Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008463.1 Hibiscus syriacus cultivar Beakdansim tig00111276_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: 1833679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:1809019 original size:42 final size:42
Alignment explanation
Indices: 1808973--1809060 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1808963 TTATATTGGC
**
1808973 GTTTTGT-CCACAAACACTTCTAATTATCCTGTCTTTAGTGGT
1 GTTTTGTGCCACAAACACCACTAATTATCCTG-CTTTAGTGGT
* * * *
1809015 GTTTTTTGCCACAAACGCCACTAATTCTCTTGCTTTAGTGGT
1 GTTTTGTGCCACAAACACCACTAATTATCCTGCTTTAGTGGT
1809057 GTTT
1 GTTT
1809061 GTAATACTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 20 0.51
43 19 0.49
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (42 bp):
GTTTTGTGCCACAAACACCACTAATTATCCTGCTTTAGTGGT
Found at i:1809027 original size:43 final size:43
Alignment explanation
Indices: 1808974--1809060 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
1808964 TATATTGGCG
**
1808974 TTTTGTCCACAAACACTTCTAATTATCCTGTCTTTAGTGGTGTT
1 TTTTGTCCACAAACACCACTAATTATCCTG-CTTTAGTGGTGTT
* * *
1809018 TTTTG-CCACAAACGCCACTAATTCTCTTGCTTTAGTGGTGTT
1 TTTTGTCCACAAACACCACTAATTATCCTGCTTTAGTGGTGTT
1809060 T
1 T
1809061 GTAATACTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 14 0.37
43 19 0.50
44 5 0.13
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.44
Consensus pattern (43 bp):
TTTTGTCCACAAACACCACTAATTATCCTGCTTTAGTGGTGTT
Found at i:1819592 original size:21 final size:21
Alignment explanation
Indices: 1819563--1819666 Score: 97
Period size: 21 Copynumber: 4.9 Consensus size: 21
1819553 CGGAAAATGA
1819563 AGCAG-GGAAACAGAGAGAGC
1 AGCAGCGGAAACAGAGAGAGC
* **
1819583 AGCAGCGGAAGCAGCTAGAGC
1 AGCAGCGGAAACAGAGAGAGC
* *
1819604 AGCAGCGGAAGCAGAGAGAGA
1 AGCAGCGGAAACAGAGAGAGC
*
1819625 AGCAGCGGCAGCACAGAGAGAG-
1 AGCAGCGG-A-AACAGAGAGAGC
1819647 -GCAGCGGCAGAACAGAGAGA
1 AGCAGCGG-A-AACAGAGAGA
1819667 AGTAATGTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
20 5 0.07
21 57 0.79
22 1 0.01
23 9 0.12
ACGTcount: A:0.39, C:0.19, G:0.40, T:0.01
Consensus pattern (21 bp):
AGCAGCGGAAACAGAGAGAGC
Found at i:1820206 original size:43 final size:42
Alignment explanation
Indices: 1820004--1820272 Score: 134
Period size: 43 Copynumber: 6.2 Consensus size: 42
1819994 CATACATTTA
* * * * * *
1820004 GCGGCGTTTTTGATAAAAACGCCGCAAAATCTCAATACATATTCT
1 GCGGCG-TTTTAATGAAAACGCCGCTAAATATCAAAACCTA-T-T
* * * * * * ** *
1820049 GCGGCGTTTTTAGGAAAACACCGGTAAAAATAAAAATTTACT
1 GCGGCGTTTTAATGAAAACGCCGCTAAATATCAAAACCTATT
* *
1820091 GCGGCGTTTTGGAA-GAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTT--AATGAAAACGCCGCTAAATATCAA-AACCTATT
* * * *
1820134 GCGGCGTTTGT-CTGCCAAATGCCGTTAAATATCAAAACCTATT
1 GCGGCGTTT-TAATG-AAAACGCCGCTAAATATCAAAACCTATT
* *
1820177 GCGGCGTTTTAATGATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTTAATGA-AAACGCCGCTAAATATCAAAACCTATT
* * * ***
1820220 GTGGCGTTTGT--TGAACAATCGCCGCTATATGTTGTAACCTATT
1 GCGGCGTTT-TAATGAA-AA-CGCCGCTAAATATCAAAACCTATT
1820263 GCGGCGTTTT
1 GCGGCGTTTT
1820273 TTGTTGAAAA
Statistics
Matches: 170, Mismatches: 42, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
41 1 0.01
42 20 0.12
43 117 0.69
44 26 0.15
45 6 0.04
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
GCGGCGTTTTAATGAAAACGCCGCTAAATATCAAAACCTATT
Found at i:1821882 original size:82 final size:80
Alignment explanation
Indices: 1821712--1822067 Score: 305
Period size: 82 Copynumber: 4.4 Consensus size: 80
1821702 AATTATTGCG
* ** * * * **
1821712 GCGTTTGTA-AAATAACACCGCTAAAGTACTACTCTGTGGCAACG-TTCTTGAAAAATGCCGCTA
1 GCGTTTGTATAAA-AACACCACTAAAGTACTACTCTGTCACGACGTTTGTTGAAAAAAGCAACTA
*
1821775 TGAATGAACCCTATT-A
65 TGGATGAA-CCTATTCA
* * * * *
1821791 TGGCATTTGTATAAAAATACCATTAAAGTACTACTCTGTCACGACATTTGTTGAAAAAAGCTACT
1 --GCGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACGACGTTTGTTGAAAAAAGCAACT
1821856 ATGGATGAACCGTATTGCA
64 ATGGATGAACC-TATT-CA
* ** *
1821875 GCGTTTGTATAAAAACGCTGCTAAAGTACTACTCTGTCGCGACGTTTGTTGAAAAACA-CAACTA
1 GCGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACGACGTTTGTTGAAAAA-AGCAACTA
1821939 TGGATGAACCCTATT-A
65 TGGATGAA-CCTATTCA
* * * * * *
1821955 TGACG-TT-TAT-AAAATACCGCTAAAGTACTACTCTGTCACAATGTTTGTTGAAAAACGCCACT
1 -G-CGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACGACGTTTGTTGAAAAAAGCAACT
* *
1822017 ATGGATGAATCTATTTCG
64 ATGGATGAACCTA-TTCA
* *
1822035 GCGTTTGTATAAAAACGCCACTAAAGTATTACT
1 GCGTTTGTATAAAAACACCACTAAAGTACTACT
1822068 TTATCGCAGA
Statistics
Matches: 224, Mismatches: 36, Indels: 30
0.77 0.12 0.10
Matches are distributed among these distances:
78 5 0.02
79 57 0.25
80 7 0.03
81 55 0.25
82 96 0.43
83 3 0.01
84 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (80 bp):
GCGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACGACGTTTGTTGAAAAAAGCAACTAT
GGATGAACCTATTCA
Found at i:1822093 original size:161 final size:164
Alignment explanation
Indices: 1821705--1822074 Score: 428
Period size: 161 Copynumber: 2.3 Consensus size: 164
1821695 CATATCAAAT
* * * * * * * *
1821705 TATTGCGGCGTTTGTA-AAATAACACCGCTAAAGTACTACTCTGTGGCAACG-TTCTTGAAAAAT
1 TATTGCAGCGTTTGTATAAA-AACGCCACTAAAGTACTACTCTATCGCGACGTTTGTTGAAAAAC
* ** * * *
1821768 GCCGCTATGAATGAACCCTATTATGGCATTTGTATAAAAATACCATTAAAGTACTACTCTGTCAC
65 ACAACTATGAATGAACCCTATTATGACAGTTGTATAAAAATACCACTAAAGTACTACTCTGTCAC
* *
1821833 GACATTTGTTGAAAAAAGCTACTATGGATGAACCG
130 AACATTTGTTGAAAAAAGCCACTATGGATGAACCG
** *
1821868 TATTGCAGCGTTTGTATAAAAACGCTGCTAAAGTACTACTCTGTCGCGACGTTTGTTGAAAAACA
1 TATTGCAGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTATCGCGACGTTTGTTGAAAAACA
* *
1821933 CAACTATGGATGAACCCTATTATGAC-GTT-TAT-AAAATACCGCTAAAGTACTACTCTGTCACA
66 CAACTATGAATGAACCCTATTATGACAGTTGTATAAAAATACCACTAAAGTACTACTCTGTCACA
** * *
1821995 ATGTTTGTTGAAAAACGCCACTATGGATGAATC-
131 ACATTTGTTGAAAAAAGCCACTATGGATGAACCG
* * * *
1822028 TATTTCGGCGTTTGTATAAAAACGCCACTAAAGTATTACTTTATCGC
1 TATTGCAGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTATCGC
1822075 AGAGTTTTGT
Statistics
Matches: 177, Mismatches: 28, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
160 40 0.23
161 55 0.31
162 3 0.02
163 44 0.25
164 35 0.20
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (164 bp):
TATTGCAGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTATCGCGACGTTTGTTGAAAAACA
CAACTATGAATGAACCCTATTATGACAGTTGTATAAAAATACCACTAAAGTACTACTCTGTCACA
ACATTTGTTGAAAAAAGCCACTATGGATGAACCG
Found at i:1822344 original size:16 final size:16
Alignment explanation
Indices: 1822323--1822362 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1822313 TGAAGCCGTT
1822323 GGGAAATAGTAAGAAG
1 GGGAAATAGTAAGAAG
1822339 GGGAAATAGTAAGAAG
1 GGGAAATAGTAAGAAG
1822355 GGGAAATA
1 GGGAAATA
1822363 ATGCCAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (16 bp):
GGGAAATAGTAAGAAG
Found at i:1822727 original size:18 final size:18
Alignment explanation
Indices: 1822704--1822739 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1822694 CATTAAATTT
1822704 TAAGTGATGTATCGTTTG
1 TAAGTGATGTATCGTTTG
1822722 TAAGTGATGTATCGTTTG
1 TAAGTGATGTATCGTTTG
1822740 CATTATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (18 bp):
TAAGTGATGTATCGTTTG
Found at i:1824229 original size:22 final size:24
Alignment explanation
Indices: 1824187--1824231 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
1824177 CAGCCTTATG
1824187 TTTTCTAACATGATAAATATAATA
1 TTTTCTAACATGATAAATATAATA
1824211 TTTT-TAACATGA-AAATATAAT
1 TTTTCTAACATGATAAATATAAT
1824232 CAATTAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.43
23 8 0.38
24 4 0.19
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (24 bp):
TTTTCTAACATGATAAATATAATA
Found at i:1831656 original size:22 final size:22
Alignment explanation
Indices: 1831628--1831671 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1831618 ATTCTGCAAG
*
1831628 GATGATAGATT-ATCTTTTCAAA
1 GATGATAAATTCA-CTTTTCAAA
1831650 GATGATAAATTCACTTTTCAAA
1 GATGATAAATTCACTTTTCAAA
1831672 ACGAAAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
GATGATAAATTCACTTTTCAAA
Found at i:1832017 original size:13 final size:13
Alignment explanation
Indices: 1832001--1832025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1831991 TGCATTCATC
1832001 ATGCATTTCATTA
1 ATGCATTTCATTA
1832014 ATGCATTTCATT
1 ATGCATTTCATT
1832026 GCATTGCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
ATGCATTTCATTA
Found at i:1832493 original size:91 final size:84
Alignment explanation
Indices: 1832414--1832582 Score: 198
Period size: 85 Copynumber: 2.0 Consensus size: 84
1832404 GTGAAGCAGA
* * * *
1832414 AAGCAAGA-ACCAAAATTTAGTTTTCACGGAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATCA
1 AAGCAAAAGACCAAAATTCAGTTTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATCA
1832478 AACTTCACAGAAGAGTAGTG
66 AACTTCAC-GAAGAGTAGTG
* * ** *
1832498 AAGCAAAAGACCAAAATCTGAG-CTCCACGAAAGAGTAGTGGAACAAATTTTTCAGCAAAGTATG
1 AAGCAAAAGACCAAAAT-TCAGTTTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATC
* *
1832562 GAACTCCACGAAAGAGTAGTG
65 AAACTTCACG-AAGAGTAGTG
1832583 GAATAAAATT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 8 0.11
85 61 0.85
86 3 0.04
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (84 bp):
AAGCAAAAGACCAAAATTCAGTTTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATCA
AACTTCACGAAGAGTAGTG
Found at i:1833123 original size:12 final size:12
Alignment explanation
Indices: 1833106--1833130 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1833096 CGTCCGAATG
1833106 ACGTTATTATAT
1 ACGTTATTATAT
1833118 ACGTTATTATAT
1 ACGTTATTATAT
1833130 A
1 A
1833131 TAATAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (12 bp):
ACGTTATTATAT
Done.