Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167952.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_212, 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: 50665
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.29
Warning! 1000 characters in sequence are not A, C, G, or T
Found at i:1521 original size:45 final size:45
Alignment explanation
Indices: 1471--1655 Score: 183
Period size: 45 Copynumber: 4.1 Consensus size: 45
1461 CTTACTTGAC
** * *
1471 CACCATCAATAGAAGATGGCCCCTGGTGTGGCCGGTTACCTCGAT
1 CACCATCGGTAGAAGATGGCCCCTGGTGTGGGCGGTTACCTCGAA
* * *
1516 CACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTGCCTCGAA
1 CACCATCGGTAGAAGATGGCCCCTGGTGTGGGCGGTTACCTCGAA
* * * * * ** * * * *
1561 CACCATCGGCACATGCTAGG-CCTTGGTGCAGGCAGTTGCCTTGAT
1 CACCATCGGTAGAAGAT-GGCCCCTGGTGTGGGCGGTTACCTCGAA
*
1606 CACCATCGGTAGAAGATGGCCCTTGGTGTGGGCGGTTACCTCGAA
1 CACCATCGGTAGAAGATGGCCCCTGGTGTGGGCGGTTACCTCGAA
1651 CACCA
1 CACCA
1656 ATGGCACATG
Statistics
Matches: 111, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
44 2 0.02
45 107 0.96
46 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.30, T:0.21
Consensus pattern (45 bp):
CACCATCGGTAGAAGATGGCCCCTGGTGTGGGCGGTTACCTCGAA
Found at i:1633 original size:135 final size:135
Alignment explanation
Indices: 1465--1729 Score: 352
Period size: 135 Copynumber: 2.0 Consensus size: 135
1455 CGGGCACTTA
* * *
1465 CTTGACCACCATCAATAGAAGATGGCCCCTGGTGTGGCCGGTTACCTCGATCACC-ATCGGTAGA
1 CTTGACCACCATCAATAGAAGATGGCCCCTGGTGTGGCCGGTTACCTCGAACACCAAT-GGCACA
* *
1529 AGATGGCCCCTAGTGCGGGCGGTTGCCTCGAACACCATCGGCACATGCTAGGCCTTGGTGCAGGC
65 AGATGGACCCTAGTGCGGGCGGTTGCCTCAAACACCATCGGCACATGCTAGGCCTTGGTGCAGGC
1594 AGTTGC
130 AGTTGC
* ** * * *
1600 CTTGATCACCATCGGTAGAAGATGGCCCTTGGTGTGGGCGGTTACCTCGAACACCAATGGCACAT
1 CTTGACCACCATCAATAGAAGATGGCCCCTGGTGTGGCCGGTTACCTCGAACACCAATGGCACAA
* * * * * * *
1665 GCTGGACCTTGGTGCGGGCGTTTGCCTCAAACACCATTGGCACATGTTGGGCCTTGGTGCAGGCA
66 GATGGACCCTAGTGCGGGCGGTTGCCTCAAACACCATCGGCACATGCTAGGCCTTGGTGCAGGCA
1730 CATGCTTCAA
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
135 109 0.98
136 2 0.02
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.22
Consensus pattern (135 bp):
CTTGACCACCATCAATAGAAGATGGCCCCTGGTGTGGCCGGTTACCTCGAACACCAATGGCACAA
GATGGACCCTAGTGCGGGCGGTTGCCTCAAACACCATCGGCACATGCTAGGCCTTGGTGCAGGCA
GTTGC
Found at i:1675 original size:45 final size:44
Alignment explanation
Indices: 1541--1724 Score: 190
Period size: 45 Copynumber: 4.1 Consensus size: 44
1531 ATGGCCCCTA
1541 GTGCGGGCGGTTGCCTCGAACACCATCGGCACATGCTAGGCCTTG
1 GTGCGGGCGGTTGCCTCGAACACCATCGGCACATGCT-GGCCTTG
* * * * * * * *
1586 GTGCAGGCAGTTGCCTTGATCACCATCGGTAGAAGATGGCCCTTG
1 GTGCGGGCGGTTGCCTCGAACACCATCGGCACATGCTGG-CCTTG
* *
1631 GTGTGGGCGGTTACCTCGAACACCAAT-GGCACATGCTGGACCTTG
1 GTGCGGGCGGTTGCCTCGAACACC-ATCGGCACATGCTGG-CCTTG
* * * *
1676 GTGCGGGCGTTTGCCTCAAACACCATTGGCACATGTTGGGCCTTG
1 GTGCGGGCGGTTGCCTCGAACACCATCGGCACATGCT-GGCCTTG
1721 GTGC
1 GTGC
1725 AGGCACATGC
Statistics
Matches: 111, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
44 4 0.04
45 103 0.93
46 4 0.04
ACGTcount: A:0.17, C:0.27, G:0.32, T:0.23
Consensus pattern (44 bp):
GTGCGGGCGGTTGCCTCGAACACCATCGGCACATGCTGGCCTTG
Found at i:1691 original size:90 final size:90
Alignment explanation
Indices: 1513--1679 Score: 266
Period size: 90 Copynumber: 1.9 Consensus size: 90
1503 CGGTTACCTC
*
1513 GATCACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTGCCTCGAACACCATCGGCACATGCT
1 GATCACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTACCTCGAACACCATCGGCACATGCT
1578 AGGCCTTGGTGCAGGCAGTTGCCTT
66 AGGCCTTGGTGCAGGCAGTTGCCTT
* * *
1603 GATCACCATCGGTAGAAGATGGCCCTTGGTGTGGGCGGTTACCTCGAACACCAAT-GGCACATGC
1 GATCACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTACCTCGAACACC-ATCGGCACATGC
1667 T-GGACCTTGGTGC
65 TAGG-CCTTGGTGC
1680 GGGCGTTTGC
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
89 2 0.03
90 67 0.94
91 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.31, T:0.22
Consensus pattern (90 bp):
GATCACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTACCTCGAACACCATCGGCACATGCT
AGGCCTTGGTGCAGGCAGTTGCCTT
Found at i:1700 original size:90 final size:90
Alignment explanation
Indices: 1516--1701 Score: 252
Period size: 90 Copynumber: 2.1 Consensus size: 90
1506 TTACCTCGAT
*
1516 CACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTGCCTCGAACACCATCGGCACATGCTAGG
1 CACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTACCTCGAACACCATCGGCACATGCTAGG
** *
1581 CCTTGGTGCAGGCAGTTGCCTTGAT
66 CCTTGGTGCAGGCAGTTGCCTCAAA
* * *
1606 CACCATCGGTAGAAGATGGCCCTTGGTGTGGGCGGTTACCTCGAACACCAAT-GGCACATGCT-G
1 CACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTACCTCGAACACC-ATCGGCACATGCTAG
*
1669 GACCTTGGTGCGGGC-GTTTGCCTCAAA
65 G-CCTTGGTGCAGGCAG-TTGCCTCAAA
1696 CACCAT
1 CACCAT
1702 TGGCACATGT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
89 3 0.04
90 80 0.94
91 2 0.02
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.22
Consensus pattern (90 bp):
CACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTACCTCGAACACCATCGGCACATGCTAGG
CCTTGGTGCAGGCAGTTGCCTCAAA
Found at i:1720 original size:90 final size:90
Alignment explanation
Indices: 1516--1723 Score: 224
Period size: 90 Copynumber: 2.3 Consensus size: 90
1506 TTACCTCGAT
* * * * * *
1516 CACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTGCCTCGAACACCATCGGCACATGCTAGG
1 CACCATCGGCACAAGATGGCCCTTGGTGTGGGCGGTTACCTCGAACACCATCGGCACATGCTAGG
** *
1581 CCTTGGTGCAGGCAGTTGCCTTGAT
66 CCTTGGTGCAGGCAGTTGCCTCAAA
* *
1606 CACCATCGGTAGAAGATGGCCCTTGGTGTGGGCGGTTACCTCGAACACCAAT-GGCACATGCT-G
1 CACCATCGGCACAAGATGGCCCTTGGTGTGGGCGGTTACCTCGAACACC-ATCGGCACATGCTAG
*
1669 GACCTTGGTGCGGGC-GTTTGCCTCAAA
65 G-CCTTGGTGCAGGCAG-TTGCCTCAAA
* * * *
1696 CACCATTGGCACATGTTGGGCCTTGGTG
1 CACCATCGGCACAAGATGGCCCTTGGTG
1724 CAGGCACATG
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
89 3 0.03
90 96 0.95
91 2 0.02
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.23
Consensus pattern (90 bp):
CACCATCGGCACAAGATGGCCCTTGGTGTGGGCGGTTACCTCGAACACCATCGGCACATGCTAGG
CCTTGGTGCAGGCAGTTGCCTCAAA
Found at i:1798 original size:68 final size:68
Alignment explanation
Indices: 1674--1802 Score: 168
Period size: 68 Copynumber: 1.9 Consensus size: 68
1664 TGCTGGACCT
* * * * *
1674 TGGTGCGGGCGTTTGCCTCAAACACCATTGGCACATGTTGGGCCTTGGTGCAGGCACATGCTTCA
1 TGGTGCGGGCGGTTGCCTCAAACACCATCGACACATGCTGGGCCTTGGTACAGGCACATGCTTCA
1739 AGC
66 AGC
* * * **
1742 TGGTGCGGGCGGTTGCCTCGACCACCATCGACACGTGCTGGGCCTTGGTATGGGCACATGC
1 TGGTGCGGGCGGTTGCCTCAAACACCATCGACACATGCTGGGCCTTGGTACAGGCACATGC
1803 CTTGACCATC
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 51 1.00
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.23
Consensus pattern (68 bp):
TGGTGCGGGCGGTTGCCTCAAACACCATCGACACATGCTGGGCCTTGGTACAGGCACATGCTTCA
AGC
Found at i:1929 original size:46 final size:45
Alignment explanation
Indices: 1849--1951 Score: 134
Period size: 46 Copynumber: 2.3 Consensus size: 45
1839 GGTGATTACA
* *
1849 TCGATCACCATCGGTAGAAGATGGCCTCTAGTGCAAGCGGTTGCC
1 TCGATCACCATCGGTACAAGATGGCCCCTAGTGCAAGCGGTTGCC
* * *
1894 TCGATCACCAATCTGTACAAGATGGCCCCTGGTGCAGGCGGTTGCC
1 TCGATCACC-ATCGGTACAAGATGGCCCCTAGTGCAAGCGGTTGCC
* *
1940 TCAAACACCATC
1 TCGATCACCATC
1952 AGCACATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 12 0.24
46 38 0.76
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.21
Consensus pattern (45 bp):
TCGATCACCATCGGTACAAGATGGCCCCTAGTGCAAGCGGTTGCC
Found at i:2089 original size:91 final size:91
Alignment explanation
Indices: 1918--2089 Score: 220
Period size: 91 Copynumber: 1.9 Consensus size: 91
1908 GTACAAGATG
* ** **
1918 GCCCCTGGTGCAGGCGGTTGCCTCAAACACCATCAGCACATGCTGGGCCTTGGTGTGGGTGGTTA
1 GCCCCTGGTGCAGGCAGTTGCCTCAAACACCATCAGCACATGCTGGGCCTTGGTACGGACGGTTA
* *
1983 CCTTGATCACTATCGGTTAGAAAATA
66 CCGTGATCACCATCGGTTAGAAAATA
** ** *
2009 GCCCCTGGTGTGGGCAGTTGCCTTGAACACCATCGGCACATGCTGGGCCTTGGTACGGACGGTTA
1 GCCCCTGGTGCAGGCAGTTGCCTCAAACACCATCAGCACATGCTGGGCCTTGGTACGGACGGTTA
2074 CCGTGAAT-ACCATCGG
66 CCGTG-ATCACCATCGG
2090 CAAGAGCTGG
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
91 66 0.97
92 2 0.03
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.24
Consensus pattern (91 bp):
GCCCCTGGTGCAGGCAGTTGCCTCAAACACCATCAGCACATGCTGGGCCTTGGTACGGACGGTTA
CCGTGATCACCATCGGTTAGAAAATA
Found at i:2139 original size:385 final size:383
Alignment explanation
Indices: 1503--2195 Score: 978
Period size: 385 Copynumber: 1.8 Consensus size: 383
1493 CTGGTGTGGC
* * *
1503 CGGTTACCTCGATCACCATCGGTAGAAGATGGCCCCTAGTGCGGGCGGTTGCCTCGAACACCATC
1 CGGTTACCTCGATCACCATCGGTACAAGATGGCCCCTAGTGCAGGCGGTTGCCTCAAACACCATC
* * * * *
1568 GGCACATGCTAGGCCTTGGTGCAGGCAGTTGCCTTGATCACCATCGGTAGAAGATGGCCCTTGGT
66 AGCACATGCTAGGCCTTGGTGCAGGCAGTTACCTTGATCACCATCGGTAGAAAATAGCCCCTGGT
* * * * *
1633 GTGGGCGGTTACCTCGAACACCAATGGCACATGCTGGACCTTGGTGCGGGCGTTTGCCTCAAACA
131 GTGGGCAGTTACCTCGAACACCAATGGCACATGCTGGACCTTGGTACGGACGGTTACCTCAAACA
* * * *
1698 CCATTGGCACATGTTGGGCCTTGGTGCAGGCACATGCTTCAAGCTGGTGCGGGCGGTTGCCTCGA
196 CCATCGGCACAAGCTGGGCCTTGGTGCAGGCACATGCCTCAAGCTGGTGCGGGCGGTTGCCTCGA
*
1763 CCACCATCGACACGTGCTGGGCCTTGGTATGGGCACATGCCTTGACCATCATTGGTAAAAGATGG
261 CCACCATCGACACATGCTGGGCCTTGGTATGGGCACATGCCTTGACCATCATTGGTAAAAGATGG
1828 CCCCTGGTATAGGTGATTACATCGATCACCATCGGTAGAAGATGGCCTCTAGTGCAAG
326 CCCCTGGTATAGGTGATTACATCGATCACCATCGGTAGAAGATGGCCTCTAGTGCAAG
* * *
1886 CGGTTGCCTCGATCACCAATCTGTACAAGATGGCCCCTGGTGCAGGCGGTTGCCTCAAACACCAT
1 CGGTTACCTCGATCACC-ATCGGTACAAGATGGCCCCTAGTGCAGGCGGTTGCCTCAAACACCAT
* ** ** *
1951 CAGCACATGCTGGGCCTTGGTGTGGGTGGTTACCTTGATCACTATCGGTTAGAAAATAGCCCCTG
65 CAGCACATGCTAGGCCTTGGTGCAGGCAGTTACCTTGATCACCATCGG-TAGAAAATAGCCCCTG
* * * *
2016 GTGTGGGCAGTTGCCTTGAACACC-ATCGGCACATGCTGGGCCTTGGTACGGACGGTTACCGT-G
129 GTGTGGGCAGTTACCTCGAACACCAAT-GGCACATGCTGGACCTTGGTACGGACGGTTACC-TCA
* * * *
2079 AATACCATCGGCA-AGAGCTGGGCCTTGGTGCAGGCACATGCCTCGAGTTGGTGTGGGCGGTTGC
192 AACACCATCGGCACA-AGCTGGGCCTTGGTGCAGGCACATGCCTCAAGCTGGTGCGGGCGGTTGC
* * *
2143 CTCGACCACCATTGGCACATGCTGGGCCTTGGTGTGGGCACATGCCTTGACCA
256 CTCGACCACCATCGACACATGCTGGGCCTTGGTATGGGCACATGCCTTGACCA
2196 CCATCGGCAC
Statistics
Matches: 267, Mismatches: 38, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
383 16 0.06
384 85 0.32
385 165 0.62
386 1 0.00
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.23
Consensus pattern (383 bp):
CGGTTACCTCGATCACCATCGGTACAAGATGGCCCCTAGTGCAGGCGGTTGCCTCAAACACCATC
AGCACATGCTAGGCCTTGGTGCAGGCAGTTACCTTGATCACCATCGGTAGAAAATAGCCCCTGGT
GTGGGCAGTTACCTCGAACACCAATGGCACATGCTGGACCTTGGTACGGACGGTTACCTCAAACA
CCATCGGCACAAGCTGGGCCTTGGTGCAGGCACATGCCTCAAGCTGGTGCGGGCGGTTGCCTCGA
CCACCATCGACACATGCTGGGCCTTGGTATGGGCACATGCCTTGACCATCATTGGTAAAAGATGG
CCCCTGGTATAGGTGATTACATCGATCACCATCGGTAGAAGATGGCCTCTAGTGCAAG
Found at i:2175 original size:45 final size:45
Alignment explanation
Indices: 2126--2250 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
2116 ATGCCTCGAG
** * * **
2126 TTGGTGTGGGCGGTTGCCTCGACCACCATTGGCACATG-CTGGGCC
1 TTGGTGTGGGCACTTGCCTCGACCACCATCGGCACAAGTC-GACCC
* *
2171 TTGGTGTGGGCACATGCCTTGACCACCATCGGCACAAGTCGACCC
1 TTGGTGTGGGCACTTGCCTCGACCACCATCGGCACAAGTCGACCC
* *
2216 TTGGTGTGGGCACTTGCCTCGATCACCGTCGGCAC
1 TTGGTGTGGGCACTTGCCTCGACCACCATCGGCAC
2251 GTGCCATGCC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 66 0.99
46 1 0.01
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.23
Consensus pattern (45 bp):
TTGGTGTGGGCACTTGCCTCGACCACCATCGGCACAAGTCGACCC
Found at i:8168 original size:27 final size:27
Alignment explanation
Indices: 8138--8193 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
8128 GTCTATCGAC
* *
8138 CTTTGTC-CCCATCCTTGGACTATTGGT
1 CTTTGTCTCCC-TCCATGGACTATCGGT
8165 CTTTGTCTCCCTCCATGGACTATCGGT
1 CTTTGTCTCCCTCCATGGACTATCGGT
8192 CT
1 CT
8194 CTGCCATCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.11, C:0.32, G:0.18, T:0.39
Consensus pattern (27 bp):
CTTTGTCTCCCTCCATGGACTATCGGT
Found at i:20558 original size:16 final size:16
Alignment explanation
Indices: 20537--20571 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20527 CATTCTCCGA
*
20537 GCTGATCGACAGATTG
1 GCTGATCGACAGACTG
20553 GCTGATCGACAGACTG
1 GCTGATCGACAGACTG
20569 GCT
1 GCT
20572 CTTGCCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (16 bp):
GCTGATCGACAGACTG
Found at i:27805 original size:24 final size:24
Alignment explanation
Indices: 27773--27826 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
27763 GCCTCCAGGC
27773 TGGCCTACAAGCTATGCGGGCATT
1 TGGCCTACAAGCTATGCGGGCATT
27797 TGGCCTACAAGCTATGCGGGCATT
1 TGGCCTACAAGCTATGCGGGCATT
27821 TGGCCT
1 TGGCCT
27827 TGTCACCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (24 bp):
TGGCCTACAAGCTATGCGGGCATT
Found at i:44145 original size:22 final size:22
Alignment explanation
Indices: 44117--44194 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
44107 ACCAGGGGCT
* * * *
44117 AGCATGTGCCAATGGTAGTCAA
1 AGCATGTGTCGATGGTGGTCGA
44139 AGCATGTGTCGATGGTGGTCGA
1 AGCATGTGTCGATGGTGGTCGA
*
44161 CGCATGTGTCGATGGTGGTCGA
1 AGCATGTGTCGATGGTGGTCGA
44183 AGCATGTGTCGA
1 AGCATGTGTCGA
44195 GACCAAGGGC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.26
Consensus pattern (22 bp):
AGCATGTGTCGATGGTGGTCGA
Done.