Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004815.1 Hibiscus syriacus cultivar Beakdansim tig00010850_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: 62370
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4690 original size:4 final size:4
Alignment explanation
Indices: 4663--4707 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
4653 CAATGACCAT
* * *
4663 CATA CGTA CCTA CATA CCTA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
4708 CCCTCTCTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.42, C:0.31, G:0.02, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:5554 original size:12 final size:12
Alignment explanation
Indices: 5539--5567 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5529 GAAACCCGAG
5539 GAGAAGAAAGAA
1 GAGAAGAAAGAA
5551 GAGAAGAAAGAA
1 GAGAAGAAAGAA
5563 GAGAA
1 GAGAA
5568 AAAAACCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
GAGAAGAAAGAA
Found at i:12933 original size:155 final size:155
Alignment explanation
Indices: 12651--12961 Score: 595
Period size: 155 Copynumber: 2.0 Consensus size: 155
12641 AGATTATATT
12651 ATAGAAGGAAATGTTGCATACTGCCTTTTAATAGAGGACGGTGAGCCATCAACATACCAGGAGGC
1 ATAGAAGGAAATGTTGCATACTGCCTTTTAATAGAGGACGGTGAGCCATCAACATACCAGGAGGC
* *
12716 AATAAACAGTTCATGTGTTTCACTGTGGATGATGGTGATGCAAGAAGAAATTGAAGCCCTTCATA
66 AATAAACAGTTCATATGTTTCACTGTGGATGATGGTGATGCAAGAAGAAATTCAAGCCCTTCATA
12781 AAAATAATACATGAGACCTTGTGCC
131 AAAATAATACATGAGACCTTGTGCC
12806 ATAGAAGGAAATGTTGCATACTGCCTTTTAATAGAGGACGGTGAGCCATCAACATACCAGGAGGC
1 ATAGAAGGAAATGTTGCATACTGCCTTTTAATAGAGGACGGTGAGCCATCAACATACCAGGAGGC
12871 AATAAACAGTTCATATGTTTCACTGTGGATGATGGTGATGCAAGAAGAAATTCAAGCCCTTCATA
66 AATAAACAGTTCATATGTTTCACTGTGGATGATGGTGATGCAAGAAGAAATTCAAGCCCTTCATA
*
12936 AAAATAATACATGGGACCTTGTGCC
131 AAAATAATACATGAGACCTTGTGCC
12961 A
1 A
12962 CTACCACAAG
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
155 153 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (155 bp):
ATAGAAGGAAATGTTGCATACTGCCTTTTAATAGAGGACGGTGAGCCATCAACATACCAGGAGGC
AATAAACAGTTCATATGTTTCACTGTGGATGATGGTGATGCAAGAAGAAATTCAAGCCCTTCATA
AAAATAATACATGAGACCTTGTGCC
Found at i:16716 original size:82 final size:82
Alignment explanation
Indices: 16608--16766 Score: 300
Period size: 82 Copynumber: 1.9 Consensus size: 82
16598 ATTTAAAATT
16608 AATTTAGAGTAAAGTTTGAATATTTATTTTTATATTAAACCTAAAAATTAATAATTCATATAAAA
1 AATTTAGAGTAAAGTTTGAATATTTATTTTTATATTAAACCTAAAAATTAATAATTCATATAAAA
16673 TGAATTATAAAATTTTA
66 TGAATTATAAAATTTTA
* *
16690 AATTTAGAGTATAGTTTGAATATTTATTTTTATATTAAATCTAAAAATTAATAATTCATATAAAA
1 AATTTAGAGTAAAGTTTGAATATTTATTTTTATATTAAACCTAAAAATTAATAATTCATATAAAA
16755 TGAATTATAAAA
66 TGAATTATAAAA
16767 CATTGTTTAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (82 bp):
AATTTAGAGTAAAGTTTGAATATTTATTTTTATATTAAACCTAAAAATTAATAATTCATATAAAA
TGAATTATAAAATTTTA
Found at i:17994 original size:20 final size:20
Alignment explanation
Indices: 17949--17994 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
17939 CTCAAATTAT
17949 ATCTCA-AACCCTAAACCTC
1 ATCTCACAACCCTAAACCTC
* *
17968 ATATCACAACCC-AATCCTC
1 ATCTCACAACCCTAAACCTC
17987 ACTCTCAC
1 A-TCTCAC
17995 TTAGAGTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (20 bp):
ATCTCACAACCCTAAACCTC
Found at i:18267 original size:2 final size:2
Alignment explanation
Indices: 18262--18290 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18252 TGTGAGTAAT
18262 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18291 TGAATAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19428 original size:33 final size:33
Alignment explanation
Indices: 19391--19455 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
19381 GGTTTTTTGG
19391 ACTCAAGGTATCTGAAAAACTCAGAATTCTTGT
1 ACTCAAGGTATCTGAAAAACTCAGAATTCTTGT
*
19424 ACTCAAGGTATCTGAAAATCTCAGAATTCTTG
1 ACTCAAGGTATCTGAAAAACTCAGAATTCTTG
19456 GAGCTGTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (33 bp):
ACTCAAGGTATCTGAAAAACTCAGAATTCTTGT
Found at i:20209 original size:36 final size:36
Alignment explanation
Indices: 20159--20234 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
20149 TTATAGCAAA
*
20159 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
20195 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
20231 AAAA
1 AAAA
20235 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:24725 original size:15 final size:15
Alignment explanation
Indices: 24707--24736 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24697 CCACGGTGCT
24707 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
24722 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
24737 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:25215 original size:36 final size:36
Alignment explanation
Indices: 25165--25240 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
25155 TTATAGCAAA
*
25165 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
25201 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
25237 AAAA
1 AAAA
25241 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:27113 original size:19 final size:19
Alignment explanation
Indices: 27054--27113 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
27044 TACTAAAACA
27054 ATAAGTAATTTGATTAATT
1 ATAAGTAATTTGATTAATT
* * * * **
27073 ATAATTATTTTTA-AAACA
1 ATAAGTAATTTGATTAATT
27091 ATAAGTAATTTGATTAATT
1 ATAAGTAATTTGATTAATT
27110 ATAA
1 ATAA
27114 TTAAATAATT
Statistics
Matches: 28, Mismatches: 12, Indels: 2
0.67 0.29 0.05
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (19 bp):
ATAAGTAATTTGATTAATT
Found at i:37400 original size:35 final size:35
Alignment explanation
Indices: 37349--37420 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
37339 AACAGTCCTT
*
37349 AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
1 AATTACATTCTAAACCCCAAATTCCAAAATAATTC
* *
37384 AATTACATTCTAAACCCCAAATTCTAAAATACTTC
1 AATTACATTCTAAACCCCAAATTCCAAAATAATTC
37419 AA
1 AA
37421 AATAATATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (35 bp):
AATTACATTCTAAACCCCAAATTCCAAAATAATTC
Found at i:38556 original size:35 final size:35
Alignment explanation
Indices: 38510--38577 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
38500 TATTATTTTG
* * * *
38510 ATTATTTTGGAATTTGGGGTTTATAATGTAATTGA
1 ATTATTTTGGAATTTAGAGTTTAGAATGAAATTGA
38545 ATTATTTTGGAATTTAGAGTTTAGAATGAAATT
1 ATTATTTTGGAATTTAGAGTTTAGAATGAAATT
38578 AAGGACTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (35 bp):
ATTATTTTGGAATTTAGAGTTTAGAATGAAATTGA
Found at i:39779 original size:93 final size:90
Alignment explanation
Indices: 39620--39804 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 90
39610 CCCCTGAAAT
39620 CTCTATGACAACCATTTGTTTTAAACACATGTTCAATCATGCTTAGAATATGAGTATACATGTGT
1 CTCTATGACAACCATTTGTTTTAAACACATGTTCAATCATGCTTAGAATATGAGTATACATGTGT
*
39685 TGAACATATTCCTTTATCCTGTACTCAC
66 TGAAC--A-TCCTTTATCCTGCACTCAC
* *
39713 CTCTATGACAGCCATTTGTTTTAAACACATGTTCGATCATGCTTAGAATATGAGTATACATGTGT
1 CTCTATGACAACCATTTGTTTTAAACACATGTTCAATCATGCTTAGAATATGAGTATACATGTGT
39778 TGAACATCCTTTATCCTGCACTCAC
66 TGAACATCCTTTATCCTGCACTCAC
39803 CT
1 CT
39805 GTTGTGAACT
Statistics
Matches: 89, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
90 20 0.22
91 1 0.01
93 68 0.76
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (90 bp):
CTCTATGACAACCATTTGTTTTAAACACATGTTCAATCATGCTTAGAATATGAGTATACATGTGT
TGAACATCCTTTATCCTGCACTCAC
Found at i:45876 original size:20 final size:20
Alignment explanation
Indices: 45851--45908 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
45841 TTTGGTTCAC
*
45851 GGAATGTAAGATTATCAGTG
1 GGAATGTAAGATTACCAGTG
45871 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
**
45891 GGAATAAAAGATTACCAG
1 GGAATGTAAGATTACCAG
45909 AGAATAGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:49487 original size:36 final size:35
Alignment explanation
Indices: 49418--49523 Score: 194
Period size: 36 Copynumber: 3.0 Consensus size: 35
49408 TTATTTATTC
*
49418 GTTAAAGATATGTGATGTGATATTTGCTTAAGTAT
1 GTTAAAGATATGTGATGTGACATTTGCTTAAGTAT
49453 GTTAAAGATATGTGATGTGACATTTTGCTTAAGTAT
1 GTTAAAGATATGTGATGTGACA-TTTGCTTAAGTAT
49489 GTTAAAGATATGTGATGTGACATTTGCTTAAGTAT
1 GTTAAAGATATGTGATGTGACATTTGCTTAAGTAT
49524 ATAGTGTCTC
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
35 34 0.49
36 35 0.51
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.42
Consensus pattern (35 bp):
GTTAAAGATATGTGATGTGACATTTGCTTAAGTAT
Found at i:56189 original size:18 final size:18
Alignment explanation
Indices: 56166--56256 Score: 110
Period size: 18 Copynumber: 4.9 Consensus size: 18
56156 ACTGAATATT
56166 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * *
56184 TGTCCCAAAGGACCATTGTT
1 TGTCCCGAAGGACCA--CTA
* *
56204 TGTTCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
56222 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
56240 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
56257 GATAATCCCT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
18 47 0.78
20 13 0.22
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:56219 original size:38 final size:38
Alignment explanation
Indices: 56164--56236 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
56154 GCACTGAATA
*
56164 TTTGTCCCGAAGGACCACTATGTCCCAAAGGACCATTG
1 TTTGTCCCGAAGAACCACTATGTCCCAAAGGACCATTG
* *
56202 TTTGTTCCGAAGAACCACTATGTCCCGAAGGACCA
1 TTTGTCCCGAAGAACCACTATGTCCCAAAGGACCA
56237 CTATATCCCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (38 bp):
TTTGTCCCGAAGAACCACTATGTCCCAAAGGACCATTG
Found at i:56501 original size:2 final size:2
Alignment explanation
Indices: 56487--56532 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
56477 ATGGAATCAC
*
56487 TA TA TA T- TA -A TA TA TA TA TA TA TA TA T- TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
56526 TG TA TA T
1 TA TA TA T
56533 GGAATCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61869 original size:22 final size:22
Alignment explanation
Indices: 61814--61875 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
61804 CATTTGTCGG
*
61814 ATGAACTGATCCCCGATGACAA
1 ATGAACTGATCTCCGATGACAA
61836 ATGAACTGATCTCCGATGACAA
1 ATGAACTGATCTCCGATGACAA
*
61858 ATGAACTGATCTCTGATG
1 ATGAACTGATCTCCGATG
61876 TATTTATGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (22 bp):
ATGAACTGATCTCCGATGACAA
Done.