Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168083.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_330, 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: 34321
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Found at i:6658 original size:22 final size:22
Alignment explanation
Indices: 6632--6675 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6622 TTCCCTCCCA
*
6632 ATATAACATCATATGTTAGGAT
1 ATATAACATCACATGTTAGGAT
*
6654 ATATAATATCACATGTTAGGAT
1 ATATAACATCACATGTTAGGAT
6676 TAAAGCCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
ATATAACATCACATGTTAGGAT
Found at i:8841 original size:3 final size:3
Alignment explanation
Indices: 8833--8905 Score: 87
Period size: 3 Copynumber: 23.7 Consensus size: 3
8823 AAATAAACCA
8833 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
*
8878 AAT AAAT AAAT AAT GAA- AAT AAA AAT AA
1 AAT -AAT -AAT AAT -AAT AAT AAT AAT AA
8906 AAATGGGCTT
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
2 4 0.06
3 47 0.75
4 12 0.19
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:9335 original size:41 final size:41
Alignment explanation
Indices: 9285--9375 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
9275 ACCTTTCAGC
9285 TTTGTCAGAATTCACTAAAATTTGATTATCAAAATTTCAAT
1 TTTGTCAGAATTCACTAAAATTTGATTATCAAAATTTCAAT
* * *
9326 TTTGCCAGAATTTACTAAAATTTGATTATCAAAATTTCAGT
1 TTTGTCAGAATTCACTAAAATTTGATTATCAAAATTTCAAT
9367 TTTGTCAGA
1 TTTGTCAGA
9376 TCTCAAGATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (41 bp):
TTTGTCAGAATTCACTAAAATTTGATTATCAAAATTTCAAT
Found at i:10530 original size:17 final size:17
Alignment explanation
Indices: 10505--10547 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
10495 TAAGTTCTCA
*
10505 TTTTT-TTTTCTCTCTT
1 TTTTTATTTTCTCTATT
* *
10521 TTTTTATTTTTTTTATT
1 TTTTTATTTTCTCTATT
10538 TTTTTATTTT
1 TTTTTATTTT
10548 TCAAGCATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTATTTTCTCTATT
Found at i:10531 original size:9 final size:9
Alignment explanation
Indices: 10519--10548 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
10509 TTTTTCTCTC
10519 TTTTTTTAT
1 TTTTTTTAT
10528 TTTTTTTA-
1 TTTTTTTAT
10536 TTTTTTTAT
1 TTTTTTTAT
10545 TTTT
1 TTTT
10549 CAAGCATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:10532 original size:8 final size:8
Alignment explanation
Indices: 10519--10548 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
10509 TTTTTCTCTC
10519 TTTTTTTA
1 TTTTTTTA
10527 TTTTTTTTA
1 -TTTTTTTA
10536 TTTTTTTA
1 TTTTTTTA
10544 TTTTT
1 TTTTT
10549 CAAGCATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:19526 original size:45 final size:44
Alignment explanation
Indices: 19455--19551 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
19445 GAATGATGCA
* * *
19455 AATGATAGTGTTAAACATGATCATGAAAATAATACATAGAAT-G
1 AATGATAATGTTAAACATGAGCATGAAAATAATACATAAAATGG
* * *
19498 ATATGATAATGTTAAAACATGAGGATGAAAATGATGCATAAAATGG
1 A-ATGATAATGTT-AAACATGAGCATGAAAATAATACATAAAATGG
19544 AATGATAA
1 AATGATAA
19552 GGAAATAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 1 0.02
44 10 0.22
45 32 0.71
46 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (44 bp):
AATGATAATGTTAAACATGAGCATGAAAATAATACATAAAATGG
Found at i:21897 original size:3 final size:3
Alignment explanation
Indices: 21889--21920 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
21879 AATAAACCCA
21889 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21921 ATGGACTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30732 original size:20 final size:21
Alignment explanation
Indices: 30699--30753 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
30689 ATAATCCTAT
* *
30699 TTTAAAATTCATTTATATTTA
1 TTTAGAATTTATTTATATTTA
30720 TTT-GAATTTATTTATATTTA
1 TTTAGAATTTATTTATATTTA
*
30740 TTTAGAGTTTATTT
1 TTTAGAATTTATTT
30754 GTTTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTAGAATTTATTTATATTTA
Found at i:32825 original size:2 final size:2
Alignment explanation
Indices: 32818--32865 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
32808 TGTTGAATTA
32818 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
32860 CT CT CT
1 CT CT CT
32866 TATTTTTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:33187 original size:70 final size:71
Alignment explanation
Indices: 33095--33233 Score: 194
Period size: 71 Copynumber: 2.0 Consensus size: 71
33085 GTTTGTATTT
*
33095 TTTCCATCTTGAGATAAAAAAATAAAATTGAA-AACAA-AGAAATATTAAATATGAAGACAAGTA
1 TTTCCATCTTGAGATAAAAAAATAAAATTGAACAA-AAGAAAAATATTAAATATGAAGACAAGTA
33158 CAAGTGG
65 CAAGTGG
* * * *
33165 TTTCCATGTTG-GAATAGAAAAATGAAATTGAACAAAAGAAAAATATTAGATATGAAGACAAGTA
1 TTTCCATCTTGAG-ATAAAAAAATAAAATTGAACAAAAGAAAAATATTAAATATGAAGACAAGTA
33229 CAAGT
65 CAAGT
33234 TTTTGAGGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
69 1 0.02
70 29 0.48
71 31 0.51
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (71 bp):
TTTCCATCTTGAGATAAAAAAATAAAATTGAACAAAAGAAAAATATTAAATATGAAGACAAGTAC
AAGTGG
Done.