Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168246.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_478, 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: 25518
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:1641 original size:21 final size:20
Alignment explanation
Indices: 1617--1656 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1607 TCTATGAGAT
1617 TATGCATGAGAATGAATGCAA
1 TATGCATGA-AATGAATGCAA
*
1638 TATGCATGAAATGCATGCA
1 TATGCATGAAATGAATGCA
1657 TACACAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (20 bp):
TATGCATGAAATGAATGCAA
Found at i:2824 original size:20 final size:21
Alignment explanation
Indices: 2781--2825 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2771 TTAAAAGATA
*
2781 AAAATTATTTTTGTTTATTTG
1 AAAATTATATTTGTTTATTTG
2802 AAAATATATATTT-TTTA-TTG
1 AAAAT-TATATTTGTTTATTTG
2822 AAAA
1 AAAA
2826 GATTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
AAAATTATATTTGTTTATTTG
Found at i:2833 original size:15 final size:14
Alignment explanation
Indices: 2813--2846 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2803 AAATATATAT
2813 TTTTTATTGAAAAGA
1 TTTTTATT-AAAAGA
*
2828 TTTTTATTTAAAGA
1 TTTTTATTAAAAGA
2842 TTTTT
1 TTTTT
2847 TATTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (14 bp):
TTTTTATTAAAAGA
Found at i:2847 original size:15 final size:15
Alignment explanation
Indices: 2811--2851 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2801 GAAAATATAT
*
2811 ATTTTTTATTGAAAAG
1 ATTTTTTATT-TAAAG
2827 A-TTTTTATTTAAAG
1 ATTTTTTATTTAAAG
2841 ATTTTTTATTT
1 ATTTTTTATTT
2852 TTTATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 17 0.74
16 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (15 bp):
ATTTTTTATTTAAAG
Found at i:2912 original size:19 final size:20
Alignment explanation
Indices: 2869--2910 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2859 TTTTGAAAAC
2869 TTTATTTACAAAGATTTTTT
1 TTTATTTACAAAGATTTTTT
2889 TTTATTTGA-AAAGATTTTTT
1 TTTATTT-ACAAAGATTTTTT
2909 TT
1 TT
2911 ATACTCGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (20 bp):
TTTATTTACAAAGATTTTTT
Found at i:3679 original size:22 final size:21
Alignment explanation
Indices: 3627--3683 Score: 89
Period size: 20 Copynumber: 2.7 Consensus size: 21
3617 AATCAAAAGA
3627 TATTTTTTGTATTCATAATAT
1 TATTTTTTGTATTCATAATAT
*
3648 T-TGTTTTGTATTCATAATATT
1 TATTTTTTGTATTCATAATA-T
3669 TATTTTTTGTATTCA
1 TATTTTTTGTATTCA
3684 ATTTTAACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 17 0.53
21 3 0.09
22 12 0.38
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.63
Consensus pattern (21 bp):
TATTTTTTGTATTCATAATAT
Found at i:5223 original size:4 final size:4
Alignment explanation
Indices: 5214--5239 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5204 GTGTATAACC
5214 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
5240 CGATAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:9981 original size:2 final size:2
Alignment explanation
Indices: 9974--10002 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9964 ATGTAATACC
9974 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10003 GTTAGATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10824 original size:30 final size:30
Alignment explanation
Indices: 10790--10860 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
10780 AAAATTTAAG
10790 ATAAAATTTTTTGAATGTTCAAAATCTTAC
1 ATAAAATTTTTTGAATGTTCAAAATCTTAC
* ** * * **
10820 ATAAAGTTACTTGAATTTTTAATGTCTTAC
1 ATAAAATTTTTTGAATGTTCAAAATCTTAC
10850 AT-AAATTTTTT
1 ATAAAATTTTTT
10861 AAAAAGATAA
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.48
Consensus pattern (30 bp):
ATAAAATTTTTTGAATGTTCAAAATCTTAC
Found at i:11034 original size:7 final size:7
Alignment explanation
Indices: 11022--11053 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
11012 AAAAAAATAA
11022 ATTTCAT
1 ATTTCAT
11029 ATTTCAT
1 ATTTCAT
11036 ATTTCAT
1 ATTTCAT
11043 ATTTCAT
1 ATTTCAT
11050 ATTT
1 ATTT
11054 TAGAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTCAT
Found at i:11640 original size:56 final size:55
Alignment explanation
Indices: 11480--11640 Score: 171
Period size: 55 Copynumber: 2.9 Consensus size: 55
11470 TATAGACTTG
* * * ** *
11480 TAATTTTTTTACCTATATTGACATTTAAAGCCCGTCAGTATAGATTTGTATGTTT
1 TAATTTTTTTACCTATATCGACAGTTAATGCCTATCAGTATAGATTTATATGTTT
* * * * * * * *
11535 TAATTTTTTCACCTAGACCGA-AGGCTAGTGCCTATTAGTATAAAATTATATGTTT
1 TAATTTTTTTACCTATATCGACA-GTTAATGCCTATCAGTATAGATTTATATGTTT
11590 TAATTTTTTTGACCTATATCGACAGTTAATGCCTATCAGTATAGATTTATA
1 TAATTTTTTT-ACCTATATCGACAGTTAATGCCTATCAGTATAGATTTATA
11641 ATTTTTCTTA
Statistics
Matches: 81, Mismatches: 22, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
54 1 0.01
55 48 0.59
56 31 0.38
57 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (55 bp):
TAATTTTTTTACCTATATCGACAGTTAATGCCTATCAGTATAGATTTATATGTTT
Found at i:11702 original size:159 final size:158
Alignment explanation
Indices: 11406--11709 Score: 364
Period size: 159 Copynumber: 1.9 Consensus size: 158
11396 ACGGTTAACA
* * * * *
11406 CCTATCAGTATAGACTTATATGTTTTAGTTTTTCTTGCCTATACTGACGGTTAATGCTCGTCAGT
1 CCTATCAGTATAAAATTATATGTTTTAATTTTTCTTGCCTATACTGACAGTTAATGCTCATCAGT
* ** * * * *
11471 ATAGACTTGTAATTTTTTTACCTATATTGACATTTAAAGCCCGTCAGTATAGATTTGTATGTTTT
66 ATAGACTTATAATTTTTTTACCTATACCGACATTT-AAGCCCATCAGTACAAACTTGTATGTTTT
11536 AATTTTTTCACCTAGACCGAAGGCTAGTG
130 AATTTTTTCACCTAGACCGAAGGCTAGTG
*
11565 CCTATTAGTATAAAATTATATGTTTTAATTTTT-TTGACCTATA-TCGACAGTTAATGC-CTATC
1 CCTATCAGTATAAAATTATATGTTTTAATTTTTCTTG-CCTATACT-GACAGTTAATGCTC-ATC
* *
11627 AGTATAGATTTATAATTTTTCTTACCTATACCGACGTTT-AGCATCCATCAGTACAAACTTGTAT
63 AGTATAGACTTATAATTTTT-TTACCTATACCGACATTTAAGC--CCATCAGTACAAACTTGTAT
* *
11691 TTTTTAATTTTTTTACCTA
125 GTTTTAATTTTTTCACCTA
11710 TACCAACGGT
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
158 8 0.07
159 66 0.54
160 48 0.39
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (158 bp):
CCTATCAGTATAAAATTATATGTTTTAATTTTTCTTGCCTATACTGACAGTTAATGCTCATCAGT
ATAGACTTATAATTTTTTTACCTATACCGACATTTAAGCCCATCAGTACAAACTTGTATGTTTTA
ATTTTTTCACCTAGACCGAAGGCTAGTG
Found at i:11744 original size:55 final size:55
Alignment explanation
Indices: 11639--11813 Score: 165
Period size: 55 Copynumber: 3.2 Consensus size: 55
11629 TATAGATTTA
* * * * * *
11639 TAATTTTTCTTACCTATACCGACGTTTAG-CATCCATCAGTACA-AACTTGTATTTTT
1 TAATTTTT-TTACCTATACCAACGGTTAGAGAT-TATCAGTATAGAA-TTGTATGTTT
* * * *
11695 TAATTTTTTTACCTATACCAACGGTTAGAGATTGTCGGTATATAATTGTATGCTT
1 TAATTTTTTTACCTATACCAACGGTTAGAGATTATCAGTATAGAATTGTATGTTT
* * ** * *
11750 TAATTTTCTTACTTATACCAATTGTTAGAGATTATCAGTATAGACTTATATGTTT
1 TAATTTTTTTACCTATACCAACGGTTAGAGATTATCAGTATAGAATTGTATGTTT
11805 TAATTTTTT
1 TAATTTTTT
11814 ATTATATTTT
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
55 85 0.88
56 12 0.12
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.46
Consensus pattern (55 bp):
TAATTTTTTTACCTATACCAACGGTTAGAGATTATCAGTATAGAATTGTATGTTT
Found at i:12045 original size:22 final size:22
Alignment explanation
Indices: 12022--12062 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
12012 AATAGCATTA
12022 AAACTACTTA-AAACTACAAGT
1 AAACTACTTATAAACTACAAGT
* *
12043 AAATTACTTATAATCTACAA
1 AAACTACTTATAAACTACAA
12063 ACTTAGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.29
Consensus pattern (22 bp):
AAACTACTTATAAACTACAAGT
Found at i:12124 original size:15 final size:15
Alignment explanation
Indices: 12104--12132 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12094 TACCAACTCT
12104 GATAAAACAAACATC
1 GATAAAACAAACATC
12119 GATAAAACAAACAT
1 GATAAAACAAACAT
12133 AAATAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.17, G:0.07, T:0.14
Consensus pattern (15 bp):
GATAAAACAAACATC
Found at i:12138 original size:15 final size:15
Alignment explanation
Indices: 12105--12140 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12095 ACCAACTCTG
**
12105 ATAAAACAAACATCG
1 ATAAAACAAACATAA
12120 ATAAAACAAACATAA
1 ATAAAACAAACATAA
12135 ATAAAA
1 ATAAAA
12141 AGTTACACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.69, C:0.14, G:0.03, T:0.14
Consensus pattern (15 bp):
ATAAAACAAACATAA
Found at i:20397 original size:109 final size:107
Alignment explanation
Indices: 20154--20414 Score: 285
Period size: 109 Copynumber: 2.4 Consensus size: 107
20144 ATTTATGAGA
* * * *
20154 AGATTATTGAAGGCGTTTTTGCCCAAAAAATACCTTGAATAATCTCTAACAAATATTGAATAGGG
1 AGATTATTGAAGGCGTTTTTGACC-AAAAATACCTTGAATAATCCCTAACAAATATTGAAGAGAG
* * * *
20219 TTATTGAAGGTATTTTTGGCCAAAAAAGCCTTGAATAATTCCT
65 TTATTGAAAGCATTTCTAGCCAAAAAAGCCTTGAATAATTCCT
* * *
20262 GGATTATTGAAGGCATTTTTGACCAAAAATGCCTTGGAATAATCCCTAACAAAATATTGAACGA-
1 AGATTATTGAAGGCGTTTTTGACCAAAAATACCTT-GAATAATCCCTAAC-AAATATTGAA-GAG
* *
20326 AGTTATTGAAAGCGTTTCTAGCCAAAAATA-TCTTGAATAATTCCT
63 AGTTATTGAAAGCATTTCTAGCCAAAAA-AGCCTTGAATAATTCCT
* * * * * *
20371 AGATTATTAAAGGTGTCTTTGGCC-AAAACACCTTCAATAATCCC
1 AGATTATTGAAGGCGTTTTTGACCAAAAATACCTTGAATAATCCC
20415 CTCCAATTTT
Statistics
Matches: 127, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
107 19 0.15
108 42 0.33
109 64 0.50
110 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (107 bp):
AGATTATTGAAGGCGTTTTTGACCAAAAATACCTTGAATAATCCCTAACAAATATTGAAGAGAGT
TATTGAAAGCATTTCTAGCCAAAAAAGCCTTGAATAATTCCT
Found at i:23098 original size:17 final size:17
Alignment explanation
Indices: 23076--23108 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
23066 TTTGTTGACC
23076 CAAATTTCATTAGTGAA
1 CAAATTTCATTAGTGAA
23093 CAAATTTCATTAGTGA
1 CAAATTTCATTAGTGA
23109 GTTAATGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
CAAATTTCATTAGTGAA
Found at i:23965 original size:24 final size:25
Alignment explanation
Indices: 23933--23979 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
23923 TAGATTGGGG
*
23933 TATTGGTTTAATAT-TATTGGTATC
1 TATTGGTTTAATATGAATTGGTATC
* *
23957 TATTTGTTTTATATGAATTGGTA
1 TATTGGTTTAATATGAATTGGTA
23980 GCTTATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.55
Consensus pattern (25 bp):
TATTGGTTTAATATGAATTGGTATC
Done.