTTATTTA
402 TATATATT
1 TATATATT
*
410 TATATAAT
1 TATATATT
*
418 TATATGTT
1 TATATATT
426 TATATATT
1 TATATATT
434 TATAT
1 TATAT
439 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (8 bp):
TATATATT
Found at i:455 original size:18 final size:20
Alignment explanation
Indices: 427--477 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
417 TTATATGTTT
427 ATATATTTATA-TTTAAAAA
1 ATATATTTATATTTTAAAAA
446 ATAT-TTTATATTTTAAAAA
1 ATATATTTATATTTTAAAAA
465 ATAATATTT-TATT
1 AT-ATATTTATATT
478 AATTTCGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.21
19 14 0.48
20 6 0.21
21 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTTATATTTTAAAAA
Found at i:1114 original size:14 final size:15
Alignment explanation
Indices: 1083--1124 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
1073 TAAAAATTTA
1083 TATATATACTTATATAAT
1 TATATATA-TT-T-TAAT
1101 TATA-ATATTTTAAT
1 TATATATATTTTAAT
1115 TATATATATT
1 TATATATATT
1125 ATATTTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 2 0.09
17 3 0.13
18 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATATATTTTAAT
Found at i:3001 original size:2 final size:2
Alignment explanation
Indices: 2994--3019 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2984 ATAATTTTAA
2994 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
3020 CCCATGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10205 original size:142 final size:142
Alignment explanation
Indices: 9949--10231 Score: 566
Period size: 142 Copynumber: 2.0 Consensus size: 142
9939 AAATTTCAAT
9949 GCCATTCCTTGCAAACCTTCCAAATCTCAAATTTCTCTTGGGTGATGAAAACAAGATGGTAGTAG
1 GCCATTCCTTGCAAACCTTCCAAATCTCAAATTTCTCTTGGGTGATGAAAACAAGATGGTAGTAG
10014 AACCTGATTCCTTTCATACTTCAATTCCAAAGTTCCAACTAAATTTCATCAGTTTGTCAAAGTGC
66 AACCTGATTCCTTTCATACTTCAATTCCAAAGTTCCAACTAAATTTCATCAGTTTGTCAAAGTGC
10079 ACAACAGATAAG
131 ACAACAGATAAG
10091 GCCATTCCTTGCAAACCTTCCAAATCTCAAATTTCTCTTGGGTGATGAAAACAAGATGGTAGTAG
1 GCCATTCCTTGCAAACCTTCCAAATCTCAAATTTCTCTTGGGTGATGAAAACAAGATGGTAGTAG
10156 AACCTGATTCCTTTCATACTTCAATTCCAAAGTTCCAACTAAATTTCATCAGTTTGTCAAAGTGC
66 AACCTGATTCCTTTCATACTTCAATTCCAAAGTTCCAACTAAATTTCATCAGTTTGTCAAAGTGC
10221 ACAACAGATAA
131 ACAACAGATAA
10232 AGGACTTAGC
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (142 bp):
GCCATTCCTTGCAAACCTTCCAAATCTCAAATTTCTCTTGGGTGATGAAAACAAGATGGTAGTAG
AACCTGATTCCTTTCATACTTCAATTCCAAAGTTCCAACTAAATTTCATCAGTTTGTCAAAGTGC
ACAACAGATAAG
Found at i:14056 original size:75 final size:73
Alignment explanation
Indices: 13912--14059 Score: 226
Period size: 74 Copynumber: 2.0 Consensus size: 73
13902 ATATATATAT
** *
13912 CTATATATATATATTCATAGAATTTTTTGGTTTTTTTCTACATTGATCCAACTAAATTTAAATAA
1 CTATATATATATATTCATAGAAAATTTTGGTTTTTTTCTACATTGATCCAACGAAATTTAAATAA
13977 AATAAAAA
66 AATAAAAA
*
13985 CTATATATATATATTCATAGAAAATTTTGGTTTTTTTTCTGCATTGATTCC-ACGAAATTTAAAT
1 CTATATATATATATTCATAGAAAATTTTGG-TTTTTTTCTACATTGA-TCCAACGAAATTTAAAT
14049 AATAATAAAAA
64 AA-AATAAAAA
14060 TAATAAAATA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
73 28 0.41
74 29 0.43
75 11 0.16
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (73 bp):
CTATATATATATATTCATAGAAAATTTTGGTTTTTTTCTACATTGATCCAACGAAATTTAAATAA
AATAAAAA
Found at i:21695 original size:26 final size:26
Alignment explanation
Indices: 21645--21710 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
21635 TTAATATAAC
*
21645 TATTAAAATAT-TAAAAATTATTTAT
1 TATTAAAATATATTAAAATTATTTAT
*
21670 TATTAAAATATATTGAAATTATTTAT
1 TATTAAAATATATTAAAATTATTTAT
*
21696 TATAAAAAT-TATTAA
1 TATTAAAATATATTAA
21711 TATAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
25 16 0.44
26 20 0.56
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TATTAAAATATATTAAAATTATTTAT
Found at i:21716 original size:15 final size:16
Alignment explanation
Indices: 21685--21794 Score: 73
Period size: 18 Copynumber: 6.6 Consensus size: 16
21675 AAATATATTG
*
21685 AAATTATTTATTATAA
1 AAATTATTTAATATAA
21701 AAATTA-TTAATATAAA
1 AAATTATTTAATAT-AA
* * *
21717 AAATAATTATATTTTAA
1 AAATTATT-TAATATAA
*
21734 TAATAATATTTAATATTAA
1 -AA-ATTATTTAATA-TAA
21753 AATATTATGTTAATATAA
1 AA-ATTAT-TTAATATAA
* *
21771 AAA-TACTTAAAAT-A
1 AAATTATTTAATATAA
21785 AAATTATTTA
1 AAATTATTTA
21795 TTATTCTTTA
Statistics
Matches: 74, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
14 4 0.05
15 17 0.23
16 15 0.20
17 4 0.05
18 21 0.28
19 13 0.18
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (16 bp):
AAATTATTTAATATAA
Found at i:21765 original size:19 final size:18
Alignment explanation
Indices: 21707--21775 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 18
21697 ATAAAAATTA
*
21707 TTAATA-TAAAA-AATAA
1 TTAATATTAAAATAATAT
*
21723 TTATATTTTAATAATAATAT
1 TTA-ATATTAA-AATAATAT
*
21743 TTAATATTAAAATATTAT
1 TTAATATTAAAATAATAT
*
21761 GTTAATATAAAAATA
1 -TTAATATTAAAATA
21776 CTTAAAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
16 3 0.07
17 2 0.05
18 10 0.23
19 21 0.49
20 7 0.16
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (18 bp):
TTAATATTAAAATAATAT
Found at i:21833 original size:19 final size:19
Alignment explanation
Indices: 21811--21909 Score: 89
Period size: 19 Copynumber: 5.3 Consensus size: 19
21801 TTTATATTGT
21811 TTATTAATATATTATAATA
1 TTATTAATATATTATAATA
*
21830 TTATT--TAT-TTGTAATA
1 TTATTAATATATTATAATA
*
21846 TTATTAATATATTAGAATA
1 TTATTAATATATTATAATA
* *
21865 TTATTTATTAATATAATAATA
1 TTA-TTAAT-ATATTATAATA
* *
21886 TTTATTTAT-TAATATAATA
1 -TTATTAATATATTATAATA
21905 TTATT
1 TTATT
21910 TATAAGTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
16 12 0.19
17 3 0.05
18 8 0.12
19 22 0.34
20 4 0.06
21 12 0.19
22 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTAATATATTATAATA
Found at i:21833 original size:35 final size:34
Alignment explanation
Indices: 21793--21914 Score: 102
Period size: 35 Copynumber: 3.4 Consensus size: 34
21783 TAAAATTATT
* * * *
21793 TATTATTCTTTATATTGTTTATTAATATATTATAA
1 TATTATTATTTATAAT-ATTATTAATATATTAGAA
*
21828 TATTATTTATTTGTAATATTATTAATATATTAGAA
1 TATTA-TTATTTATAATATTATTAATATATTAGAA
* * *
21863 TATTATTTATTAATATAATAATATTTATTTATTA-ATA
1 TATTA-TTATT--TATAATATTATTAATATATTAGA-A
*
21900 TAATATTATTTATAA
1 TATTATTATTTATAA
21915 GTAAAATTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
34 5 0.07
35 32 0.44
36 14 0.19
37 22 0.30
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (34 bp):
TATTATTATTTATAATATTATTAATATATTAGAA
Found at i:21890 original size:22 final size:22
Alignment explanation
Indices: 21846--21912 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
21836 ATTTGTAATA
*
21846 TTATTAATATATTAGA-ATATTAT
1 TTATTAATATAATA-ATAT-TTAT
21869 TTATTAATATAATAATATTTAT
1 TTATTAATATAATAATATTTAT
*
21891 TTATTAATATAATATTATTTAT
1 TTATTAATATAATAATATTTAT
21913 AAGTAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
22 26 0.63
23 15 0.37
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (22 bp):
TTATTAATATAATAATATTTAT
Found at i:22052 original size:40 final size:41
Alignment explanation
Indices: 21973--22052 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 41
21963 CTCTTTTTCA
* * *
21973 AAAAATATCTTTCCTTTTTTTAAATCTGTAAGATAATTTTG
1 AAAAATAACTTTCATTTTTTTAAATCAGTAAGATAATTTTG
* *
22014 AAAAATAACTTT-ATTTTTTATAGATCAGTAA-ATTATTTT
1 AAAAATAACTTTCATTTTTT-TAAATCAGTAAGATAATTTT
22053 TTTGTTGACC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
40 13 0.39
41 20 0.61
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (41 bp):
AAAAATAACTTTCATTTTTTTAAATCAGTAAGATAATTTTG
Found at i:23439 original size:8 final size:8
Alignment explanation
Indices: 23439--23475 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
23429 TATTTATTTA
23439 TATATATT
1 TATATATT
*
23447 TATATAAT
1 TATATATT
*
23455 TATATGTT
1 TATATATT
23463 TATATATT
1 TATATATT
23471 TATAT
1 TATAT
23476 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (8 bp):
TATATATT
Found at i:23488 original size:17 final size:18
Alignment explanation
Indices: 23464--23501 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23454 TTATATGTTT
23464 ATATATTTATATTTAAAAA
1 ATAT-TTTATATTTAAAAA
*
23483 ATATTTTTTATTTAAAAA
1 ATATTTTATATTTAAAAA
23501 A
1 A
23502 ATAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTTTATATTTAAAAA
Found at i:23511 original size:20 final size:18
Alignment explanation
Indices: 23464--23514 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
23454 TTATATGTTT
23464 ATATATTTATATTTAAAAA
1 ATATATTT-TATTTAAAAA
*
23483 ATATTTTTTATTTAAAAAA
1 ATATATTTTATTT-AAAAA
23502 ATAATATTTTATT
1 AT-ATATTTTATT
23515 AATTTCGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.18
19 14 0.50
20 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATATTTTATTTAAAAA
Found at i:24140 original size:14 final size:15
Alignment explanation
Indices: 24109--24150 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
24099 TAAAAATTTA
24109 TATATATACTTATATAAT
1 TATATATA-TT-T-TAAT
24127 TATA-ATATTTTAAT
1 TATATATATTTTAAT
24141 TATATATATT
1 TATATATATT
24151 ATATTTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 2 0.09
17 3 0.13
18 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATATATTTTAAT
Found at i:24283 original size:20 final size:20
Alignment explanation
Indices: 24238--24276 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
24228 ATACAATAAA
24238 AAAT-TAAAAAAAAAATTTT
1 AAATATAAAAAAAAAATTTT
24257 AAATATAAAAATAAAAATTT
1 AAATATAAAAA-AAAAATTT
24277 ATATATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATAAAAAAAAAATTTT
Found at i:24309 original size:14 final size:15
Alignment explanation
Indices: 24278--24319 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
24268 TAAAAATTTA
24278 TATATATACTTATATAAT
1 TATATATA-TT-T-TAAT
24296 TATA-ATATTTTAAT
1 TATATATATTTTAAT
24310 TATATATATT
1 TATATATATT
24320 ATATTTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 2 0.09
17 3 0.13
18 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATATATTTTAAT
Found at i:24479 original size:14 final size:15
Alignment explanation
Indices: 24448--24489 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
24438 TAAAAATTTA
24448 TATATATACTTATATAAT
1 TATATATA-TT-T-TAAT
24466 TATA-ATATTTTAAT
1 TATATATATTTTAAT
24480 TATATATATT
1 TATATATATT
24490 ATATTTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 2 0.09
17 3 0.13
18 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATATATTTTAAT
Found at i:24508 original size:170 final size:170
Alignment explanation
Indices: 24046--24550 Score: 922
Period size: 169 Copynumber: 3.0 Consensus size: 170
24036 GCCATCTATC
24046 AAACTTAATTTATACAATAAAAAATTAAAAAATCTTTTTTTAAAATATAAAAATAAAAATTTATA
1 AAACTTAATTTATACAATAAAAAATTAAAAAATCTTTTTTT-AAATATAAAAATAAAAATTTATA
24111 TATATACTTATATAATTATAATATTTTAATTATATATATTATATTTGAGTCGAGCTGGACTTGGA
65 TATATACTTATATAATTATAATATTTTAATTATATATATTATATTTGAGTCGAGCTGGACTTGGA
24176 TTTTAATTTTTTTGTTTAATACTTAGTCCAAAATTTCCATT
130 TTTTAATTTTTTTGTTTAATACTTAGTCCAAAATTTCCATT
****
24217 AAACTTAATTTATACAATAAAAAATTAAAAAA-AAAATTTTAAATATAAAAATAAAAATTTATAT
1 AAACTTAATTTATACAATAAAAAATTAAAAAATCTTTTTTTAAATATAAAAATAAAAATTTATAT
*
24281 ATATACTTATATAATTATAATATTTTAATTATATATATTATATTTGAGTCAAGCTGGACTTGGAT
66 ATATACTTATATAATTATAATATTTTAATTATATATATTATATTTGAGTCGAGCTGGACTTGGAT
* *
24346 TTTAATTTTTTTGTTTAATGCTTAGTCCAAAATTTTCATT
131 TTTAATTTTTTTGTTTAATACTTAGTCCAAAATTTCCATT
24386 AAACTTAATTTATACAATAAAAAATTAAAAAATCTTTTTTTAAATATAAAAATAAAAATTTATAT
1 AAACTTAATTTATACAATAAAAAATTAAAAAATCTTTTTTTAAATATAAAAATAAAAATTTATAT
24451 ATATACTTATATAATTATAATATTTTAATTATATATATTATATTTGAGTCGAGCTGGACTTGGAT
66 ATATACTTATATAATTATAATATTTTAATTATATATATTATATTTGAGTCGAGCTGGACTTGGAT
*
24516 TTTAATTTTTTTGTTTAATATTTAGTCCAAAATTT
131 TTTAATTTTTTTGTTTAATACTTAGTCCAAAATTT
24551 AAACAGGCCT
Statistics
Matches: 319, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
169 158 0.50
170 129 0.40
171 32 0.10
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (170 bp):
AAACTTAATTTATACAATAAAAAATTAAAAAATCTTTTTTTAAATATAAAAATAAAAATTTATAT
ATATACTTATATAATTATAATATTTTAATTATATATATTATATTTGAGTCGAGCTGGACTTGGAT
TTTAATTTTTTTGTTTAATACTTAGTCCAAAATTTCCATT
Found at i:25391 original size:31 final size:29
Alignment explanation
Indices: 25356--25414 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
25346 ATGAATGATC
25356 TTTAAATTATAATAAAATATT-TAATATAATA
1 TTTAAATT-TAA-AAAAT-TTATAATATAATA
*
25387 TTTAAATTTTAAAAATTTATAATATAAT
1 TTTAAATTTAAAAAATTTATAATATAAT
25415 GTCAAATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 14 0.54
30 2 0.08
31 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAAATTTAAAAAATTTATAATATAATA
Done.