Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001299.1 Hibiscus syriacus cultivar Beakdansim tig00002538_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: 69476
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:2629 original size:19 final size:20
Alignment explanation
Indices: 2583--2621 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2573 TTGTAAACCC
*
2583 ATAAAATATTGTTTATATAA
1 ATAAAATATTGTTAATATAA
2603 ATAAAATATT-TTAATATAA
1 ATAAAATATTGTTAATATAA
2622 TAATAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
ATAAAATATTGTTAATATAA
Found at i:4618 original size:137 final size:137
Alignment explanation
Indices: 4358--4618 Score: 398
Period size: 137 Copynumber: 1.9 Consensus size: 137
4348 ACCTAAGTGC
* * * *
4358 CGAAATGGAAATTCACAAACTTATTATAAATTCCATGGATGCACACATAGTGTCGAAAGTACATA
1 CGAAATGGAAATTCACAAACTCATTATAAATACCATGGATGCACACATAGTGCCGAAAGTACACA
* * *
4423 TAGTATTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCTTCATACAAAAA
66 TAGTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGACAACCATCATACAAAAA
4488 CGTATGT
131 CGTATGT
* * *
4495 CGAAATGGTAATTCACAAACTCATTATTAATACCATGGTTGCACATC-TAGTGCCGAAAGTACAC
1 CGAAATGGAAATTCACAAACTCATTATAAATACCATGGATGCACA-CATAGTGCCGAAAGTACAC
* *
4559 ATAGTACTGATACGAAAATGCAACATATGCATTAAACAAAATTGATCTACAACCATCATA
65 ATAGTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGACAACCATCATA
4619 TACAATGTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
137 110 0.99
138 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (137 bp):
CGAAATGGAAATTCACAAACTCATTATAAATACCATGGATGCACACATAGTGCCGAAAGTACACA
TAGTACTGATACGAAAATGCAACATATGCATTAAACAAAATCGATCGACAACCATCATACAAAAA
CGTATGT
Found at i:20511 original size:16 final size:16
Alignment explanation
Indices: 20490--20523 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
20480 ATAAAAGGAG
20490 GATATGTACATGGTGA
1 GATATGTACATGGTGA
20506 GATATGTACATGGTGA
1 GATATGTACATGGTGA
20522 GA
1 GA
20524 CGTTGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.29
Consensus pattern (16 bp):
GATATGTACATGGTGA
Found at i:23311 original size:29 final size:29
Alignment explanation
Indices: 23279--23360 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
23269 CCAAAATATA
23279 AAACTTTTAAAATTTATATTTTGGTCC-A-T
1 AAACTTTTAAAATTTATATTTT-G-CCTACT
*
23308 AAACTTTTACAAAGTTTATACTTTGCCTACT
1 AAACTTTTA-AAA-TTTATATTTTGCCTACT
* *
23339 AAACTCTCAAAATTTATATTTT
1 AAACTTTTAAAATTTATATTTT
23361 AGCCACAAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 20 0.44
30 8 0.18
31 17 0.38
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (29 bp):
AAACTTTTAAAATTTATATTTTGCCTACT
Found at i:27164 original size:22 final size:23
Alignment explanation
Indices: 27079--27168 Score: 60
Period size: 22 Copynumber: 3.9 Consensus size: 23
27069 GGGTATATAT
*
27079 TATATTTAAATGACATATATAT-CA
1 TATATTTAAA--ACATATATATAAA
* * *
27103 TATTTTTGAAAATATACATATAAA
1 TATATTT-AAAACATATATATAAA
* ** *
27127 TATATATAGTA-TTATATATAAA
1 TATATTTAAAACATATATATAAA
27149 TATATTTAAAA-ATATATATA
1 TATATTTAAAACATATATATA
27169 GCTTGAAGGA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
22 25 0.50
23 10 0.20
24 12 0.24
25 3 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (23 bp):
TATATTTAAAACATATATATAAA
Found at i:35641 original size:103 final size:103
Alignment explanation
Indices: 35462--35679 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
35452 GTAGAGGGTC
35462 TATGTGGTCCTTCGGGACAAATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACAAATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
35527 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* *
35565 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACAAATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
35630 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
35668 TATGTAGTCCTT
1 TATGTGGTCCTT
35680 AGAGACAACT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACAAATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:35729 original size:23 final size:23
Alignment explanation
Indices: 35703--35763 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
35693 TATGGAACTT
*
35703 CGGTGCATTTCTATGCGGCACTA
1 CGGTGCATTTCTACGCGGCACTA
* * *
35726 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCATTTCTACGCGGCACTA
*
35749 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
35764 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGCACTA
Found at i:38875 original size:24 final size:24
Alignment explanation
Indices: 38848--38901 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
38838 TAAATGAACA
*
38848 AACATAAACAAACGAAA-GTAAACG
1 AACATAAACAAAC-AAACATAAACG
* **
38872 AACAAAAATGAACAAACATAAACG
1 AACATAAACAAACAAACATAAACG
38896 AACATA
1 AACATA
38902 TCATCAAACG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.65, C:0.17, G:0.09, T:0.09
Consensus pattern (24 bp):
AACATAAACAAACAAACATAAACG
Found at i:38898 original size:14 final size:14
Alignment explanation
Indices: 38833--38899 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
38823 AGATTGAGCT
*
38833 AAACATAAATGAAC
1 AAACATAAACGAAC
*
38847 AAACATAAACAAAC
1 AAACATAAACGAAC
*
38861 GAAA-GTAAACGAAC
1 -AAACATAAACGAAC
*
38875 --A-A-AAATGAAC
1 AAACATAAACGAAC
38885 AAACATAAACGAAC
1 AAACATAAACGAAC
38899 A
1 A
38900 TATCATCAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
10 7 0.17
11 1 0.02
12 1 0.02
13 1 0.02
14 28 0.68
15 3 0.07
ACGTcount: A:0.66, C:0.16, G:0.09, T:0.09
Consensus pattern (14 bp):
AAACATAAACGAAC
Found at i:48744 original size:15 final size:15
Alignment explanation
Indices: 48724--48753 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48714 AATTACGATT
*
48724 TTCCATTGAAATATC
1 TTCCATTAAAATATC
48739 TTCCATTAAAATATC
1 TTCCATTAAAATATC
48754 CCATTGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (15 bp):
TTCCATTAAAATATC
Found at i:50156 original size:18 final size:18
Alignment explanation
Indices: 50130--50173 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
50120 GTGAAGTATG
*
50130 AATGGTGTTGTCGTGGAA
1 AATGTTGTTGTCGTGGAA
*
50148 AATGTTGTTGTCGTGGTA
1 AATGTTGTTGTCGTGGAA
*
50166 AGTGTTGT
1 AATGTTGT
50174 AAGGTTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.05, G:0.36, T:0.41
Consensus pattern (18 bp):
AATGTTGTTGTCGTGGAA
Found at i:55009 original size:21 final size:21
Alignment explanation
Indices: 54985--55024 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
54975 GTTTGCAAAC
54985 ATTACCCTCAATATCAATATT
1 ATTACCCTCAATATCAATATT
55006 ATTACCCTCAATATCAATA
1 ATTACCCTCAATATCAATA
55025 CCAAGGCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTACCCTCAATATCAATATT
Done.