Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006593.1 Hibiscus syriacus cultivar Beakdansim tig00016173_pilon, 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: 59219
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:5775 original size:20 final size:20
Alignment explanation
Indices: 5750--5789 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5740 GTCATAACAT
5750 AAAATTATTAGTCTTTGTAA
1 AAAATTATTAGTCTTTGTAA
5770 AAAATTATTAGTCTTTGTAA
1 AAAATTATTAGTCTTTGTAA
5790 GAGCTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (20 bp):
AAAATTATTAGTCTTTGTAA
Found at i:7955 original size:24 final size:22
Alignment explanation
Indices: 7904--7965 Score: 54
Period size: 24 Copynumber: 2.6 Consensus size: 22
7894 TTTAAGTATG
* *
7904 ATTT-ATAAAAATAAAATTAAG
1 ATTTAATATAAATAAAATTAAA
7925 ATATTAATATAAATCAAAATTAATA
1 AT-TTAATATAAAT-AAAATTAA-A
7950 ATTTAAGTATTAAATA
1 ATTTAA-TA-TAAATA
7966 CATAATTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
21 2 0.06
22 2 0.06
23 7 0.21
24 12 0.36
25 5 0.15
26 5 0.15
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (22 bp):
ATTTAATATAAATAAAATTAAA
Found at i:8767 original size:18 final size:18
Alignment explanation
Indices: 8744--8785 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
8734 GATGAATTAA
*
8744 AATTTTAAAATATATGAT
1 AATTTTAAAATATATGAC
*
8762 AATTTTGAAATATATGAC
1 AATTTTAAAATATATGAC
8780 AATTTT
1 AATTTT
8786 TAATAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (18 bp):
AATTTTAAAATATATGAC
Found at i:9102 original size:41 final size:42
Alignment explanation
Indices: 9023--9108 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 42
9013 TGGCCTGGCC
* * * *
9023 TATTTAACTAAACAGTCCAGGCCCATGCCTTTTTAAAAG-CT
1 TATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGCCT
**
9064 TATTTAACTAAACAGGCCAGGCTTAGGCCTATTAAAAAGCCT
1 TATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGCCT
9106 TAT
1 TAT
9109 AAGCCTGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
41 33 0.87
42 5 0.13
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (42 bp):
TATTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGCCT
Found at i:15349 original size:31 final size:31
Alignment explanation
Indices: 15311--15398 Score: 133
Period size: 31 Copynumber: 2.8 Consensus size: 31
15301 TAAAAATTTA
*
15311 GGTACTAAAATGAAACAATAAGTTAAAAAT-G
1 GGTACTAAAATGAAACAAAAAG-TAAAAATCG
*
15342 GGTACTAAAATGAAACAAAAAGTAAACATCG
1 GGTACTAAAATGAAACAAAAAGTAAAAATCG
*
15373 GGTACTAAAATGAAATAAAAAGTAAA
1 GGTACTAAAATGAAACAAAAAGTAAA
15399 TATTAGGTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
30 6 0.11
31 47 0.89
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.19
Consensus pattern (31 bp):
GGTACTAAAATGAAACAAAAAGTAAAAATCG
Found at i:27186 original size:30 final size:30
Alignment explanation
Indices: 27136--27215 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 30
27126 ATATTTTTTT
* * *
27136 TAATATTTTCGATTATTTTTTAGCGTCTAG
1 TAATATTTTCGATCATTTTTTAACGTCTAA
* *
27166 TAATGTTTTTGATCATTTTTTAACGTCTAA
1 TAATATTTTCGATCATTTTTTAACGTCTAA
* *
27196 TAATATATTCGGTCATTTTT
1 TAATATTTTCGATCATTTTT
27216 CGAAAATCCA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.54
Consensus pattern (30 bp):
TAATATTTTCGATCATTTTTTAACGTCTAA
Found at i:44099 original size:8 final size:8
Alignment explanation
Indices: 44028--44098 Score: 124
Period size: 8 Copynumber: 8.9 Consensus size: 8
44018 TACATGCATA
*
44028 CATACATA
1 CATACATG
44036 CATACATG
1 CATACATG
44044 CATACATG
1 CATACATG
44052 CATACATG
1 CATACATG
44060 CATACATG
1 CATACATG
44068 CATACATG
1 CATACATG
44076 CATACATG
1 CATACATG
*
44084 CATACATA
1 CATACATG
44092 CATACAT
1 CATACAT
44099 AAACTTGTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 61 1.00
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.25
Consensus pattern (8 bp):
CATACATG
Found at i:53512 original size:16 final size:16
Alignment explanation
Indices: 53483--53523 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
53473 CGTTCATTTA
53483 ATAAAC-AA-ACGAAC
1 ATAAACGAACACGAAC
53497 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
53513 ATAAACGAACA
1 ATAAACGAACA
53524 ATTTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.24
15 2 0.08
16 17 0.68
ACGTcount: A:0.61, C:0.22, G:0.10, T:0.07
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:53612 original size:16 final size:16
Alignment explanation
Indices: 53591--53635 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
53581 TAATAAATTA
53591 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
53607 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
53623 ACGAATATAAACG
1 ACGAACATAAACG
53636 TTGGAGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.56, C:0.20, G:0.13, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:57059 original size:13 final size:14
Alignment explanation
Indices: 57029--57061 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
57019 TTGTTGTCCT
57029 TTTTATTTTGATAA
1 TTTTATTTTGATAA
57043 -TTTATTTTGA-AA
1 TTTTATTTTGATAA
57055 TTTTATT
1 TTTTATT
57062 AATTAGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 16 0.89
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (14 bp):
TTTTATTTTGATAA
Found at i:58266 original size:41 final size:42
Alignment explanation
Indices: 58188--58283 Score: 144
Period size: 41 Copynumber: 2.3 Consensus size: 42
58178 CCATTCCTTA
58188 AAATTCTGC-AATTAAACCAAATCACCATGAAAAACTAAACC
1 AAATTCTGCAAATTAAACCAAATCACCATGAAAAACTAAACC
*
58229 AAATTCTGCAAATTAAAACCAAATCA-CATG-AACACTAAACC
1 AAATTCTGCAAATT-AAACCAAATCACCATGAAAAACTAAACC
*
58270 AAAATCTGCAAATT
1 AAATTCTGCAAATT
58284 CAAGTCTACC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
41 32 0.63
42 8 0.16
43 11 0.22
ACGTcount: A:0.51, C:0.23, G:0.05, T:0.21
Consensus pattern (42 bp):
AAATTCTGCAAATTAAACCAAATCACCATGAAAAACTAAACC
Found at i:59044 original size:2 final size:2
Alignment explanation
Indices: 59037--59062 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59027 TTAACCCATA
59037 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
59063 TGATTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.