Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009434.1 Hibiscus syriacus cultivar Beakdansim tig00113490_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: 30464
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:5508 original size:8 final size:8
Alignment explanation
Indices: 5495--5522 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5485 AGATTCTCCC
5495 ATATGTAT
1 ATATGTAT
5503 ATATGTAT
1 ATATGTAT
5511 ATATGTAT
1 ATATGTAT
5519 ATAT
1 ATAT
5523 CTTCTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:9044 original size:8 final size:8
Alignment explanation
Indices: 9031--9087 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 8
9021 AAAATGAGTG
9031 AAAATGAA
1 AAAATGAA
9039 AAAATG-A
1 AAAATGAA
9046 AAAAT-AA
1 AAAATGAA
9053 AAAAT-AA
1 AAAATGAA
9060 AAAATG--
1 AAAATGAA
9066 --AATGAAA
1 AAAATG-AA
9073 AAAATGAA
1 AAAATGAA
9081 AAAATGA
1 AAAATGA
9088 GGGTTCAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
4 4 0.10
7 19 0.45
8 15 0.36
9 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (8 bp):
AAAATGAA
Found at i:9061 original size:21 final size:20
Alignment explanation
Indices: 9031--9083 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
9021 AAAATGAGTG
9031 AAAATGAAAAAATGAAAAATAA
1 AAAATG-AAAAATGAAAAA-AA
* **
9053 AAAATAAAAAATGAATGAAA
1 AAAATGAAAAATGAAAAAAA
9073 AAAATGAAAAA
1 AAAATGAAAAA
9084 ATGAGGGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 12 0.44
21 10 0.37
22 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.13
Consensus pattern (20 bp):
AAAATGAAAAATGAAAAAAA
Found at i:9084 original size:21 final size:22
Alignment explanation
Indices: 9031--9087 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
9021 AAAATGAGTG
9031 AAAATGAAAAAATGAAAAATAA
1 AAAATGAAAAAATGAAAAATAA
**
9053 AAAAT-AAAAAATGAATGA-AA
1 AAAATGAAAAAATGAAAAATAA
9073 AAAATGAAAAAATGA
1 AAAATGAAAAAATGA
9088 GGGTTCAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 7 0.22
21 20 0.62
22 5 0.16
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (22 bp):
AAAATGAAAAAATGAAAAATAA
Found at i:10165 original size:55 final size:55
Alignment explanation
Indices: 10086--10454 Score: 514
Period size: 55 Copynumber: 6.7 Consensus size: 55
10076 CCAACGATAA
* *
10086 TTGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
10141 TTGAAGATCGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* *
10196 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGCAGACACGTTTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
10251 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AAATAGGGAGCAGACACGATTG
* *
10307 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACATGATTA
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * ** *
10362 TCG-AGAATCGTTTGAGTCTTGTACTCTCTGGAA-AAATGGGGAGCAGACACGATTG
1 TTGAAG-ATTGTTCGAGTCTCATACTCTCT-GAAGAAATAGGGAGCAGACACGATTG
** * * *
10417 ACGAAGATT-TTCGAGT-T-TTACTCCCTGAAGCAATAGGG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGG
10455 GATAAAACCA
Statistics
Matches: 284, Mismatches: 25, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
51 3 0.01
52 13 0.05
53 1 0.00
54 8 0.03
55 201 0.71
56 58 0.20
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
Found at i:10389 original size:166 final size:165
Alignment explanation
Indices: 10086--10454 Score: 514
Period size: 166 Copynumber: 2.2 Consensus size: 165
10076 CCAACGATAA
* *
10086 TTGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATCG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATCG
* * *
10151 TTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTC
66 TTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTATCGAAGATCGTTCGAGTCTC
*
10216 ATACTCTCT-GAAGAAATAGAGAGCAGACACGTTTG
131 ATACTCTCTGGAA-AAATAGAGAGCAGACACGATTG
*
10251 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGATT
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AAATAGGGAGCAGACACGATTGTTGAAGATC
* *
10316 GTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACATGATTATCG-AGAATCGTTTGAGTC
65 GTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTATCGAAG-ATCGTTCGAGTC
** * *
10380 TTGTACTCTCTGGAAAAATGGGGAGCAGACACGATTG
129 TCATACTCTCTGGAAAAATAGAGAGCAGACACGATTG
** * * *
10417 ACGAAGATT-TTCGAGT-T-TTACTCCCTGAAGCAATAGGG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGG
10455 GATAAAACCA
Statistics
Matches: 183, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
162 7 0.04
163 11 0.06
164 1 0.01
165 40 0.22
166 121 0.66
167 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (165 bp):
TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATCG
TTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTATCGAAGATCGTTCGAGTCTC
ATACTCTCTGGAAAAATAGAGAGCAGACACGATTG
Found at i:16950 original size:21 final size:21
Alignment explanation
Indices: 16917--16959 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16907 TCTCGTTTAT
* * *
16917 CGCTTTTGTGGTCATAGCGGG
1 CGCTATTGCGGTCATAGAGGG
16938 CGCTATTGCGGTCATAGAGGG
1 CGCTATTGCGGTCATAGAGGG
16959 C
1 C
16960 ACTTTTGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.21, G:0.37, T:0.28
Consensus pattern (21 bp):
CGCTATTGCGGTCATAGAGGG
Found at i:17417 original size:21 final size:21
Alignment explanation
Indices: 17373--17435 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
17363 TTCTGATATA
*
17373 CCCGCTAT-AGCCACAAAAGTG
1 CCCGCTATGA-CCACAAAAGCG
* * *
17394 CCCTCTATGACCGCAATAGCG
1 CCCGCTATGACCACAAAAGCG
17415 CCCGCTATGACCACAAAAGCG
1 CCCGCTATGACCACAAAAGCG
17436 ATAAACGAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.37, G:0.19, T:0.14
Consensus pattern (21 bp):
CCCGCTATGACCACAAAAGCG
Found at i:18294 original size:21 final size:21
Alignment explanation
Indices: 18270--18321 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
18260 TCCTAATCCT
18270 TAAATCTTAAACTATAAAT-AC
1 TAAATCTTAAACTAT-AATCAC
* * *
18291 TAAACCTTAAACTCTAATCCC
1 TAAATCTTAAACTATAATCAC
18312 TAAATCTTAA
1 TAAATCTTAA
18322 GTCATAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATCTTAAACTATAATCAC
Found at i:18309 original size:42 final size:42
Alignment explanation
Indices: 18262--18390 Score: 136
Period size: 42 Copynumber: 3.1 Consensus size: 42
18252 ACCCTAAATC
*
18262 CTAATCCTTAAATCTTAAACTATAAATACTAAACCTTAAACT
1 CTAATCCTTAAATCTTAAACTATAAACACTAAACCTTAAACT
* * *
18304 CTAATCCCTAAATCTT-AAGTCATAAACACTAAACCCTAAACT
1 CTAATCCTTAAATCTTAAACT-ATAAACACTAAACCTTAAACT
* * * * ** *
18346 TTAATCTTTAAATCCTAAGCCGTAAGCACTAAACCTTAAAC-
1 CTAATCCTTAAATCTTAAACTATAAACACTAAACCTTAAACT
18387 CTAA
1 CTAA
18391 ACCCTAAACT
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
41 6 0.09
42 63 0.90
43 1 0.01
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.29
Consensus pattern (42 bp):
CTAATCCTTAAATCTTAAACTATAAACACTAAACCTTAAACT
Found at i:19673 original size:12 final size:12
Alignment explanation
Indices: 19649--19682 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
19639 GTTTCGGGAG
19649 AGAAGAGAGAGGA
1 AGAAGA-AGAGGA
19662 AGAAGAAGAGGA
1 AGAAGAAGAGGA
19674 AGAAGAAGA
1 AGAAGAAGA
19683 TGCATAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AGAAGAAGAGGA
Found at i:19869 original size:11 final size:11
Alignment explanation
Indices: 19807--19874 Score: 66
Period size: 11 Copynumber: 6.2 Consensus size: 11
19797 TTCGTTTTCA
*
19807 AGCTTGAATCA
1 AGCTTGAATCG
*
19818 AGTTTGAATCG
1 AGCTTGAATCG
** *
19829 AGCTCAAAATTG
1 AGCT-TGAATCG
*
19841 AGCTTGAACCG
1 AGCTTGAATCG
19852 AGC-TGAATCG
1 AGCTTGAATCG
19862 AGCTTGAATCG
1 AGCTTGAATCG
19873 AG
1 AG
19875 TTTTAATTGA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
10 9 0.20
11 27 0.61
12 8 0.18
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (11 bp):
AGCTTGAATCG
Found at i:20088 original size:2 final size:2
Alignment explanation
Indices: 20081--20132 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
20071 ACCCCTACAC
20081 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
20123 AT AT AT AT AT
1 AT AT AT AT AT
20133 CCATTTGGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20647 original size:24 final size:25
Alignment explanation
Indices: 20587--20654 Score: 93
Period size: 24 Copynumber: 2.7 Consensus size: 25
20577 ATGACAATAA
20587 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTTTT-AA-TAAGTTAAT
* *
20614 AATAAGATATATTTAATAAGTTAAT
1 AATAAAATATTTTTAATAAGTTAAT
20639 -ATAAAATATTTTTAAT
1 AATAAAATATTTTTAAT
20655 TTAATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 14 0.38
25 9 0.24
26 2 0.05
27 12 0.32
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
AATAAAATATTTTTAATAAGTTAAT
Found at i:20669 original size:24 final size:25
Alignment explanation
Indices: 20637--20691 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
20627 TAATAAGTTA
* *
20637 ATATA-AAATATTTTTAATTTAA-T
1 ATATATAAATATTATAAATTTAAGT
20660 ATATATAAATATTATAAATTTAAGT
1 ATATATAAATATTATAAATTTAAGT
*
20685 ATTTATA
1 ATATATA
20692 CGCTAAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 5 0.19
24 15 0.56
25 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATATATAAATATTATAAATTTAAGT
Found at i:22084 original size:7 final size:7
Alignment explanation
Indices: 22072--22103 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
22062 TTATATTATC
22072 ATCTGCA
1 ATCTGCA
22079 ATCTGCA
1 ATCTGCA
22086 ATCTGCA
1 ATCTGCA
22093 ATCTGCA
1 ATCTGCA
22100 ATCT
1 ATCT
22104 TTAACTAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (7 bp):
ATCTGCA
Found at i:28681 original size:82 final size:80
Alignment explanation
Indices: 28483--28681 Score: 224
Period size: 82 Copynumber: 2.5 Consensus size: 80
28473 TATATCCTTC
* * *
28483 AAATTCCTAAAA-ACAAGCTAAAGATAAT-TCTTAAAATAATACTTAAATCCTAATTAGAACAAT
1 AAATTCCTAAAACA-AAGATAAA-ATAATATCTTAAAATAATACATAAATCCTAATTAAAACAAT
28546 AAAAACTATTTAAACTA
64 AAAAACTATTTAAACTA
* ** * * *
28563 AAATTCCTAAAACAAAGATAAGATAAATATAATAAAATAATATCATAAATCTTAATTAAAATATT
1 AAATTCCTAAAACAAAGATAAAAT-AATATCTTAAAATAATA-CATAAATCCTAATTAAAACAAT
*
28628 TAAAACTATTTAAACTA
64 AAAAACTATTTAAACTA
*
28645 AAATTCCTAAAGATAAA-ATTAAAATAATATCTTAAAA
1 AAATTCCTAAA-ACAAAGA-TAAAATAATATCTTAAAA
28682 CATGAGTTTA
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
79 2 0.02
80 21 0.21
81 12 0.12
82 55 0.56
83 9 0.09
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (80 bp):
AAATTCCTAAAACAAAGATAAAATAATATCTTAAAATAATACATAAATCCTAATTAAAACAATAA
AAACTATTTAAACTA
Done.