Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168188.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_425, 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: 27308
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Found at i:365 original size:85 final size:85
Alignment explanation
Indices: 265--435 Score: 279
Period size: 85 Copynumber: 2.0 Consensus size: 85
255 AAGCTATCGA
* * * *
265 ACGTGTTCTAAGTGCATGGATAATCCAGTCTTCCTGCTTTTCACAAACGTCAAAGCAGACTAAGA
1 ACGTGTTCTAAGTGCATGGATAATCAAATCATCCTGCTTTTCACAAACATCAAAGCAGACTAAGA
*
330 ACTTTTAAGTCAAGAAAACT
66 AATTTTAAGTCAAGAAAACT
* *
350 ACGTGTTCTAAGTGCATGGATAATCAAATCATCCTGCTTTTCACAAACATCGAAGCGGACTAAGA
1 ACGTGTTCTAAGTGCATGGATAATCAAATCATCCTGCTTTTCACAAACATCAAAGCAGACTAAGA
415 AATTTTAAGTCAAGAAAACT
66 AATTTTAAGTCAAGAAAACT
435 A
1 A
436 ATCACCGTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (85 bp):
ACGTGTTCTAAGTGCATGGATAATCAAATCATCCTGCTTTTCACAAACATCAAAGCAGACTAAGA
AATTTTAAGTCAAGAAAACT
Found at i:662 original size:13 final size:14
Alignment explanation
Indices: 638--667 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
628 ATTTTATTTT
638 TTTAATGTATTTAA
1 TTTAATGTATTTAA
652 TTTAATG-ATTTAA
1 TTTAATGTATTTAA
665 TTT
1 TTT
668 TATTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTAATGTATTTAA
Found at i:669 original size:14 final size:15
Alignment explanation
Indices: 637--669 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
627 CATTTTATTT
637 TTTTAATGTATTTAA
1 TTTTAATGTATTTAA
652 -TTTAATG-ATTTAA
1 TTTTAATGTATTTAA
665 TTTTA
1 TTTTA
670 TTATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTAATGTATTTAA
Found at i:3621 original size:19 final size:19
Alignment explanation
Indices: 3583--3622 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3573 ATCTAGAAAT
*
3583 TTTTAAATTTTTCAATGAA
1 TTTTAAATTTTTCAACGAA
*
3602 TTTTAAATTTTTTAACGAA
1 TTTTAAATTTTTCAACGAA
3621 TT
1 TT
3623 CATTTAGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTAAATTTTTCAACGAA
Found at i:9577 original size:26 final size:27
Alignment explanation
Indices: 9545--9603 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
9535 ATCAGATAAT
* *
9545 TAATAAT-AAAATCAAGATAAAT-AGTA
1 TAATAATAAAAAT-AAAATAAATAAGGA
9571 TAATAATAAAAATAAAATAAATAAGGA
1 TAATAATAAAAATAAAATAAATAAGGA
9598 TAATAA
1 TAATAA
9604 GAATACGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (27 bp):
TAATAATAAAAATAAAATAAATAAGGA
Found at i:15727 original size:2 final size:2
Alignment explanation
Indices: 15720--15748 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15710 ATGATCTGGA
15720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15749 ATTTATAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19030 original size:3 final size:3
Alignment explanation
Indices: 19017--19050 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
19007 TTTTAATTTT
*
19017 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19051 CTTATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:19068 original size:8 final size:8
Alignment explanation
Indices: 19001--19091 Score: 75
Period size: 8 Copynumber: 11.4 Consensus size: 8
18991 TAATTTTAGT
19001 TTTAATT-
1 TTTAATTA
*
19008 TTTAATTT
1 TTTAATTA
19016 TTTATCATTA
1 TTTA--ATTA
19026 -TT-ATTA
1 TTTAATTA
*
19032 TTATTATTA
1 TT-TAATTA
*
19041 TTATTATTA
1 TT-TAATTA
19050 TCTT-ATT-
1 T-TTAATTA
19057 TTTAATTA
1 TTTAATTA
19065 TTTAATTA
1 TTTAATTA
19073 TTTAATTA
1 TTTAATTA
19081 TTTAATTA
1 TTTAATTA
19089 TTT
1 TTT
19092 TCGTCATTTT
Statistics
Matches: 74, Mismatches: 1, Indels: 17
0.80 0.01 0.18
Matches are distributed among these distances:
6 6 0.08
7 12 0.16
8 35 0.47
9 17 0.23
10 4 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAATTA
Found at i:20126 original size:9 final size:8
Alignment explanation
Indices: 20113--20143 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
20103 TTTCAAACCA
20113 AAAAAATT
1 AAAAAATT
20121 AAAAAATT
1 AAAAAATT
20129 AAAAAATAT
1 AAAAAAT-T
20138 AAAAAA
1 AAAAAA
20144 AAACATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (8 bp):
AAAAAATT
Found at i:20406 original size:159 final size:162
Alignment explanation
Indices: 20181--20472 Score: 432
Period size: 159 Copynumber: 1.8 Consensus size: 162
20171 ATTAAATACA
* * * * *
20181 AATTATCCAATGATGAGATTTTTTAGAAATTTCAAATGGTAAATTTTCTAAGAACTCTTGAGGTG
1 AATTATCCAAAGATGAGATCTCTTAGAAATTTCAAATGGTAAATATTCTAAGAAATCTTGAGGTG
* * *
20246 AGAAATTTTATTTAAGTTTGGCCCCAAATTGTGGAATAATTTAGAT-AAAA-TTTCAATAAAAAT
66 AGAAATTTTATCTAAATTTGG-CCCAAATGGTGGAATAATTTAGATGAAAATTTTCAATAAAAAT
20309 AATTGTATAAAATTTGGATTGTAAATATTTGAT
130 AATTGTATAAAATTTGGATTGTAAATATTTGAT
20342 AATTATCCAAAGATGAGA-CTCTTAGAAATTTCAAATGGTAAA-ATTCTAAGAAATCTCT-AGGT
1 AATTATCCAAAGATGAGATCTCTTAGAAATTTCAAATGGTAAATATTCTAAGAAATCT-TGAGGT
* * *
20404 GAGAAATTTTCTCTAAATTTGGCCCAAATGGTGGAATAGTTTAGATGAAAATTTTCAATAAAAGT
65 GAGAAATTTTATCTAAATTTGGCCCAAATGGTGGAATAATTTAGATGAAAATTTTCAATAAAAAT
20469 AATT
130 AATT
20473 ATTATTATTT
Statistics
Matches: 117, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
158 22 0.19
159 39 0.33
160 39 0.33
161 17 0.15
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (162 bp):
AATTATCCAAAGATGAGATCTCTTAGAAATTTCAAATGGTAAATATTCTAAGAAATCTTGAGGTG
AGAAATTTTATCTAAATTTGGCCCAAATGGTGGAATAATTTAGATGAAAATTTTCAATAAAAATA
ATTGTATAAAATTTGGATTGTAAATATTTGAT
Found at i:21679 original size:51 final size:51
Alignment explanation
Indices: 21614--21714 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
21604 TCACAACATG
** *
21614 CATCCTCATGTTTTAAGCATTATCATGTTACATCATTCTATGCATCATTTC
1 CATCCTCATGTTTTAAGCATTATCAAATCACATCATTCTATGCATCATTTC
* * *
21665 CATCCTCATGTTTTAAGCATTATTAAATCATATCATTTTATGCATCATTT
1 CATCCTCATGTTTTAAGCATTATCAAATCACATCATTCTATGCATCATTT
21715 TCATAATCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (51 bp):
CATCCTCATGTTTTAAGCATTATCAAATCACATCATTCTATGCATCATTTC
Found at i:21725 original size:51 final size:51
Alignment explanation
Indices: 21619--21726 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 51
21609 ACATGCATCC
** * **
21619 TCATGTTTTAAGCATTATCATGTTACATCATTCTATGCATCATTTCCATCC
1 TCATGTTTTAAGCATTATCAAATCACATCATTCTATGCATCATTTCCATAA
* * * *
21670 TCATGTTTTAAGCATTATTAAATCATATCATTTTATGCATCATTTTCATAA
1 TCATGTTTTAAGCATTATCAAATCACATCATTCTATGCATCATTTCCATAA
21721 TCATGT
1 TCATGT
21727 CTAACACCAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (51 bp):
TCATGTTTTAAGCATTATCAAATCACATCATTCTATGCATCATTTCCATAA
Done.