Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002009.1 Hibiscus syriacus cultivar Beakdansim tig00004107_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: 65925
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3030 original size:54 final size:54
Alignment explanation
Indices: 2942--3293 Score: 490
Period size: 54 Copynumber: 6.5 Consensus size: 54
2932 TATATGTTGC
* *
2942 AATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATTAGTTTGTG
1 AATTACCGTATCGGCACTATGTGTGCAACCCAAGTAATTCATAATTAGTTTGTG
** * * * * *
2996 AATTGTCGTATTGGCACTATGTGTGCAACCTAAGTTATTCATAATGACTTTGTG
1 AATTACCGTATCGGCACTATGTGTGCAACCCAAGTAATTCATAATTAGTTTGTG
*
3050 AATTACCGTATCAGCACTATGTGTGCAACCCACA-TAATTCATAATTAGTTTGTG
1 AATTACCGTATCGGCACTATGTGTGCAACCCA-AGTAATTCATAATTAGTTTGTG
* * * *
3104 AATTACCGTATCGGCACTATGTGTGCAACCTACGTAATTTATAATTTGTTTGTG
1 AATTACCGTATCGGCACTATGTGTGCAACCCAAGTAATTCATAATTAGTTTGTG
*
3158 AATTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATTAGTTTGTG
1 AATTACCGTATCGGCACTATGTGTGCAACCCAAGTAATTCATAATTAGTTTGTG
* * * * *
3212 AATTACCATATCGACACTATGTGTACAACCCACGTAATTCATAATGAGTTTGTG
1 AATTACCGTATCGGCACTATGTGTGCAACCCAAGTAATTCATAATTAGTTTGTG
* *
3266 AATTACCGTATCGACACTATGAGTGCAA
1 AATTACCGTATCGGCACTATGTGTGCAA
3294 AACCATGAAA
Statistics
Matches: 268, Mismatches: 28, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
54 267 1.00
55 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (54 bp):
AATTACCGTATCGGCACTATGTGTGCAACCCAAGTAATTCATAATTAGTTTGTG
Found at i:5409 original size:19 final size:18
Alignment explanation
Indices: 5375--5411 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5365 AACCTAAGAC
5375 AAAATAATATAATAATAA
1 AAAATAATATAATAATAA
*
5393 AAAATTATATAAATAATAA
1 AAAATAATAT-AATAATAA
5412 TTTTTAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATAATATAATAATAA
Found at i:11039 original size:18 final size:18
Alignment explanation
Indices: 11018--11061 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
11008 GTTGTTTTTA
*
11018 AAATAAAAGATAATAATT
1 AAATAAAAGAAAATAATT
*
11036 AAATAAAAAGAAAATATTT
1 AAAT-AAAAGAAAATAATT
11055 AAATAAA
1 AAATAAA
11062 TAATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:11957 original size:53 final size:52
Alignment explanation
Indices: 11860--11962 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 52
11850 AATGAAAATA
* *
11860 CTTAAACTATTTAAACTAAAATACTAAAAATAAAGATAAGATAAAATATAACT
1 CTTAAAATATTTAAACTAAAATACTAAAAATAAACATAAGATAAAA-ATAACT
* * * *
11913 CTTAAAATATTTAAACTAAAATCCTAGAGATAAACAT-GGAATAAAAATAA
1 CTTAAAATATTTAAACTAAAATACTAAAAATAAACATAAG-ATAAAAATAA
11963 TCCTAAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
52 5 0.12
53 38 0.88
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (52 bp):
CTTAAAATATTTAAACTAAAATACTAAAAATAAACATAAGATAAAAATAACT
Found at i:16852 original size:18 final size:18
Alignment explanation
Indices: 16831--16873 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
16821 GTTATTTTTA
*
16831 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
16849 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
16867 AAATAAA
1 AAATAAA
16874 TAATTTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:23397 original size:90 final size:92
Alignment explanation
Indices: 23236--23402 Score: 259
Period size: 90 Copynumber: 1.8 Consensus size: 92
23226 AACTGCGTCC
* *
23236 GTAGGGCTTACCCTAAGCACAAAGCAAAAGGAAGTCAACCTAAGGATATTCCTTGGGGCCTATGG
1 GTAGGGCTTACCCTAAGCACAAAGCAAAAGGAAGCCAACCTAAGGATATGCCTTGGGGCCTATGG
23301 GCCTACCTAAGGATATTCTTTGGGTCT
66 GCCTACCTAAGGATATTCTTTGGGTCT
* * *
23328 GTAGGG-TTACCCTAAGCAGACTA-CAAAGGGAA-CCAACCTAAGGATATGCCTTGGGGCCTATG
1 GTAGGGCTTACCCTAAGCACA-AAGCAAAAGGAAGCCAACCTAAGGATATGCCTTGGGGCCTATG
23390 GGCCTACCTAAGG
65 GGCCTACCTAAGG
23403 GTATCCTTAG
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
90 41 0.59
91 21 0.30
92 7 0.10
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (92 bp):
GTAGGGCTTACCCTAAGCACAAAGCAAAAGGAAGCCAACCTAAGGATATGCCTTGGGGCCTATGG
GCCTACCTAAGGATATTCTTTGGGTCT
Found at i:24804 original size:27 final size:27
Alignment explanation
Indices: 24737--24804 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
24727 AATTCTAGGG
*
24737 TTTAGAGGTACTTTAGGCCATTTTACAC
1 TTTAGGGGTA-TTTAGGCCATTTTACAC
* *
24765 TTTA-GGGTCATTTTGGTCATTTTACAC
1 TTTAGGGGT-ATTTAGGCCATTTTACAC
24792 TTTAGGGGTATTT
1 TTTAGGGGTATTT
24805 CTATAATTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 26 0.74
28 9 0.26
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTAGGGGTATTTAGGCCATTTTACAC
Found at i:25724 original size:23 final size:23
Alignment explanation
Indices: 25697--25753 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
25687 GTCAACGGTT
*
25697 AACGGTTTAACTCGGTCAAAGTC
1 AACGGGTTAACTCGGTCAAAGTC
*
25720 AACGGGTTGACTCGGTCAAAGTC
1 AACGGGTTAACTCGGTCAAAGTC
*
25743 AACGAGTTAAC
1 AACGGGTTAAC
25754 CCAGTGAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (23 bp):
AACGGGTTAACTCGGTCAAAGTC
Found at i:36500 original size:14 final size:14
Alignment explanation
Indices: 36481--36527 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
36471 AAGCCAACAG
*
36481 GTTGACTCGGATGA
1 GTTGACTCAGATGA
*
36495 GTTGACTCAGATTA
1 GTTGACTCAGATGA
* *
36509 GTTGACTTAGACGA
1 GTTGACTCAGATGA
36523 GTTGA
1 GTTGA
36528 ATTAGTTTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.32
Consensus pattern (14 bp):
GTTGACTCAGATGA
Found at i:40588 original size:45 final size:45
Alignment explanation
Indices: 40519--40806 Score: 398
Period size: 45 Copynumber: 6.4 Consensus size: 45
40509 AATACACCAT
* *
40519 TATACACTTT-AATCTATAGCATACTTTTCTGCTGATAATGCACCCA
1 TATACA-TTTCAA-CTATAGTATACTTTTCTGTTGATAATGCACCCA
* * * *
40565 TATGCATTTCGACTATAGTATACTTTTCTGTTGAAAATGTACCCA
1 TATACATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
40610 TATACATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
1 TATACATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
* * *
40655 TATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACTCA
1 TATACATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
* * * * *
40700 TGTTCATTTCAACTATAGTATACTTTTCTATCGATAATGTACCCA
1 TATACATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
* *
40745 TATACATTTCAACTATAGTATACTTTTTTTGTTGATAATGTACCCA
1 TATACATTTCAACTATAGTATAC-TTTTCTGTTGATAATGCACCCA
40791 TATACATTTCAACTAT
1 TATACATTTCAACTAT
40807 GGCATCCTTT
Statistics
Matches: 215, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
45 174 0.81
46 41 0.19
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.41
Consensus pattern (45 bp):
TATACATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
Found at i:40685 original size:90 final size:90
Alignment explanation
Indices: 40519--40843 Score: 420
Period size: 90 Copynumber: 3.6 Consensus size: 90
40509 AATACACCAT
* *
40519 TATACACTTT-AATCTATAGCATACTTTTCTGCTGATAATGCACCCATATGCATTTCGACTATAG
1 TATACA-TTTCAA-CTATAGCATACTTTTCTGCCGATAATGCACCCATATGCATTTCAACTATAG
*
40583 TATACTTTTCTGTTGAAAATGTACCCA
64 TATACTTTTCTGTTGATAATGTACCCA
* ** *
40610 TATACATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCA
1 TATACATTTCAACTATAGCATACTTTTCTGCCGATAATGCACCCATATGCATTTCAACTATAGTA
* *
40675 TACTTTTCTGTTGATAATGCACTCA
66 TACTTTTCTGTTGATAATGTACCCA
* * * ** * *
40700 TGTTCATTTCAACTATAGTATACTTTTCTATCGATAATGTACCCATATACATTTCAACTATAGTA
1 TATACATTTCAACTATAGCATACTTTTCTGCCGATAATGCACCCATATGCATTTCAACTATAGTA
*
40765 TACTTTTTTTGTTGATAATGTACCCA
66 TAC-TTTTCTGTTGATAATGTACCCA
* * *
40791 TATACATTTCAACTATGGCAT-CCTTTCATGCCAATAATGCACCCATATGCATT
1 TATACATTTCAACTATAGCATACTTTTC-TGCCGATAATGCACCCATATGCATT
40844 ATTATTTTCA
Statistics
Matches: 204, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
90 140 0.69
91 64 0.31
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (90 bp):
TATACATTTCAACTATAGCATACTTTTCTGCCGATAATGCACCCATATGCATTTCAACTATAGTA
TACTTTTCTGTTGATAATGTACCCA
Found at i:41278 original size:20 final size:20
Alignment explanation
Indices: 41253--41306 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
41243 GACCCTTCAA
41253 TATCGATACCCCTA-TCATGG
1 TATCGATACCCCTACT-ATGG
*
41273 TATCGATACTACCCTACTTTGG
1 TATCGATAC--CCCTACTATGG
41295 TATCGATACCCC
1 TATCGATACCCC
41307 CTTCCAGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 12 0.40
22 17 0.57
23 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (20 bp):
TATCGATACCCCTACTATGG
Found at i:41367 original size:95 final size:95
Alignment explanation
Indices: 41253--41470 Score: 237
Period size: 95 Copynumber: 2.3 Consensus size: 95
41243 GACCCTTCAA
* * *
41253 TATCGATACCCCTATCATGGTATCGATACTACCCTACTT-TGGTA-TCGATACCCCCT-TCCAGT
1 TATCGATACCCCTACCATGGTATCGATACTACCATA-TTATGGTACT-GATA-CCCCTATACAGT
* **
41315 ATCAATACCAAATTTAGATTTGATGTGT-CCCAG
63 ATCAATACCAAAATTAGATTCAATGT-TACCCAG
* * * **
41348 TATCGATACCCTTACCATGGTATTGATACTACTATATTATGGTACTGATACCCCTATATGGTATC
1 TATCGATACCCCTACCATGGTATCGATACTACCATATTATGGTACTGATACCCCTATACAGTATC
* **
41413 AATACCAAAATTAGGTTCAATGTTACCTGG
66 AATACCAAAATTAGATTCAATGTTACCCAG
*
41443 TATCGATACCCCAACCATGGTATCGATA
1 TATCGATACCCCTACCATGGTATCGATA
41471 GCACCTCGTT
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
94 8 0.08
95 93 0.91
96 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (95 bp):
TATCGATACCCCTACCATGGTATCGATACTACCATATTATGGTACTGATACCCCTATACAGTATC
AATACCAAAATTAGATTCAATGTTACCCAG
Found at i:41404 original size:22 final size:22
Alignment explanation
Indices: 41364--41406 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41354 TACCCTTACC
* *
41364 ATGGTATTGATACTACTATATT
1 ATGGTACTGATACCACTATATT
*
41386 ATGGTACTGATACCCCTATAT
1 ATGGTACTGATACCACTATAT
41407 GGTATCAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (22 bp):
ATGGTACTGATACCACTATATT
Found at i:42545 original size:2 final size:2
Alignment explanation
Indices: 42538--42591 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
42528 TTTTATTGTC
42538 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
42580 AT AT AT AT AT AT
1 AT AT AT AT AT AT
42592 TAATTTTATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43021 original size:31 final size:31
Alignment explanation
Indices: 42981--43046 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
42971 AAGTAATAAT
* *
42981 TTGGTCACTAACGTTATCGATTTGTAACAAA
1 TTGGCCACTAACGTTATCGATTTATAACAAA
* *
43012 TTGGCCACTAATGTTATCGATTTATAACTAA
1 TTGGCCACTAACGTTATCGATTTATAACAAA
43043 TTGG
1 TTGG
43047 TCATTGGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (31 bp):
TTGGCCACTAACGTTATCGATTTATAACAAA
Found at i:45746 original size:19 final size:20
Alignment explanation
Indices: 45714--45761 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
45704 AATGATTTTC
* * *
45714 TTTTGAAATCAAAATTG-GA
1 TTTTGAAAACAAAAATGAAA
*
45733 TTTTGAAAAGAAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
45753 TTTTGAAAA
1 TTTTGAAAA
45762 ATTAGTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.33
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:49894 original size:64 final size:63
Alignment explanation
Indices: 49823--49973 Score: 189
Period size: 64 Copynumber: 2.3 Consensus size: 63
49813 ATAGTCAATA
* *
49823 TTGCATTTAGATAA-CGCATAGCAGAGTCAATATTCCATT-AAGATAATACATAGTAGAGTTAGT
1 TTGCATTTAGATAATCACA-AG-AGAGTCAATATTACATTCAA-ATAATACATAGTAGAGTTAGT
49886 G
63 G
* * *
49887 TTGCATTTAGATAATTCACAAGAGCGTCAGTATTACATTCAAATAATGCATAGTAGAGTTAGTG
1 TTGCATTTAGATAA-TCACAAGAGAGTCAATATTACATTCAAATAATACATAGTAGAGTTAGTG
*
49951 TTGCATTCAGATAATGCACAAGA
1 TTGCATTTAGATAAT-CACAAGA
49974 TTGTTAGTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 69 0.90
65 4 0.05
66 3 0.04
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (63 bp):
TTGCATTTAGATAATCACAAGAGAGTCAATATTACATTCAAATAATACATAGTAGAGTTAGTG
Found at i:49966 original size:32 final size:32
Alignment explanation
Indices: 49780--49968 Score: 137
Period size: 32 Copynumber: 5.9 Consensus size: 32
49770 TGAGGCACAA
* * * * *
49780 CAGAGTTAGTTTTGCATTCATATAGTGCATAA
1 CAGAGTCAGTATTGCATTCAGATAATGCATAG
* * * *
49812 CATAGTCAATATTGCATTTAGATAACGCATAG
1 CAGAGTCAGTATTGCATTCAGATAATGCATAG
* * * *
49844 CAGAGTCAATATTCCATTAAGATAATACATAG
1 CAGAGTCAGTATTGCATTCAGATAATGCATAG
* * * * * *
49876 TAGAGTTAGTGTTGCATTTAGATAATTCACAAG
1 CAGAGTCAGTATTGCATTCAGATAATGCA-TAG
* * *
49909 -AGCGTCAGTATTACATTCAAATAATGCATAG
1 CAGAGTCAGTATTGCATTCAGATAATGCATAG
* * *
49940 TAGAGTTAGTGTTGCATTCAGATAATGCA
1 CAGAGTCAGTATTGCATTCAGATAATGCA
49969 CAAGATTGTT
Statistics
Matches: 120, Mismatches: 35, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
31 2 0.02
32 116 0.97
33 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
CAGAGTCAGTATTGCATTCAGATAATGCATAG
Done.