Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003725.1 Hibiscus syriacus cultivar Beakdansim tig00007966_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: 75489
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6041 original size:19 final size:20
Alignment explanation
Indices: 5996--6043 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5986 TGTACTATGC
* *
5996 TTGAAATTAATGCTAGAGTG
1 TTGAAATTGATGCTAGAATG
*
6016 TTGAAATTGATGTTAGAATG
1 TTGAAATTGATGCTAGAATG
6036 -TGAAATTG
1 TTGAAATTG
6044 GGTCACTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (20 bp):
TTGAAATTGATGCTAGAATG
Found at i:9280 original size:2 final size:2
Alignment explanation
Indices: 9269--9303 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
9259 ATCAATCATA
9269 AT AT -T 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
9304 GTTATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9582 original size:15 final size:16
Alignment explanation
Indices: 9548--9582 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
9538 CAAAATCCTC
*
9548 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTCAAA
9564 TTTTCTTTCTC-CAAA
1 TTTTCTTTCTCTCAAA
9579 TTTT
1 TTTT
9583 ATCATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTCTTTCTCTCAAA
Found at i:11191 original size:19 final size:20
Alignment explanation
Indices: 11146--11192 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
11136 TATACTATGC
*
11146 TTGAAATTAATGTTAGAGTG
1 TTGAAATTAATGTTAGAATG
*
11166 TTGAAATTTATGTTAGAATG
1 TTGAAATTAATGTTAGAATG
11186 -TGAAATT
1 TTGAAATT
11193 GGGTCACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGAAATTAATGTTAGAATG
Found at i:14659 original size:2 final size:2
Alignment explanation
Indices: 14648--14708 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
14638 ATCAATCATA
14648 AT AT -T 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
14689 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
14709 GTTATATTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:19738 original size:2 final size:2
Alignment explanation
Indices: 19731--19756 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19721 ATAATATGAC
19731 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
19757 GTTATATTTA
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
Found at i:20021 original size:16 final size:16
Alignment explanation
Indices: 20000--20034 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19990 CAAAATCCTC
*
20000 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTAAAT
20016 TTTTCTTTCTCTAAAT
1 TTTTCTTTCTCTAAAT
20032 TTT
1 TTT
20035 CTCATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTCTTTCTCTAAAT
Found at i:21642 original size:19 final size:20
Alignment explanation
Indices: 21597--21644 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
21587 TGTACTATGC
* *
21597 TTGAAATTAATGTTAGAGTG
1 TTGAAATTGATGTTAGAATG
21617 TTGAAATTGATGTTAGAATG
1 TTGAAATTGATGTTAGAATG
21637 -TGAAATTG
1 TTGAAATTG
21645 GGTCGCATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
TTGAAATTGATGTTAGAATG
Found at i:24730 original size:15 final size:16
Alignment explanation
Indices: 24696--24732 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
24686 CAAAATCCTC
*
24696 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTCAAA
24712 TTTTCTTTCTC-CAAA
1 TTTTCTTTCTCTCAAA
24727 TTTTCT
1 TTTTCT
24733 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTCTTTCTCTCAAA
Found at i:26340 original size:19 final size:20
Alignment explanation
Indices: 26295--26342 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
26285 TGTACTATGC
* *
26295 TTGAAATTAATGTTAGAGTG
1 TTGAAATTGATGTTAGAATG
26315 TTGAAATTGATGTTAGAATG
1 TTGAAATTGATGTTAGAATG
26335 -TGAAATTG
1 TTGAAATTG
26343 GGTCACTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
TTGAAATTGATGTTAGAATG
Found at i:28646 original size:19 final size:19
Alignment explanation
Indices: 28622--28666 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
28612 GAACGCTGGA
28622 AACCGGTTTTGACCGGATT
1 AACCGGTTTTGACCGGATT
*
28641 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGATT
*
28660 GACCGGT
1 AACCGGT
28667 CACGACCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (19 bp):
AACCGGTTTTGACCGGATT
Found at i:28655 original size:10 final size:10
Alignment explanation
Indices: 28623--28666 Score: 56
Period size: 9 Copynumber: 4.6 Consensus size: 10
28613 AACGCTGGAA
28623 ACCGGTTTTG
1 ACCGGTTTTG
* *
28633 ACCGG-ATTA
1 ACCGGTTTTG
28642 ACCGGTTTTG
1 ACCGGTTTTG
28652 ACCGG-TTTG
1 ACCGGTTTTG
28661 ACCGGT
1 ACCGGT
28667 CACGACCCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 16 0.57
10 12 0.43
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.32
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:28687 original size:13 final size:13
Alignment explanation
Indices: 28669--28732 Score: 74
Period size: 13 Copynumber: 4.5 Consensus size: 13
28659 TGACCGGTCA
*
28669 CGACCCGTTTACC
1 CGACCCGTTGACC
28682 CGACCCGTTGACCCGACC
1 CGACCCGTTG-----ACC
28700 CGACCCGTTGACC
1 CGACCCGTTGACC
28713 CGACCCGTTGACC
1 CGACCCGTTGACC
28726 CGACCCG
1 CGACCCG
28733 ACCCGTTGAC
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
13 32 0.71
18 13 0.29
ACGTcount: A:0.16, C:0.48, G:0.22, T:0.14
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:28693 original size:31 final size:31
Alignment explanation
Indices: 28669--28743 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
28659 TGACCGGTCA
*
28669 CGACCCGTTTACCCGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACCCGTTGACCCGACC
28700 CGACCCGTTGACCCGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACCCGTTGACCCGACC
28731 CGACCCGTTGACC
1 CGACCCGTTGACC
28744 GTTGACCGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.16, C:0.48, G:0.21, T:0.15
Consensus pattern (31 bp):
CGACCCGTTGACCCGACCCGTTGACCCGACC
Found at i:28702 original size:18 final size:18
Alignment explanation
Indices: 28679--28743 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
28669 CGACCCGTTT
28679 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
28697 ACCCGACCCGTT-----G
1 ACCCGACCCGTTGACCCG
28710 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
28728 ACCCGACCCGTTGACC
1 ACCCGACCCGTTGACC
28744 GTTGACCGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
13 13 0.31
18 29 0.69
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:28812 original size:29 final size:29
Alignment explanation
Indices: 28751--28826 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
28741 ACCGTTGACC
*** *
28751 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
28780 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
28809 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
28827 TTTTTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:41679 original size:31 final size:31
Alignment explanation
Indices: 41641--41702 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
41631 TAACATATGA
41641 TTGAAGCTAGCACATAAAGAATTACATCAAT
1 TTGAAGCTAGCACATAAAGAATTACATCAAT
* *
41672 TTGAAGCTAGCTCATAAAGAATTACGTCAAT
1 TTGAAGCTAGCACATAAAGAATTACATCAAT
41703 AGGTTTCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (31 bp):
TTGAAGCTAGCACATAAAGAATTACATCAAT
Found at i:44583 original size:38 final size:36
Alignment explanation
Indices: 44466--44584 Score: 109
Period size: 38 Copynumber: 3.3 Consensus size: 36
44456 TTTTATGAAC
44466 CAAAGATGAAATTACCATGTGCAAAGTTGGCCACCTA
1 CAAAGATGAAATTACC-TGTGCAAAGTTGGCCACCTA
* * ** *
44503 CCAAAGATGAATTTTCCAAT---AAGTTGGCCACCAA
1 -CAAAGATGAAATTACCTGTGCAAAGTTGGCCACCTA
* * *
44537 CCAAGATGAAATTCCCTTGTGCAAAGTTGGTCACCTA
1 CAAAGATGAAATTACC-TGTGCAAAGTTGGCCACCTA
44574 CTAAAGATGAA
1 C-AAAGATGAA
44585 TTTTTCAACT
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
33 13 0.21
34 14 0.22
37 14 0.22
38 22 0.35
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.24
Consensus pattern (36 bp):
CAAAGATGAAATTACCTGTGCAAAGTTGGCCACCTA
Found at i:63624 original size:26 final size:26
Alignment explanation
Indices: 63586--63638 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
63576 AATGACTTAA
63586 GAATATCACCAAGCCTATG-AATGAAT
1 GAATATCACCAAG-CTATGAAATGAAT
*
63612 GAATATC-CTCAAGCTTTGAAATGAAT
1 GAATATCAC-CAAGCTATGAAATGAAT
63638 G
1 G
63639 GAAATACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (26 bp):
GAATATCACCAAGCTATGAAATGAAT
Found at i:73922 original size:79 final size:79
Alignment explanation
Indices: 73834--73986 Score: 216
Period size: 79 Copynumber: 1.9 Consensus size: 79
73824 AGGTGTTTAC
* * * * *
73834 AAATTAAGCTCACAAAAACAATCTATGTACAAGAGAAAAGAAATAACAAAGAATTAAAAGTTTTT
1 AAATAAAGCTCACAAAAACAATATATGTACAAGAGAAAAGAAAGAACAAAGAATGAAAAGCTTTT
73899 CTCGTGATCCTATT
66 CTCGTGATCCTATT
* * * *
73913 AAATAAAGCTTACAAAAACACTATATGTATAAGAGAAAAGAAAGAACGAAGAATGAAAAGCTTTT
1 AAATAAAGCTCACAAAAACAATATATGTACAAGAGAAAAGAAAGAACAAAGAATGAAAAGCTTTT
*
73978 CTCTTGATC
66 CTCGTGATC
73987 ATTGTTGATT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (79 bp):
AAATAAAGCTCACAAAAACAATATATGTACAAGAGAAAAGAAAGAACAAAGAATGAAAAGCTTTT
CTCGTGATCCTATT
Done.