Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168076.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_324, 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: 34606
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:831 original size:30 final size:30
Alignment explanation
Indices: 795--853 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
785 GAGGATAGGA
795 TAATAATCATTTTATATCATATTTGGTTTG
1 TAATAATCATTTTATATCATATTTGGTTTG
825 TAATAATCATTTTATATCATATTTGGTTT
1 TAATAATCATTTTATATCATATTTGGTTT
854 ATATCTAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (30 bp):
TAATAATCATTTTATATCATATTTGGTTTG
Found at i:1819 original size:11 final size:10
Alignment explanation
Indices: 1805--1849 Score: 58
Period size: 9 Copynumber: 4.5 Consensus size: 10
1795 TTAGAGGGTG
1805 AAAAGAGAGAT
1 AAAA-AGAGAT
1816 -AAAAGAGAAT
1 AAAAAGAG-AT
1826 AAAAAGAGAT
1 AAAAAGAGAT
1836 AAAAA-AGAT
1 AAAAAGAGAT
1845 AAAAA
1 AAAAA
1850 TAAATAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 13 0.41
10 12 0.38
11 7 0.22
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (10 bp):
AAAAAGAGAT
Found at i:1835 original size:20 final size:19
Alignment explanation
Indices: 1805--1849 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1795 TTAGAGGGTG
*
1805 AAAAGAGAGATAAAAGAGAAT
1 AAAA-AGAGATAAAAAAG-AT
1826 AAAAAGAGATAAAAAAGAT
1 AAAAAGAGATAAAAAAGAT
1845 AAAAA
1 AAAAA
1850 TAAATAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (19 bp):
AAAAAGAGATAAAAAAGAT
Found at i:4390 original size:41 final size:42
Alignment explanation
Indices: 4305--4387 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
4295 TGCCTTCTTT
* * *
4305 ATATAAACACTATTATATGAGAAAGAAACGGTTCCGATTGAA
1 ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
4347 ATATAAACACTATTATACGAG-AAG-AACAGTTCCAATTGAA
1 ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
4387 A
1 A
4388 ATACTGTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 15 0.39
41 3 0.08
42 20 0.53
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.25
Consensus pattern (42 bp):
ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
Found at i:7317 original size:2 final size:2
Alignment explanation
Indices: 7304--7337 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
7294 ATTCTTTTTC
* *
7304 AT AT AT AC AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7338 GATAAAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10204 original size:42 final size:42
Alignment explanation
Indices: 10118--10201 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
10108 TTGCTTCTTT
* *
10118 ATATAAACACTATTATATGAGAAAGAAACGGTTCCAATTGAA
1 ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
10160 ATATAAACACTATTATACGAGAAAG-AACAGTTCCAATTGAA
1 ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
10201 A
1 A
10202 ATACTGTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 16 0.40
42 24 0.60
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (42 bp):
ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
Found at i:16691 original size:23 final size:24
Alignment explanation
Indices: 16629--16694 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 24
16619 TTTTTCAATT
*
16629 TAAAATAAGAAATAATAAGAGTAAA
1 TAAAATAAGAAA-AATAACAGTAAA
16654 TAAAAATAA-ACAAAATAACA-TAAA
1 T-AAAATAAGA-AAAATAACAGTAAA
16678 TAAAATAAGAAAAATAA
1 TAAAATAAGAAAAATAA
16695 AGTCAAAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 14 0.38
24 6 0.16
25 8 0.22
26 9 0.24
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (24 bp):
TAAAATAAGAAAAATAACAGTAAA
Found at i:17318 original size:52 final size:51
Alignment explanation
Indices: 17190--17321 Score: 126
Period size: 52 Copynumber: 2.6 Consensus size: 51
17180 TTTATTTTCG
*
17190 TTTTAATGAAAATTGATTCTGAAATCAAA-TTCCAAAATCTCTCCCTATCA
1 TTTTAATGAAAATTGATTCTGAAATTAAATTTCCAAAATCTCTCCCTATCA
* ** * * *
17240 ATTTAATGTGAATTGATTAT-ATAATTAAATTTCGACAATCTCTCCAC-ATCA
1 TTTTAATGAAAATTGATTCTGA-AATTAAATTTCCAAAATCTCTCC-CTATCA
** *
17291 TTTTTAATGCCAATTGATTCTGGAATTAAAT
1 -TTTTAATGAAAATTGATTCTGAAATTAAAT
17322 CTAAAAAATC
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
49 1 0.02
50 22 0.34
51 17 0.26
52 25 0.38
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (51 bp):
TTTTAATGAAAATTGATTCTGAAATTAAATTTCCAAAATCTCTCCCTATCA
Found at i:18565 original size:32 final size:32
Alignment explanation
Indices: 18522--18586 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
18512 CATAGCTAAA
18522 TTATTTCTTGTTATGCAAGTTAGGTTATTACT
1 TTATTTCTTGTTATGCAAGTTAGGTTATTACT
*
18554 TTATTTTTTGTTATGCAAGTTAGGTTATTACT
1 TTATTTCTTGTTATGCAAGTTAGGTTATTACT
18586 T
1 T
18587 GGTTAAACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.08, G:0.15, T:0.55
Consensus pattern (32 bp):
TTATTTCTTGTTATGCAAGTTAGGTTATTACT
Found at i:20862 original size:27 final size:27
Alignment explanation
Indices: 20824--20880 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
20814 GGATCAAGGT
20824 ATTTAGTATTAAATGATGTTAGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
*
20851 ATTTAGTATTAAATGATGTTTGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
20878 ATT
1 ATT
20881 CAATTAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (27 bp):
ATTTAGTATTAAATGATGTTAGCCCAC
Found at i:27073 original size:11 final size:10
Alignment explanation
Indices: 27057--27101 Score: 58
Period size: 9 Copynumber: 4.5 Consensus size: 10
27047 TTAGAAGGTG
27057 AAAAGAGAGAT
1 AAAA-AGAGAT
27068 -AAAAGAGAAT
1 AAAAAGAG-AT
27078 AAAAAGAGAT
1 AAAAAGAGAT
27088 AAAAA-AGAT
1 AAAAAGAGAT
27097 AAAAA
1 AAAAA
27102 TAAATAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 13 0.41
10 12 0.38
11 7 0.22
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (10 bp):
AAAAAGAGAT
Found at i:27087 original size:20 final size:19
Alignment explanation
Indices: 27057--27101 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
27047 TTAGAAGGTG
*
27057 AAAAGAGAGATAAAAGAGAAT
1 AAAA-AGAGATAAAAAAG-AT
27078 AAAAAGAGATAAAAAAGAT
1 AAAAAGAGATAAAAAAGAT
27097 AAAAA
1 AAAAA
27102 TAAATAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (19 bp):
AAAAAGAGATAAAAAAGAT
Found at i:29608 original size:41 final size:40
Alignment explanation
Indices: 29557--29640 Score: 125
Period size: 39 Copynumber: 2.1 Consensus size: 40
29547 TGCTTCTTTT
* *
29557 ATATAAACACTATTATATGAGAAAGAAACGGTTCCAATTGAA
1 ATATAAACACTATTATACGAG-AAG-AACAGTTCCAATTGAA
29599 ATAT-AACACTATTATACGAGAAGAACAGTTCCAATTGAA
1 ATATAAACACTATTATACGAGAAGAACAGTTCCAATTGAA
29638 ATA
1 ATA
29641 CTGTGTTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
39 18 0.45
40 3 0.08
41 15 0.38
42 4 0.10
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (40 bp):
ATATAAACACTATTATACGAGAAGAACAGTTCCAATTGAA
Found at i:32584 original size:2 final size:2
Alignment explanation
Indices: 32571--32604 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
32561 ATTCTTTTTC
* *
32571 AT AT AT AC AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32605 GATAAAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33334 original size:20 final size:19
Alignment explanation
Indices: 33284--33322 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33274 TCTAATTAAA
33284 ATCACTTCT-TTTTGGTTAG
1 ATCA-TTCTCTTTTGGTTAG
*
33303 ATCATTTTCTTTTGGTTAG
1 ATCATTCTCTTTTGGTTAG
33322 A
1 A
33323 ATATATCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.54
Consensus pattern (19 bp):
ATCATTCTCTTTTGGTTAG
Done.