Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168156.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_397, 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: 29030
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:1212 original size:26 final size:26
Alignment explanation
Indices: 1179--1236 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
1169 GGTCCAAAAT
*
1179 TCAAGGGGCCAACTTTAGCCATTTCA
1 TCAAGGGGCCAACTTTAGCCATTTAA
1205 TCAAGGGGCCAACTTTAGCCATTTAA
1 TCAAGGGGCCAACTTTAGCCATTTAA
1231 TCAAGG
1 TCAAGG
1237 TTCCCAATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (26 bp):
TCAAGGGGCCAACTTTAGCCATTTAA
Found at i:17491 original size:60 final size:61
Alignment explanation
Indices: 17420--17563 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 61
17410 TATGTTATTT
* ** *
17420 AAAGCATGCAATTACGGTGTTTATTTAAA-GAAATGCCATAATTGAGTAT-TTTAAATTT-TA
1 AAAGCAAGCAATTACGGCATTT-TTTAAATGAAATGCCATAATTGAATATATTT-AATTTCTA
* * * *
17480 AAAGCAAGCAATTATGGCATTTTTTAAATTAAATGTCGTAATTGAATATATTTAATTTCTA
1 AAAGCAAGCAATTACGGCATTTTTTAAATGAAATGCCATAATTGAATATATTTAATTTCTA
*
17541 AATGCAAGCAATTACGGCATTTT
1 AAAGCAAGCAATTACGGCATTTT
17564 CTTTAAACCA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
59 6 0.08
60 39 0.55
61 26 0.37
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (61 bp):
AAAGCAAGCAATTACGGCATTTTTTAAATGAAATGCCATAATTGAATATATTTAATTTCTA
Found at i:17612 original size:63 final size:59
Alignment explanation
Indices: 17456--17616 Score: 169
Period size: 63 Copynumber: 2.6 Consensus size: 59
17446 AAAGAAATGC
* * * ** **
17456 CATAATTGAGTATTTTAAATTTTAAAAGCAAGCAATTATGGCATTTTTTAAATTAAATGT
1 CATAATTGAATATTTT-AATTTTAAATGCAAGCAATTACGGCATTTTTTAAACCAAACAT
*
17516 CGTAATTGAATATATTTAATTTCTAAATGCAAGCAATTACGGCATTTTCTTTAAACCAAACAT
1 CATAATTGAATAT-TTTAATTT-TAAATGCAAGCAATTACGGCA-TTT-TTTAAACCAAACAT
* *
17579 CATAATTGAATATTTTCAATTATTGAATCCAAGCAATT
1 CATAATTGAATATTTT-AATT-TTAAATGCAAGCAATT
17617 CCATCGTTTC
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
60 16 0.19
61 22 0.26
62 6 0.07
63 39 0.46
64 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (59 bp):
CATAATTGAATATTTTAATTTTAAATGCAAGCAATTACGGCATTTTTTAAACCAAACAT
Found at i:17752 original size:125 final size:124
Alignment explanation
Indices: 17450--17754 Score: 280
Period size: 125 Copynumber: 2.5 Consensus size: 124
17440 TTATTTAAAG
* * * **
17450 AAATGCCATAATTGAGTATTTTAAATTTTAAAAGCAAGCAATTATGGCATTT-TTTAAATTAAAT
1 AAATGTCATAATTGAGTATTTTCAATTTTAAATGCAAGCAATTATGATATTTCTTTAAATTAAAT
*
17514 GTCGTAATTGAATATATTTAATTTCTAAATGCAAGCAATTACGGCATTTTCTTTAAACC
66 GTCATAATTGAATATATTTAATTTCTAAATGCAAGCAATTACGGCATTTTCTTTAAACC
** * * * ** * * *
17573 AAACATCATAATTGAATATTTTCAATTATTGAATCCAAGCAATT-CCATCGTTTCTTTCATTTAA
1 AAATGTCATAATTGAGTATTTTCAATT-TTAAATGCAAGCAATTATGAT-ATTTCTTTAAATTAA
* * * * ** **
17637 ATG-CAATAATTG-AT-TTTTTCAAAATTT-TAAATGCAAGCAATTATGGCCTTTTTTTTTTATT
64 ATGTC-ATAATTGAATATATTT---AATTTCTAAATGCAAGCAATTACGGCATTTTCTTTAAACC
*
17698 AAATGTCATAATTGAGTATATTCAATTTCTAAATGCAAGCAATTATGATATTTCTTT
1 AAATGTCATAATTGAGTATTTTCAATTT-TAAATGCAAGCAATTATGATATTTCTTT
17755 TAACTAAAGC
Statistics
Matches: 140, Mismatches: 33, Indels: 16
0.74 0.17 0.08
Matches are distributed among these distances:
123 26 0.19
124 20 0.14
125 87 0.62
126 7 0.05
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (124 bp):
AAATGTCATAATTGAGTATTTTCAATTTTAAATGCAAGCAATTATGATATTTCTTTAAATTAAAT
GTCATAATTGAATATATTTAATTTCTAAATGCAAGCAATTACGGCATTTTCTTTAAACC
Found at i:27396 original size:21 final size:21
Alignment explanation
Indices: 27372--27416 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
27362 TTTTTTTTAA
*
27372 TTTTAGGGCTTCA-TTTAGGGT
1 TTTTA-GGCTTCATTTTAGGCT
*
27393 TTTTAGGTTTCATTTTAGGCT
1 TTTTAGGCTTCATTTTAGGCT
27414 TTT
1 TTT
27417 AGTTTAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.13, C:0.09, G:0.22, T:0.56
Consensus pattern (21 bp):
TTTTAGGCTTCATTTTAGGCT
Found at i:27416 original size:20 final size:19
Alignment explanation
Indices: 27393--27472 Score: 56
Period size: 21 Copynumber: 4.0 Consensus size: 19
27383 CATTTAGGGT
27393 TTTTAGGTTTCATTTTAGG
1 TTTTAGGTTTCATTTTAGG
*
27412 CTTTTA-GTTTAGGATTTT-GG
1 -TTTTAGGTTT--CATTTTAGG
* *
27432 TTTTAGGGTTTCACTTAAGGG
1 TTTTA-GGTTTCATTTTA-GG
*
27453 TTTAAGGTTTCAATTTTAGG
1 TTTTAGGTTTC-ATTTTAGG
27473 GTTTCATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
19 12 0.26
20 15 0.33
21 19 0.41
ACGTcount: A:0.19, C:0.06, G:0.24, T:0.51
Consensus pattern (19 bp):
TTTTAGGTTTCATTTTAGG
Found at i:27483 original size:60 final size:60
Alignment explanation
Indices: 27372--27489 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
27362 TTTTTTTTAA
* * *
27372 TTTTAGGGCTTCATTTAGGGTTTTTAGGTTTCATTTTAGGCTTTTAGTTTAGGATTTTGG
1 TTTTAGGGCTTCATTAAGGGTTTTAAGGTTTCATTTTAGGCTTTCAGTTTAGGATTTTGG
* * *
27432 TTTTAGGGTTTCACTTAAGGG-TTTAAGGTTTCAATTTTAGGGTTTCA-TTTAGGCTTTT
1 TTTTAGGGCTTCA-TTAAGGGTTTTAAGGTTTC-ATTTTAGGCTTTCAGTTTAGGATTTT
27490 ACTTACAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 32 0.64
61 18 0.36
ACGTcount: A:0.17, C:0.08, G:0.24, T:0.52
Consensus pattern (60 bp):
TTTTAGGGCTTCATTAAGGGTTTTAAGGTTTCATTTTAGGCTTTCAGTTTAGGATTTTGG
Found at i:27883 original size:3 final size:3
Alignment explanation
Indices: 27868--27903 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
27858 TAAAATTTTC
*
27868 ATT ATT CTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27904 TATTTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.