Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167976.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_234, 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: 45432
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Found at i:8808 original size:45 final size:45
Alignment explanation
Indices: 8758--8862 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
8748 AAAGTAGCTT
*
8758 ATGCCAATGATGGTCGAGACATGTGCCCGAACCATGCACCAACAC
1 ATGCCAATGATGGTAGAGACATGTGCCCGAACCATGCACCAACAC
* * * * * * *
8803 GTGCCAATGATGGTAGAGGCATGTGCTCGCACTATGCACTAACAT
1 ATGCCAATGATGGTAGAGACATGTGCCCGAACCATGCACCAACAC
*
8848 ATGCCATTGATGGTA
1 ATGCCAATGATGGTA
8863 AGTCCTTGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (45 bp):
ATGCCAATGATGGTAGAGACATGTGCCCGAACCATGCACCAACAC
Found at i:18876 original size:45 final size:45
Alignment explanation
Indices: 18818--18907 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
18808 TGTGCCAATT
18818 GTGGTCGAGGCAAGTGCCCATACCAAAGGCCAGCTTGTGTCGATG
1 GTGGTCGAGGCAAGTGCCCATACCAAAGGCCAGCTTGTGTCGATG
* * *
18863 GTGGTTGATGCAAGTGCTCATACCAAAGGCCAGCTTGTGTCGATG
1 GTGGTCGAGGCAAGTGCCCATACCAAAGGCCAGCTTGTGTCGATG
18908 ATAGTCAAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.23
Consensus pattern (45 bp):
GTGGTCGAGGCAAGTGCCCATACCAAAGGCCAGCTTGTGTCGATG
Found at i:18926 original size:45 final size:45
Alignment explanation
Indices: 18825--18932 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
18815 ATTGTGGTCG
* * * **
18825 AGGCAAGTGCCCATACCAAAGGCCAGCTTGTGTCGATGGTGGTTG
1 AGGCAAGTGCTCATACCAAAGGCCAGCTTGTGTCGATGATAGTCA
*
18870 ATGCAAGTGCTCATACCAAAGGCCAGCTTGTGTCGATGATAGTCA
1 AGGCAAGTGCTCATACCAAAGGCCAGCTTGTGTCGATGATAGTCA
*
18915 AGGCATA-TGCTCGTACCA
1 AGGCA-AGTGCTCATACCA
18933 TGTGCCAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 53 0.98
46 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (45 bp):
AGGCAAGTGCTCATACCAAAGGCCAGCTTGTGTCGATGATAGTCA
Found at i:40082 original size:28 final size:29
Alignment explanation
Indices: 40050--40122 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 29
40040 TTTCATTCTT
*
40050 TTTTTATTATTATTATATAATTTTG-TTA
1 TTTTTATTATTATTATATAATTCTGTTTA
* *
40078 TTTTTTTTATTATTATATAGTTCTGTTTA
1 TTTTTATTATTATTATATAATTCTGTTTA
* *
40107 TTATTATTATTGTTAT
1 TTTTTATTATTATTAT
40123 TATTAATCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.25, C:0.01, G:0.05, T:0.68
Consensus pattern (29 bp):
TTTTTATTATTATTATATAATTCTGTTTA
Found at i:40453 original size:19 final size:21
Alignment explanation
Indices: 40408--40446 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40398 AATAAAAGGG
40408 AACAAACACAATAAAAAAAAT
1 AACAAACACAATAAAAAAAAT
40429 AACAAACACAA-AAAAAAA
1 AACAAACACAATAAAAAAA
40447 TTTCAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.05
Consensus pattern (21 bp):
AACAAACACAATAAAAAAAAT
Found at i:40931 original size:25 final size:25
Alignment explanation
Indices: 40903--40964 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
40893 TAGGTTTTTC
* *
40903 TTTTTCTTTTT-ATTTTCCATTTTGA
1 TTTTTATTTTTAATTTT-CATGTTGA
* *
40928 TTTTGATTTTTAATTTTTATGTTGA
1 TTTTTATTTTTAATTTTCATGTTGA
40953 TTTTTATGTTTT
1 TTTTTAT-TTTT
40965 TTTTTATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 21 0.70
26 9 0.30
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.73
Consensus pattern (25 bp):
TTTTTATTTTTAATTTTCATGTTGA
Found at i:40943 original size:19 final size:19
Alignment explanation
Indices: 40921--40958 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40911 TTTATTTTCC
*
40921 ATTTTGATTTTGATTTTTA
1 ATTTTGATGTTGATTTTTA
*
40940 ATTTTTATGTTGATTTTTA
1 ATTTTGATGTTGATTTTTA
40959 TGTTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (19 bp):
ATTTTGATGTTGATTTTTA
Found at i:40981 original size:19 final size:19
Alignment explanation
Indices: 40959--40995 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40949 TTGATTTTTA
* *
40959 TGTTTTTTTTTATTATTAT
1 TGTTATTTTATATTATTAT
40978 TGTTATTTTATATTATTA
1 TGTTATTTTATATTATTA
40996 CTAGTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (19 bp):
TGTTATTTTATATTATTAT
Done.