Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167980.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_238, 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: 44700
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:373 original size:25 final size:24
Alignment explanation
Indices: 317--378 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
307 TGTTTTGACT
* *
317 TTATATT-TTT-TATTTATTTATG
1 TTATATTGTTTATTTTTATTTATC
*
339 TTATTTTGTTTATTTTTATTTACTC
1 TTATATTGTTTATTTTTATTTA-TC
364 TTATATTG-TTATTTT
1 TTATATTGTTTATTTT
379 AAATTGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 6 0.18
23 3 0.09
24 16 0.48
25 8 0.24
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.73
Consensus pattern (24 bp):
TTATATTGTTTATTTTTATTTATC
Found at i:4240 original size:42 final size:41
Alignment explanation
Indices: 4178--4261 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 41
4168 AACACAGTAT
* * *
4178 TTTCAATTGGAACTGTTCTTTCTCGTATAATAGTGTTTATA
1 TTTCAATCGGAACCGTTCTTTCTCATATAATAGTGTTTATA
4219 TTTCAATCGGAACCGTTTCTTTCTCATATAATAGTGTTTATA
1 TTTCAATCGGAACCG-TTCTTTCTCATATAATAGTGTTTATA
4261 T
1 T
4262 AAAGAAGCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 13 0.33
42 26 0.67
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (41 bp):
TTTCAATCGGAACCGTTCTTTCTCATATAATAGTGTTTATA
Found at i:4657 original size:22 final size:22
Alignment explanation
Indices: 4623--4670 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
4613 GAAATATATT
4623 AATTTTAATTTATCTAA-AATAA
1 AATTTTAATTTATCTAATAA-AA
*
4645 AATTTT-ATATTATTTAATAAAA
1 AATTTTAAT-TTATCTAATAAAA
4667 AATT
1 AATT
4671 ATTTAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 2 0.09
22 19 0.83
23 2 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTTTAATTTATCTAATAAAA
Found at i:6755 original size:9 final size:9
Alignment explanation
Indices: 6718--6756 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
6708 TCTTATTTAT
*
6718 TTTTATCTT
1 TTTTATCTC
6727 TTTTATCTC
1 TTTTATCTC
6736 TTTTTATTCTC
1 -TTTTA-TCTC
6747 TTTTATCTC
1 TTTTATCTC
6756 T
1 T
6757 CTCTTTTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 13 0.48
10 10 0.37
11 4 0.15
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATCTC
Found at i:6758 original size:11 final size:10
Alignment explanation
Indices: 6717--6756 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
6707 TTCTTATTTA
6717 TTTTTATCT-
1 TTTTTATCTC
6726 TTTTTATCTC
1 TTTTTATCTC
6736 TTTTTAT-TC
1 TTTTTATCTC
6745 TCTTTTATCTC
1 T-TTTTATCTC
6756 T
1 T
6757 CTCTTTTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 12 0.43
10 13 0.46
11 3 0.11
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTATCTC
Found at i:7748 original size:30 final size:30
Alignment explanation
Indices: 7712--7770 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
7702 GTTTAGATAT
7712 AAACCAAATATGATATAAAATGATTATTAC
1 AAACCAAATATGATATAAAATGATTATTAC
7742 AAACCAAATATGATATAAAATGATTATTA
1 AAACCAAATATGATATAAAATGATTATTA
7771 TCCTATCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.54, C:0.08, G:0.07, T:0.31
Consensus pattern (30 bp):
AAACCAAATATGATATAAAATGATTATTAC
Found at i:10751 original size:27 final size:27
Alignment explanation
Indices: 10721--10777 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
10711 AACTTAATTG
10721 AATGTGGGCAAACATCATTTAATACTA
1 AATGTGGGCAAACATCATTTAATACTA
*
10748 AATGTGGGCTAACATCATTTAATACTA
1 AATGTGGGCAAACATCATTTAATACTA
10775 AAT
1 AAT
10778 ACCTTGATCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (27 bp):
AATGTGGGCAAACATCATTTAATACTA
Found at i:13067 original size:32 final size:32
Alignment explanation
Indices: 13026--13090 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
13016 AGGTTTAACC
13026 AAGTAATAACCTAACTTGCATAACAAGAAATA
1 AAGTAATAACCTAACTTGCATAACAAGAAATA
13058 AAGTAATAACCTAACTTGCATAACAAGAAATA
1 AAGTAATAACCTAACTTGCATAACAAGAAATA
13090 A
1 A
13091 TTTAGCTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.54, C:0.15, G:0.09, T:0.22
Consensus pattern (32 bp):
AAGTAATAACCTAACTTGCATAACAAGAAATA
Found at i:15974 original size:23 final size:25
Alignment explanation
Indices: 15947--16011 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 25
15937 CTGTTTGACT
*
15947 TTATTTTTCTTATTTTAT-TTA-TG
1 TTATTTTTCTTATTTTATATTACTC
15970 TTATTTTGT-TTATTTT-TATTACTC
1 TTATTTT-TCTTATTTTATATTACTC
15994 TTATTATTTCTTATTTTA
1 TTATT-TTTCTTATTTTA
16012 AATTGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 1 0.03
23 17 0.49
24 8 0.23
25 9 0.26
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.72
Consensus pattern (25 bp):
TTATTTTTCTTATTTTATATTACTC
Found at i:22868 original size:22 final size:22
Alignment explanation
Indices: 22834--22897 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 22
22824 GAAATATATT
22834 AATTTTA-ATTTATCTAAAATAA
1 AATTTTATA-TTATCTAAAATAA
*
22856 AATTTTATATTAT-T-TAATAA
1 AATTTTATATTATCTAAAATAA
*
22876 AAATTTAT-TTA-CTAAATATAA
1 AATTTTATATTATCTAAA-ATAA
22897 A
1 A
22898 TATAAGATGC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
19 4 0.11
20 13 0.37
21 6 0.17
22 11 0.31
23 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTTTATATTATCTAAAATAA
Found at i:23410 original size:6 final size:7
Alignment explanation
Indices: 23389--23413 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
23379 TTTACTATTT
23389 AATTAAA
1 AATTAAA
23396 AATTAAA
1 AATTAAA
23403 AATTAAA
1 AATTAAA
23410 AATT
1 AATT
23414 TATCCTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:24974 original size:20 final size:19
Alignment explanation
Indices: 24941--24985 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
24931 TTCTTATTTA
*
24941 TTTTTATCTTTTTTATCTC
1 TTTTTATCTCTTTTATCTC
24960 TTTTTATTCTCTTTTATCTC
1 TTTTTA-TCTCTTTTATCTC
24980 TCTTTT
1 T-TTTT
24986 CACCCTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 13 0.57
21 4 0.17
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTATCTCTTTTATCTC
Found at i:24979 original size:9 final size:9
Alignment explanation
Indices: 24942--24980 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
24932 TCTTATTTAT
*
24942 TTTTATCTT
1 TTTTATCTC
24951 TTTTATCTC
1 TTTTATCTC
24960 TTTTTATTCTC
1 -TTTTA-TCTC
24971 TTTTATCTC
1 TTTTATCTC
24980 T
1 T
24981 CTTTTCACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 13 0.48
10 10 0.37
11 4 0.15
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATCTC
Found at i:29081 original size:26 final size:24
Alignment explanation
Indices: 29052--29099 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
29042 AACTTAATTG
29052 AATGTGGGCAAACATCATTTAATAAT
1 AATGTGGG-AAA-ATCATTTAATAAT
*
29078 AATGTGGGATAATCATTTAATA
1 AATGTGGGAAAATCATTTAATA
29100 CTAAATACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 2 0.10
26 8 0.38
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (24 bp):
AATGTGGGAAAATCATTTAATAAT
Found at i:34181 original size:23 final size:24
Alignment explanation
Indices: 34155--34220 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 24
34145 TGTTTTGACT
*
34155 TTATTTTTCTTATTTTATTTA-TG
1 TTATTTTTCTTATTTTATTTACTC
34178 TTATTTTGT-TTATTTTTATTTACTC
1 TTATTTT-TCTTA-TTTTATTTACTC
34203 TTATTATTTCTTATTTTA
1 TTATT-TTTCTTATTTTA
34221 AATTGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 10 0.27
24 10 0.27
25 12 0.32
26 5 0.14
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (24 bp):
TTATTTTTCTTATTTTATTTACTC
Found at i:40652 original size:42 final size:41
Alignment explanation
Indices: 40590--40673 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 41
40580 AACACAGTAT
* * *
40590 TTTCAATTGGAACTGTTCTTTCTCGTATAATAGTGTTTATA
1 TTTCAATCGGAACCGTTCTTTCTCATATAATAGTGTTTATA
40631 TTTCAATCGGAACCGTTTCTTTCTCATATAATAGTGTTTATA
1 TTTCAATCGGAACCG-TTCTTTCTCATATAATAGTGTTTATA
40673 T
1 T
40674 AAAGAAGCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 13 0.33
42 26 0.67
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (41 bp):
TTTCAATCGGAACCGTTCTTTCTCATATAATAGTGTTTATA
Found at i:41059 original size:21 final size:21
Alignment explanation
Indices: 41035--41096 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
41025 GAAATATATT
41035 AATTTTAATTATCTAAAATAA
1 AATTTTAATTATCTAAAATAA
*
41056 AATTTTATATTAT-T-TAATAA
1 AATTTTA-ATTATCTAAAATAA
*
41076 AA-TTTATTTA-CTAAATATAA
1 AATTTTAATTATCTAAA-ATAA
41096 A
1 A
41097 TATATAGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
18 4 0.12
19 5 0.15
20 12 0.35
21 8 0.24
22 5 0.15
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTAATTATCTAAAATAA
Done.