Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168219.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_453, 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: 26314
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Found at i:23681 original size:30 final size:30
Alignment explanation
Indices: 23647--23774 Score: 116
Period size: 30 Copynumber: 4.2 Consensus size: 30
23637 TTATCTTCTT
*
23647 CACCAACACCACCACCACCACCAACACCAA
1 CACCAACACCACCACCACCACCACCACCAA
*
23677 CACCAACACCACCACCACCACC-CTCATCATCAT
1 CACCAACACCACCACCACCACCAC-CA-C--CAA
* * * *
23710 CATCACCATCACCATCACCACCACCACCAA
1 CACCAACACCACCACCACCACCACCACCAA
* * *
23740 C-CTCATCATCACCATCACCACCACCACCAA
1 CAC-CAACACCACCACCACCACCACCACCAA
23770 CACCA
1 CACCA
23775 CCCTCGTCAT
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
30 56 0.68
31 2 0.02
32 1 0.01
33 22 0.27
34 1 0.01
ACGTcount: A:0.37, C:0.55, G:0.00, T:0.09
Consensus pattern (30 bp):
CACCAACACCACCACCACCACCACCACCAA
Found at i:23716 original size:27 final size:27
Alignment explanation
Indices: 23683--23921 Score: 115
Period size: 27 Copynumber: 9.1 Consensus size: 27
23673 CCAACACCAA
*
23683 CACCACCACCACCACCCTCATCATCAT
1 CACCACCAACACCACCCTCATCATCAT
* * *
23710 CATCACCATCACCA---TCA-C--CAC
1 CACCACCAACACCACCCTCATCATCAT
* * * *
23731 CACCACCAAC-CTCATCATCACCATCAC
1 CACCACCAACAC-CACCCTCATCATCAT
* * * *
23758 CACCACCACCAACACCAC-CCTCGTCAT
1 CACCACCAACACCACC-CTCATCATCAT
* *
23785 CACCACCACCACCA-CCT--TCGTCAT
1 CACCACCAACACCACCCTCATCATCAT
* * *
23809 CACCACCACCACCAACGTCATCATCAT
1 CACCACCAACACCACCCTCATCATCAT
* * *
23836 CGCCACCAACACCACTTTCGTCATCAACAT
1 CACCACCAACACCAC---CCTCATCATCAT
* *
23866 CGCCACCAACACCACCCTCGTCATCAT
1 CACCACCAACACCACCCTCATCATCAT
* * *
23893 C-CTCACCAACAACACCTTCTTCATCAT
1 CAC-CACCAACACCACCCTCATCATCAT
23920 CA
1 CA
23922 GAATCATCAT
Statistics
Matches: 168, Mismatches: 26, Indels: 35
0.73 0.11 0.15
Matches are distributed among these distances:
20 1 0.01
21 12 0.07
23 1 0.01
24 27 0.16
25 4 0.02
26 2 0.01
27 95 0.57
30 26 0.15
ACGTcount: A:0.30, C:0.51, G:0.03, T:0.16
Consensus pattern (27 bp):
CACCACCAACACCACCCTCATCATCAT
Found at i:23776 original size:24 final size:24
Alignment explanation
Indices: 23648--23824 Score: 108
Period size: 24 Copynumber: 7.2 Consensus size: 24
23638 TATCTTCTTC
* *
23648 ACCAACACCACCACCACCACCAAC
1 ACCAACACCACCATCACCACCACC
* *
23672 ACCAACACCAACACCACCACCACC
1 ACCAACACCACCATCACCACCACC
** * * * *
23696 ACCCTCATCATCATCATCACCATC
1 ACCAACACCACCATCACCACCACC
* *
23720 ACCATCACCACCACCACCA--ACC
1 ACCAACACCACCATCACCACCACC
* * *
23742 -TCATCATCACCATCACCACCACC
1 ACCAACACCACCATCACCACCACC
* *
23765 ACCAACACCACCCTCGTCATCACCACC
1 ACCAACACCA--C-CATCACCACCACC
* *
23792 ACCACCACCTTCGTCATCACCACCACC
1 ACCAACACC-AC--CATCACCACCACC
23819 ACCAAC
1 ACCAAC
23825 GTCATCATCA
Statistics
Matches: 117, Mismatches: 28, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
21 15 0.13
22 2 0.02
23 3 0.03
24 59 0.50
26 2 0.02
27 36 0.31
ACGTcount: A:0.34, C:0.55, G:0.01, T:0.10
Consensus pattern (24 bp):
ACCAACACCACCATCACCACCACC
Found at i:23785 original size:36 final size:36
Alignment explanation
Indices: 23653--23800 Score: 153
Period size: 36 Copynumber: 4.2 Consensus size: 36
23643 TCTTCACCAA
* *
23653 CACCACCACCACCACCAACAC-CA--A-CACCAACAC
1 CACCACCACCAACACCAAC-CTCATCATCACCATCAC
* * *
23686 CACCACCACC-ACCCTCATCATCATCATCACCATCAC
1 CACCACCACCAACAC-CAACCTCATCATCACCATCAC
* *
23722 CATCACCACCACCACCAACCTCATCATCACCATCAC
1 CACCACCACCAACACCAACCTCATCATCACCATCAC
* * *
23758 CACCACCACCAACACCACCCTCGTCATCACCACCAC
1 CACCACCACCAACACCAACCTCATCATCACCATCAC
23794 CACCACC
1 CACCACC
23801 TTCGTCATCA
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
32 2 0.02
33 15 0.16
35 1 0.01
36 74 0.79
37 2 0.02
ACGTcount: A:0.34, C:0.56, G:0.01, T:0.09
Consensus pattern (36 bp):
CACCACCACCAACACCAACCTCATCATCACCATCAC
Found at i:23820 original size:3 final size:3
Alignment explanation
Indices: 23647--23800 Score: 98
Period size: 3 Copynumber: 51.3 Consensus size: 3
23637 TTATCTTCTT
* * * *
23647 CAC CAA CAC CAC CAC CAC CAC CAA CAC CAA CAC CAA CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
* * * * * *
23695 CAC C-C TCAT CAT CAT CAT CAC CAT CAC CAT CAC CAC CAC CAC CAAC
1 CAC CAC -CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C-AC
* * * * * ** *
23741 C-T CAT CAT CAC CAT CAC CAC CAC CAC CAA CAC CAC C-C TCGT CAT
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC -CAC CAC
23785 CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC C
23801 TTCGTCATCA
Statistics
Matches: 122, Mismatches: 23, Indels: 12
0.78 0.15 0.08
Matches are distributed among these distances:
2 3 0.02
3 116 0.95
4 3 0.02
ACGTcount: A:0.34, C:0.56, G:0.01, T:0.09
Consensus pattern (3 bp):
CAC
Found at i:23841 original size:21 final size:21
Alignment explanation
Indices: 23662--23845 Score: 113
Period size: 21 Copynumber: 8.8 Consensus size: 21
23652 ACACCACCAC
* ** *
23662 CACCACCAACACCAACACCAA
1 CACCACCACCACCAACGTCAT
* *
23683 CACCACCACCACCACCCTCAT
1 CACCACCACCACCAACGTCAT
* * * * **
23704 CATCATCATCACCATCACCAT
1 CACCACCACCACCAACGTCAT
*
23725 CACCACCACCACCAACCTCAT
1 CACCACCACCACCAACGTCAT
* * *
23746 CATCACCATCACC-AC--CAC
1 CACCACCACCACCAACGTCAT
* **
23764 CACCAACACCACCCTCGTCAT
1 CACCACCACCACCAACGTCAT
*
23785 CACCACCACCACCACCTTCGTCAT
1 CACCACCACCACCA---ACGTCAT
23809 CACCACCACCACCAACGTCAT
1 CACCACCACCACCAACGTCAT
* * *
23830 CATCATCGCCACCAAC
1 CACCACCACCACCAAC
23846 ACCACTTTCG
Statistics
Matches: 126, Mismatches: 31, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
18 12 0.10
19 1 0.01
20 2 0.02
21 90 0.71
24 21 0.17
ACGTcount: A:0.33, C:0.53, G:0.02, T:0.12
Consensus pattern (21 bp):
CACCACCACCACCAACGTCAT
Found at i:23843 original size:30 final size:30
Alignment explanation
Indices: 23716--23900 Score: 112
Period size: 30 Copynumber: 6.4 Consensus size: 30
23706 TCATCATCAC
* * *
23716 CATCACCATCACCACCACCACCAACCTCAT
1 CATCATCACCACCACCACCACCAACGTCAT
* * ** *
23746 CATCACCATCACCACCACCACCAACACCAC
1 CATCATCACCACCACCACCACCAACGTCAT
* * *
23776 CCTCGTCATCACCACCACCACC-AC--C-T
1 CATCATCACCACCACCACCACCAACGTCAT
* *
23802 --TCGTCATCACCACCACCACCAACGTCAT
1 CATCATCACCACCACCACCACCAACGTCAT
* * ***
23830 CATCATCGCCACCAACACCACTTTCGTCAT
1 CATCATCACCACCACCACCACCAACGTCAT
* * * **
23860 CAACATCGCCACCAACACCACCCTCGTCAT
1 CATCATCACCACCACCACCACCAACGTCAT
*
23890 CATCCTCACCA
1 CATCATCACCA
23901 ACAACACCTT
Statistics
Matches: 129, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
24 20 0.16
25 2 0.02
27 2 0.02
28 1 0.01
29 2 0.02
30 102 0.79
ACGTcount: A:0.30, C:0.51, G:0.04, T:0.15
Consensus pattern (30 bp):
CATCATCACCACCACCACCACCAACGTCAT
Found at i:23859 original size:24 final size:24
Alignment explanation
Indices: 23761--23918 Score: 118
Period size: 24 Copynumber: 6.1 Consensus size: 24
23751 CCATCACCAC
*
23761 CACCACCAACACCACCCTCGTCAT
1 CACCACCAACACCACCTTCGTCAT
*
23785 CACCACCACCACCACCTTCGTCAT
1 CACCACCAACACCACCTTCGTCAT
* * *
23809 CACCACCACCACCAACGTCATCATCAT
1 CACCACCAACACC-AC--CTTCGTCAT
* *
23836 CGCCACCAACACCACTTTCGTCAT
1 CACCACCAACACCACCTTCGTCAT
*
23860 CAACATCGCCACCAACACCACCCTCGTCAT
1 ---CA---CCACCAACACCACCTTCGTCAT
* *
23890 CATCCTCACCAACAACACCTTCTTCAT
1 CA--C-CACCAACACCACCTTCGTCAT
23917 CA
1 CA
23919 TCAGAATCAT
Statistics
Matches: 107, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
24 41 0.38
25 2 0.02
26 3 0.03
27 41 0.38
30 20 0.19
ACGTcount: A:0.29, C:0.49, G:0.04, T:0.17
Consensus pattern (24 bp):
CACCACCAACACCACCTTCGTCAT
Found at i:23906 original size:30 final size:30
Alignment explanation
Indices: 23809--23960 Score: 133
Period size: 30 Copynumber: 4.9 Consensus size: 30
23799 CCTTCGTCAT
* *
23809 CACCACCACCACCAACGTCATCATCATCGC
1 CACCAACACCACCATCGTCATCATCATCGC
** *
23839 CACCAACACCACTTTCGTCATCAACATCGC
1 CACCAACACCACCATCGTCATCATCATCGC
* * *
23869 CACCAACACCACCCTCGTCATCATCCTCAC
1 CACCAACACCACCATCGTCATCATCATCGC
* * * *
23899 CAACAACACCTTCTTCATCATCAGAATCATCATCAC
1 CACCAACACC-AC--CATCGTC---ATCATCATCGC
*
23935 CACCAACACCACCTTCGTCATCATCA
1 CACCAACACCACCATCGTCATCATCA
23961 GAATCGTCAC
Statistics
Matches: 97, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
30 66 0.68
31 1 0.01
33 10 0.10
35 1 0.01
36 19 0.20
ACGTcount: A:0.31, C:0.45, G:0.05, T:0.19
Consensus pattern (30 bp):
CACCAACACCACCATCGTCATCATCATCGC
Found at i:23929 original size:39 final size:39
Alignment explanation
Indices: 23886--23975 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
23876 ACCACCCTCG
*
23886 TCATCATC-CTCACCAACAACACCTTCTTCATCATCAGAA
1 TCATCATCAC-CACCAACAACACCTTCGTCATCATCAGAA
*
23925 TCATCATCACCACCAACACCACCTTCGTCATCATCAGAA
1 TCATCATCACCACCAACAACACCTTCGTCATCATCAGAA
* *
23964 TCGTCACCACCA
1 TCATCATCACCA
23976 TCTCCATCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 45 0.98
40 1 0.02
ACGTcount: A:0.32, C:0.41, G:0.04, T:0.22
Consensus pattern (39 bp):
TCATCATCACCACCAACAACACCTTCGTCATCATCAGAA
Done.