Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000794.1 Hibiscus syriacus cultivar Beakdansim tig00001537_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: 52102
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:104 original size:25 final size:25
Alignment explanation
Indices: 67--137 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 25
57 TTAAATTCAT
67 AATATTTTATATATATTAACTTAAAA
1 AATATTTT-TATATATTAACTTAAAA
***
93 AATA-TTTT-TATATT-ACTTTTTA
1 AATATTTTTATATATTAACTTAAAA
115 AATATATTTTAT-TATTAACTTAA
1 AATAT-TTTTATATATTAACTTAA
138 TTTAAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
22 9 0.25
23 6 0.17
24 9 0.25
25 8 0.22
26 4 0.11
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
AATATTTTTATATATTAACTTAAAA
Found at i:146 original size:29 final size:28
Alignment explanation
Indices: 82--184 Score: 85
Period size: 27 Copynumber: 3.9 Consensus size: 28
72 TTTATATATA
*
82 TTAACTTAAAAA-ATATTTTTATATT-AC
1 TTAATTTAAAAATATATTTTT-TATTAAC
109 TT--TTT--AAATATATTTTATTATTAAC
1 TTAATTTAAAAATATATTTT-TTATTAAC
* **
134 TTAATTTAAAAATAT-TTTTTTTTTATT
1 TTAATTTAAAAATATATTTTTTATTAAC
* *
161 TTCATTTAAAAATATATATTTTAT
1 TTAATTTAAAAATATATTTTTTAT
185 GTTAAAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
23 3 0.05
24 11 0.18
25 7 0.11
27 24 0.39
28 10 0.16
29 6 0.10
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (28 bp):
TTAATTTAAAAATATATTTTTTATTAAC
Found at i:148 original size:27 final size:25
Alignment explanation
Indices: 90--153 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 25
80 TATTAACTTA
90 AAAAATATTTTTATATT-ACTT-TTT
1 AAAAATATTTTT-TATTAACTTATTT
*
114 AAATATATTTTATTATTAACTTAATTT
1 AAAAATATTTT-TTATTAACTT-ATTT
141 AAAAATATTTTTT
1 AAAAATATTTTTT
154 TTTTATTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 14 0.41
25 5 0.15
26 2 0.06
27 13 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (25 bp):
AAAAATATTTTTTATTAACTTATTT
Found at i:953 original size:16 final size:17
Alignment explanation
Indices: 918--954 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
908 ATGGGATGAA
918 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
935 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
951 AAAA
1 AAAA
955 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:994 original size:15 final size:15
Alignment explanation
Indices: 974--1003 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
964 ACTACCATAA
*
974 TATTATTTTTTATAT
1 TATTATATTTTATAT
989 TATTATATTTTATAT
1 TATTATATTTTATAT
1004 ATAAATAATA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATATTTTATAT
Found at i:11701 original size:182 final size:182
Alignment explanation
Indices: 11394--11726 Score: 519
Period size: 182 Copynumber: 1.8 Consensus size: 182
11384 CCTTGCTAAA
* * *
11394 CACCCAATTCATTCACTAGCCCAGTAAGCCATAAAGCTTCTTTTGCATATTCAGATGCTTCCATG
1 CACCCAATTCATTCACTAGCCCAGTAAGCCATAAAACTTCTTTTGCAGATTCAGATGCTTCCATA
*
11459 TATTCAGCTTCAGTTGTAGATAATGCCACAATAGATTGAATAGTTGACTTCCAACATATAGGCCC
66 TATTCAGCTTCAGTTGTAGATAATGCCACAATAGATTGAACAGTTGACTTCCAACATATAGGCCC
11524 TCCACCAAGAGTAAAAACATACACAATCACAATGCAATTTTGAACTGGACCT
131 TCCACCAAGAGTAAAAACATACACAATCACAATGCAATTTTGAACTGGACCT
* * * * *
11576 CACCCAATTCATTTACTGGCCCAGTAAGCCATAAAACGTT-TTTTGCAGCTTTAGATG-TTGTCA
1 CACCCAATTCATTCACTAGCCCAGTAAGCCATAAAAC-TTCTTTTGCAGATTCAGATGCTT-CCA
* *
11639 TATATTTAGCTTCAGTTGTAGATAATGTCACAATAGACTT-AACAGTTGACTTCCAACATATAGG
64 TATATTCAGCTTCAGTTGTAGATAATGCCACAATAGA-TTGAACAGTTGACTTCCAACATATAGG
11703 CCCTCCACCAAGAGTAAAAACATA
128 CCCTCCACCAAGAGTAAAAACATA
11727 TCCAATTGTA
Statistics
Matches: 137, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
181 2 0.01
182 131 0.96
183 4 0.03
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (182 bp):
CACCCAATTCATTCACTAGCCCAGTAAGCCATAAAACTTCTTTTGCAGATTCAGATGCTTCCATA
TATTCAGCTTCAGTTGTAGATAATGCCACAATAGATTGAACAGTTGACTTCCAACATATAGGCCC
TCCACCAAGAGTAAAAACATACACAATCACAATGCAATTTTGAACTGGACCT
Found at i:16932 original size:28 final size:29
Alignment explanation
Indices: 16900--16956 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
16890 TTTTATTATT
16900 AATTTACGGTCTAGGATATAA-GGTTTAG
1 AATTTACGGTCTAGGATATAAGGGTTTAG
* * * *
16928 AATTTATGTTTTAGGATTTAAGGGTTTAG
1 AATTTACGGTCTAGGATATAAGGGTTTAG
16957 GGTCTTGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.42
Consensus pattern (29 bp):
AATTTACGGTCTAGGATATAAGGGTTTAG
Found at i:18879 original size:15 final size:15
Alignment explanation
Indices: 18859--18888 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18849 ATTCATTTAC
18859 ACCCATATATTCAAT
1 ACCCATATATTCAAT
18874 ACCCATATATTCAAT
1 ACCCATATATTCAAT
18889 CGCTAAAAAA
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:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (15 bp):
ACCCATATATTCAAT
Found at i:19950 original size:103 final size:102
Alignment explanation
Indices: 19684--19970 Score: 367
Period size: 102 Copynumber: 2.8 Consensus size: 102
19674 GGAGAAAAAC
* * * *
19684 AAACATCAAGATCAGGCAAGCACAGATGCATATATGAATTCATCGAGAACAACCGAGCTAATACT
1 AAACAACAAGATCAAGCAAGCACAGATGCATATATGAAGTCATCGAGAACAACCGAGCTAAAACT
* * ** * * *
19749 AGAAACGGTCAAAATACCTGAACACGACGGGTCGAGA
66 AGAGATGCCCAAAATACCTGAACACCACGGATCCAGA
* *
19786 AAACAGCAAGATCAAGCAAGCACATATGCATATATGAAGTCATCGAGAACAACCGAGCTAAAACT
1 AAACAACAAGATCAAGCAAGCACAGATGCATATATGAAGTCATCGAGAACAACCGAGCTAAAACT
* * *
19851 AGAGATTCCCAAAATACCTGAACCCCATGGATCCAGA
66 AGAGATGCCCAAAATACCTGAACACCACGGATCCAGA
* * * *
19888 AAACAACAAGATCAAGCAAAGCACAGATGCATATATAAAGTCACCGAGAACCACCGAGCTAAAAT
1 AAACAACAAGATCAAGC-AAGCACAGATGCATATATGAAGTCATCGAGAACAACCGAGCTAAAAC
**
19953 TAGAGATGATCAAAATAC
65 TAGAGATGCCCAAAATAC
19971 TCAAATCCGG
Statistics
Matches: 160, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
102 103 0.64
103 57 0.36
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.15
Consensus pattern (102 bp):
AAACAACAAGATCAAGCAAGCACAGATGCATATATGAAGTCATCGAGAACAACCGAGCTAAAACT
AGAGATGCCCAAAATACCTGAACACCACGGATCCAGA
Found at i:30291 original size:21 final size:20
Alignment explanation
Indices: 30257--30305 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
30247 ATCCCTATGC
* *
30257 AAAAGGATCAATCCCTTTGA
1 AAAATGATCAATCCCATTGA
* *
30277 TCAAATGATCGATCCCATTGA
1 -AAAATGATCAATCCCATTGA
30298 AAAATGAT
1 AAAATGAT
30306 TTATTCTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (20 bp):
AAAATGATCAATCCCATTGA
Found at i:36752 original size:60 final size:60
Alignment explanation
Indices: 36661--36796 Score: 164
Period size: 60 Copynumber: 2.3 Consensus size: 60
36651 CTAAACTATA
* * * * *
36661 ACCCTCATTTTATAGTAGTCCTTAAATTTTTGAATATTCTAATTTCATCCTCAAAATATG
1 ACCCTCATTCTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCTCAAAATATG
* * * * **
36721 ACTCTCATTCTAAATTAATCCTTATACTTTTGAATATTCTAATTTCATTCTTAAGCTATG
1 ACCCTCATTCTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCTCAAAATATG
*
36781 ACCCTCTTTCTAAATT
1 ACCCTCATTCTAAATT
36797 GGTATACAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (60 bp):
ACCCTCATTCTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCTCAAAATATG
Found at i:41833 original size:51 final size:49
Alignment explanation
Indices: 41773--41893 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 49
41763 ATACTTACAC
* * **
41773 CATATTTATACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAAAA
1 CATACTTATACCGGTGTAAGTGAATAAAAT-AAAAAGCGTAG-AAGTAAAA
* * * *
41824 TATACTTATATCGTTGTAAGTGAATAATATAAAAAGCGTAGAAGTAAAA
1 CATACTTATACCGGTGTAAGTGAATAAAATAAAAAGCGTAGAAGTAAAA
* *
41873 CATACTTACACTGGTGTAAGT
1 CATACTTATACCGGTGTAAGT
41894 ATGTATATCT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
49 22 0.39
50 10 0.18
51 25 0.44
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.30
Consensus pattern (49 bp):
CATACTTATACCGGTGTAAGTGAATAAAATAAAAAGCGTAGAAGTAAAA
Found at i:41891 original size:49 final size:51
Alignment explanation
Indices: 41784--41893 Score: 127
Period size: 49 Copynumber: 2.2 Consensus size: 51
41774 ATATTTATAC
* ** * *
41784 CGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAAAATATACTTATAT
1 CGGTGTAAGTGAATAAAATAAAAAAGCGTAGCAAGTAAAACATACTTACAT
* *
41835 CGTTGTAAGTGAATAATAT-AAAAAGCGTAG-AAGTAAAACATACTTACA-
1 CGGTGTAAGTGAATAAAATAAAAAAGCGTAGCAAGTAAAACATACTTACAT
41883 CTGGTGTAAGT
1 C-GGTGTAAGT
41894 ATGTATATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 1 0.02
49 22 0.44
50 10 0.20
51 17 0.34
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (51 bp):
CGGTGTAAGTGAATAAAATAAAAAAGCGTAGCAAGTAAAACATACTTACAT
Found at i:48598 original size:2 final size:2
Alignment explanation
Indices: 48591--48631 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
48581 GTTATTAATT
48591 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
48632 TAATGTGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50080 original size:2 final size:2
Alignment explanation
Indices: 50073--50107 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50063 TCAATCTACA
50073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50108 CTAAATTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.