Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168482.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_80, 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: 113083
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.29
Warning! 3000 characters in sequence are not A, C, G, or T
Found at i:18160 original size:43 final size:44
Alignment explanation
Indices: 18112--18220 Score: 152
Period size: 44 Copynumber: 2.5 Consensus size: 44
18102 ACTAATGCTG
*
18112 ATCGAGGCATATGCTCGCACAA-GTCTAGATTATGCCAATGTTA
1 ATCGAGGCATGTGCTCGCACAAGGTCTAGATTATGCCAATGTTA
*
18155 ATCGAGGCATGTGC-C-CACAATAGGTCTAGATTATGCCAATGTTG
1 ATCGAGGCATGTGCTCGCAC-A-AGGTCTAGATTATGCCAATGTTA
*
18199 ATCAAGGCATGTGCTCGCACAA
1 ATCGAGGCATGTGCTCGCACAA
18221 AGGGCCAACA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
41 3 0.05
42 2 0.03
43 14 0.24
44 34 0.59
45 2 0.03
46 3 0.05
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (44 bp):
ATCGAGGCATGTGCTCGCACAAGGTCTAGATTATGCCAATGTTA
Found at i:18241 original size:45 final size:44
Alignment explanation
Indices: 18142--18243 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
18132 AAGTCTAGAT
* * * * *
18142 TATGCCAATGTTAATCGAGGCATGTGCCCACAATAGGTCTAGAT
1 TATGCCAATGTTGATCAAGGCATGTGCCCACAATAGGGCCAGAA
18186 TATGCCAATGTTGATCAAGGCATGTGCTCGCACAA-AGGGCCA-ACA
1 TATGCCAATGTTGATCAAGGCATGTGC-C-CACAATAGGGCCAGA-A
18231 TATGCCAATGTTG
1 TATGCCAATGTTG
18244 GTTGAGGCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
44 26 0.52
45 19 0.38
46 5 0.10
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (44 bp):
TATGCCAATGTTGATCAAGGCATGTGCCCACAATAGGGCCAGAA
Found at i:18269 original size:45 final size:45
Alignment explanation
Indices: 18220--18333 Score: 111
Period size: 45 Copynumber: 2.5 Consensus size: 45
18210 TGCTCGCACA
* ** *
18220 AAGGGCCAACATATGCCAATGTTGGTTGAGGCAAATGCCCATACC
1 AAGGGCCAACATATGCCAATGATGGTCAAGCCAAATGCCCATACC
* * * * *
18265 AAGGGCCAGCTTATGCCGATGATGGTCAAGCCAAGTGTCCATACC
1 AAGGGCCAACATATGCCAATGATGGTCAAGCCAAATGCCCATACC
* * * *
18310 AAAGGCCAACTTGTGCTAATGATG
1 AAGGGCCAACATATGCCAATGATG
18334 TTTAAAGCCT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (45 bp):
AAGGGCCAACATATGCCAATGATGGTCAAGCCAAATGCCCATACC
Found at i:32697 original size:45 final size:45
Alignment explanation
Indices: 32612--32709 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
32602 TAGCACAAGT
* * ** *
32612 TGGCCTTTGGTATGGACACTTGGCTTGACCATCATCGGCATAAGC
1 TGGCCCTTGGTATGGACACTTGCCTCAACCAACATCGGCATAAGC
* * * * *
32657 TGGCCCTTGGTATGGGCATTTGCCTCAACCAACATTGGCATATGT
1 TGGCCCTTGGTATGGACACTTGCCTCAACCAACATCGGCATAAGC
32702 TGGCCCTT
1 TGGCCCTT
32710 TGTGCGAGCA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (45 bp):
TGGCCCTTGGTATGGACACTTGCCTCAACCAACATCGGCATAAGC
Found at i:64304 original size:36 final size:36
Alignment explanation
Indices: 64190--64306 Score: 155
Period size: 36 Copynumber: 3.2 Consensus size: 36
64180 CACCATTAAT
*
64190 AGATGCTAGCCTATTGTTGCCTCAGACACCACCAGT
1 AGATGCTAGCCTATTGTTGCCTCAGACACCACCAGC
64226 AGATGCTAGCCTATTGTTGCCTCAGACACCACCAGC
1 AGATGCTAGCCTATTGTTGCCTCAGACACCACCAGC
* * * * * *
64262 ATATGCTAGCCCATTATTACCTTAGACACC-CTTAGC
1 AGATGCTAGCCTATTGTTGCCTCAGACACCAC-CAGC
64298 AGATGCTAG
1 AGATGCTAG
64307 TGTCATTGGT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
35 1 0.01
36 71 0.99
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (36 bp):
AGATGCTAGCCTATTGTTGCCTCAGACACCACCAGC
Found at i:70932 original size:13 final size:13
Alignment explanation
Indices: 70914--70946 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
70904 ATATCTCAAG
70914 GCCTCATCCTTTA
1 GCCTCATCCTTTA
70927 GCCTCATCCTTTA
1 GCCTCATCCTTTA
70940 GCCTCAT
1 GCCTCAT
70947 TCTAGGTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.39, G:0.09, T:0.36
Consensus pattern (13 bp):
GCCTCATCCTTTA
Found at i:82002 original size:36 final size:36
Alignment explanation
Indices: 81962--82064 Score: 134
Period size: 36 Copynumber: 2.9 Consensus size: 36
81952 ACACCATTAA
81962 TAGATGCTAGCCTATTGTTGCCTTAGACACCACCAG
1 TAGATGCTAGCCTATTGTTGCCTTAGACACCACCAG
* *
81998 TAGATGCTAGCCTATTGTTGCCTCAGACACCACTAG
1 TAGATGCTAGCCTATTGTTGCCTTAGACACCACCAG
* * * * * *
82034 CATATGCTGGCCCATTATTACCTTAGACACC
1 TAGATGCTAGCCTATTGTTGCCTTAGACACC
82065 CTTAGCAGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.28
Consensus pattern (36 bp):
TAGATGCTAGCCTATTGTTGCCTTAGACACCACCAG
Found at i:111109 original size:45 final size:44
Alignment explanation
Indices: 111060--111222 Score: 137
Period size: 45 Copynumber: 3.6 Consensus size: 44
111050 CATTATCGAG
*
111060 GGCACTTACCTTAACCACCATTGGCACAAGCTAGCTCTTGGTATA
1 GGCACTTACCTCAACCACCATTGGCACAAGCTAGC-CTTGGTATA
* * * *
111105 GGCACTTGCCTCAACCACCATTAGCACATGCTAGCCGTTGGTGTA
1 GGCACTTACCTCAACCACCATTGGCACAAGCTAGCC-TTGGTATA
* * * * ** * * *
111150 GGCACATGCCTCAATCAACATTGGCTGAAGATGGCCCTTGGTATG
1 GGCACTTACCTCAACCACCATTGGCACAAGCTAG-CCTTGGTATA
* * * *
111195 GGTAGTTACCTTAAACACCATTGGCACA
1 GGCACTTACCTCAACCACCATTGGCACA
111223 TGCTGGCCCT
Statistics
Matches: 91, Mismatches: 25, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
44 1 0.01
45 88 0.97
46 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (44 bp):
GGCACTTACCTCAACCACCATTGGCACAAGCTAGCCTTGGTATA
Done.