Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168064.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_313, 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: 35916
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:2386 original size:28 final size:28
Alignment explanation
Indices: 2370--2423 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
2360 TATGTTAAAG
2370 TATACTTGTCATCCAGCAAATAGGAAAC
1 TATACTTGTCATCCAGCAAATAGGAAAC
2398 TATACTTGTCATCCAGCAAATAGGAA
1 TATACTTGTCATCCAGCAAATAGGAA
2424 TGCTCTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (28 bp):
TATACTTGTCATCCAGCAAATAGGAAAC
Found at i:3569 original size:3 final size:3
Alignment explanation
Indices: 3561--3587 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3551 TGGCAAACTT
3561 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
3588 AGAACTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:5520 original size:14 final size:15
Alignment explanation
Indices: 5503--5534 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
5493 CCTCTCAGTT
5503 TTTGCTTTTTT-TTC
1 TTTGCTTTTTTGTTC
5517 TTTGCTTTTTTGTTC
1 TTTGCTTTTTTGTTC
5532 TTT
1 TTT
5535 TTAGCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.78
Consensus pattern (15 bp):
TTTGCTTTTTTGTTC
Found at i:8843 original size:10 final size:11
Alignment explanation
Indices: 8815--8843 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
8805 GTACTTAATG
8815 AACTTTTTTAA
1 AACTTTTTTAA
8826 AACTTTTTTAA
1 AACTTTTTTAA
8837 AACTTTT
1 AACTTTT
8844 ATTTTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (11 bp):
AACTTTTTTAA
Found at i:10603 original size:34 final size:34
Alignment explanation
Indices: 10560--10628 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
10550 ACATTTATAC
10560 CTTTTATTATTTTTTAATTTTTAAAAATACATTG
1 CTTTTATTATTTTTTAATTTTTAAAAATACATTG
10594 CTTTTATTATTTTTTAATTTTTAAAAATACATTG
1 CTTTTATTATTTTTTAATTTTTAAAAATACATTG
10628 C
1 C
10629 AAGCTTGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (34 bp):
CTTTTATTATTTTTTAATTTTTAAAAATACATTG
Found at i:10791 original size:14 final size:14
Alignment explanation
Indices: 10735--10791 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 14
10725 TTGTCTTCAA
10735 TTTTTTATATGTATT
1 TTTTTTATAT-TATT
*
10750 TTTTATTATTTTATT
1 TTTT-TTATATTATT
10765 CTTTTTTGCATATTATT
1 -TTTTTT--ATATTATT
*
10782 TATTTTATAT
1 TTTTTTATAT
10792 GAAAATAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 4 0.11
15 10 0.29
16 14 0.40
17 7 0.20
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (14 bp):
TTTTTTATATTATT
Found at i:13614 original size:13 final size:13
Alignment explanation
Indices: 13596--13622 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13586 ACATTATATA
13596 AAATTAAAATTTT
1 AAATTAAAATTTT
13609 AAATTAAAATTTT
1 AAATTAAAATTTT
13622 A
1 A
13623 TTTATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTAAAATTTT
Found at i:13642 original size:8 final size:8
Alignment explanation
Indices: 13619--13669 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
13609 AAATTAAAAT
*
13619 TTTATTTA
1 TTTATATA
*
13627 TATATATA
1 TTTATATA
13635 TTTATATA
1 TTTATATA
*
13643 ATTATATA
1 TTTATATA
*
13651 TTTAAATA
1 TTTATATA
13659 TTTATAT-
1 TTTATATA
13666 TTTA
1 TTTA
13670 AAAAATAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
7 4 0.11
8 32 0.89
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTATATA
Found at i:13648 original size:16 final size:16
Alignment explanation
Indices: 13629--13684 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
13619 TTTATTTATA
*
13629 TATATATTTATATAAT
1 TATATATTTAAATAAT
*
13645 TATATATTTAAATATT
1 TATATATTTAAATAAT
*
13661 TATAT-TTTAAAAAAT
1 TATATATTTAAATAAT
*
13676 AATA-ATTTA
1 TATATATTTA
13685 TTAATTTCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 15 0.44
16 19 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:16938 original size:24 final size:24
Alignment explanation
Indices: 16902--16949 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
16892 CTTTAAAAAA
16902 AAAAATCAGATTTT-AATTTTTAT
1 AAAAATCAGATTTTAAATTTTTAT
*
16925 AAAAATCAATATTTTGAAATTTTTA
1 AAAAATC-AGATTTT-AAATTTTTA
16950 AAGTTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
26 8 0.38
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (24 bp):
AAAAATCAGATTTTAAATTTTTAT
Found at i:16951 original size:24 final size:23
Alignment explanation
Indices: 16902--16951 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
16892 CTTTAAAAAA
*
16902 AAAAATCAGATTTTAATTTTTAT
1 AAAAATCAGATTTTAAATTTTAT
*
16925 AAAAATCAATATTTTGAAATTTT-T
1 AAAAATC-AGATTTT-AAATTTTAT
16949 AAA
1 AAA
16952 GTTTTTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 10 0.43
25 6 0.26
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (23 bp):
AAAAATCAGATTTTAAATTTTAT
Found at i:16990 original size:22 final size:20
Alignment explanation
Indices: 16963--17034 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 20
16953 TTTTTTCATA
16963 TTTTTAAAATATTAAATTTAAT
1 TTTTTAAAATA--AAATTTAAT
*
16985 TTTTTAAAATAAAATTTAAAAA
1 TTTTTAAAATAAAATTT--AAT
** *
17007 TTTTT-AAATATGATTTTAT
1 TTTTTAAAATAAAATTTAAT
17026 TTTTTAAAA
1 TTTTTAAAA
17035 ATTCAATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 6 0.14
20 9 0.21
21 9 0.21
22 18 0.43
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (20 bp):
TTTTTAAAATAAAATTTAAT
Found at i:17226 original size:19 final size:19
Alignment explanation
Indices: 17183--17226 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17173 ACAAAATATT
* *
17183 AATTTTAATATTTTTTTAA
1 AATTTTAAAATTTTTATAA
**
17202 CGTTTTAAAATTTTTATAA
1 AATTTTAAAATTTTTATAA
17221 AATTTT
1 AATTTT
17227 CTATATTTTA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
AATTTTAAAATTTTTATAA
Found at i:17329 original size:20 final size:20
Alignment explanation
Indices: 17287--17330 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
17277 TATTTTGTAT
* *
17287 TTTTAAAAAGAGTTTATAAA
1 TTTTAAAAAAAGTTTACAAA
* *
17307 TTTTAAAAAAATTTTACATA
1 TTTTAAAAAAAGTTTACAAA
17327 TTTT
1 TTTT
17331 TTTATGTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
TTTTAAAAAAAGTTTACAAA
Found at i:18040 original size:20 final size:20
Alignment explanation
Indices: 18014--18068 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
18004 GAATTATCAA
18014 ATTAATAAAATTAATATTAT
1 ATTAATAAAATTAATATTAT
* * *
18034 GTTAATAAAATCAACATTAT
1 ATTAATAAAATTAATATTAT
*
18054 ATCAATAAAATTAAT
1 ATTAATAAAATTAAT
18069 GATCACATCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (20 bp):
ATTAATAAAATTAATATTAT
Found at i:21426 original size:58 final size:58
Alignment explanation
Indices: 21356--21472 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
21346 GAAACTTCAT
21356 ATCTAAACGCTTTTCTGTATCCTCCATCTAGGAATCATCAGGTTTTAGAAACTGTTGA
1 ATCTAAACGCTTTTCTGTATCCTCCATCTAGGAATCATCAGGTTTTAGAAACTGTTGA
* * *
21414 ATCTAAATGCTTTTCTGTATCCTCTATCTAGGAATCATTAGGTTTTAGAAACTGTTGA
1 ATCTAAACGCTTTTCTGTATCCTCCATCTAGGAATCATCAGGTTTTAGAAACTGTTGA
21472 A
1 A
21473 GTCATCACTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (58 bp):
ATCTAAACGCTTTTCTGTATCCTCCATCTAGGAATCATCAGGTTTTAGAAACTGTTGA
Found at i:23528 original size:5 final size:5
Alignment explanation
Indices: 23518--23554 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
23508 GGAATCTGGG
*
23518 TCTTT TCTTT TCTTT TCTTT TTTTT TCTTT CTCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT -TCTTT T
23555 TTGGGATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:34861 original size:21 final size:21
Alignment explanation
Indices: 34835--34874 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34825 TGATAAGAAT
34835 GTTGCC-CATTCTTCGTTATAA
1 GTTGCCTCATTCTTC-TTATAA
*
34856 GTTGCCTCATTTTTCTTAT
1 GTTGCCTCATTCTTCTTAT
34875 CAAACAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.15, C:0.23, G:0.12, T:0.50
Consensus pattern (21 bp):
GTTGCCTCATTCTTCTTATAA
Done.