Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001879.1 Hibiscus syriacus cultivar Beakdansim tig00003815_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: 72063
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:7130 original size:19 final size:19
Alignment explanation
Indices: 7106--7143 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
7096 GATTTCATTG
7106 ATAAAAGGAAATGTTGTTT
1 ATAAAAGGAAATGTTGTTT
*
7125 ATAAAAGGGAATGTTGTTT
1 ATAAAAGGAAATGTTGTTT
7144 CTCTTACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (19 bp):
ATAAAAGGAAATGTTGTTT
Found at i:14665 original size:12 final size:12
Alignment explanation
Indices: 14648--14672 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14638 AAAGAAAAGA
14648 TTGCAGACACTG
1 TTGCAGACACTG
14660 TTGCAGACACTG
1 TTGCAGACACTG
14672 T
1 T
14673 ATGTGATGCA
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:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TTGCAGACACTG
Found at i:22581 original size:21 final size:21
Alignment explanation
Indices: 22525--22581 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
22515 GGATGCAACC
* *
22525 ACTGCTCCACTTGATTCTTCC
1 ACTGCTCCAATTGATTCTTCA
* *
22546 ACGGCTCCAACTGATTCTTCA
1 ACTGCTCCAATTGATTCTTCA
*
22567 ACTGCTCTAATTGAT
1 ACTGCTCCAATTGAT
22582 CCTTAGCTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (21 bp):
ACTGCTCCAATTGATTCTTCA
Found at i:22598 original size:54 final size:54
Alignment explanation
Indices: 22534--22639 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
22524 CACTGCTCCA
* *
22534 CTTGATTCTTCCACGGCTCCAACTGATTCTTCAACTGCTCTAATTGATCCTTAG
1 CTTGATTCTTCCACGGCTCCAACTGAATCTTAAACTGCTCTAATTGATCCTTAG
* *
22588 CTTGATTCTTCCACGGCTCCAATTGAATCTTAAACTGCTCTAATTGCTCCTT
1 CTTGATTCTTCCACGGCTCCAACTGAATCTTAAACTGCTCTAATTGATCCTT
22640 CCACTGTTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (54 bp):
CTTGATTCTTCCACGGCTCCAACTGAATCTTAAACTGCTCTAATTGATCCTTAG
Found at i:40754 original size:8 final size:7
Alignment explanation
Indices: 40739--40864 Score: 64
Period size: 7 Copynumber: 17.3 Consensus size: 7
40729 ATTTTGCTTG
40739 AAGAAAA
1 AAGAAAA
40746 AATGAAAA
1 AA-GAAAA
* *
40754 AA-TAAT
1 AAGAAAA
*
40760 AATAAAA
1 AAGAAAA
*
40767 ATGAGAAA
1 AAGA-AAA
40775 AAG-AAA
1 AAGAAAA
40781 AAGAAGAA
1 AAGAA-AA
40789 AAGAAGAA
1 AAGAA-AA
40797 AAGAAAA
1 AAGAAAA
40804 AATGAGAAA
1 AA-GA-AAA
40813 AA-ATAAA
1 AAGA-AAA
40820 AATGGAAAA
1 AA--GAAAA
*
40829 AA-AAGA
1 AAGAAAA
40835 AAGAAAA
1 AAGAAAA
40842 ATA-AAAA
1 A-AGAAAA
*
40849 GAGAAAA
1 AAGAAAA
*
40856 ATGAAAA
1 AAGAAAA
40863 AA
1 AA
40865 AAAGAGAGAA
Statistics
Matches: 92, Mismatches: 14, Indels: 26
0.70 0.11 0.20
Matches are distributed among these distances:
6 16 0.17
7 35 0.38
8 30 0.33
9 10 0.11
10 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (7 bp):
AAGAAAA
Found at i:40867 original size:38 final size:38
Alignment explanation
Indices: 40760--40867 Score: 114
Period size: 38 Copynumber: 2.7 Consensus size: 38
40750 AAAAAATAAT
*
40760 AATAAAAATGAGAAAAA-GAAAAAGAAGAAAAGAAGAAA
1 AATAAAAATGAGAAAAATGAAAAA-AAAAAAAGAAGAAA
*
40798 AGA-AAAAATGAGAAAAAATAAAAATGGAAAAAAAAGAAAGAAA
1 A-ATAAAAATGAG-AAAAATGAAAA---AAAAAAAAG-AAGAAA
40841 AATAAAAA-GAGAAAAATGAAAAAAAAA
1 AATAAAAATGAGAAAAATGAAAAAAAAA
40868 GAGAGAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 16
0.76 0.04 0.21
Matches are distributed among these distances:
38 15 0.25
39 6 0.10
40 4 0.07
41 10 0.17
42 11 0.19
43 13 0.22
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (38 bp):
AATAAAAATGAGAAAAATGAAAAAAAAAAAAGAAGAAA
Found at i:42415 original size:107 final size:102
Alignment explanation
Indices: 42194--42555 Score: 325
Period size: 104 Copynumber: 3.4 Consensus size: 102
42184 GAAGCAAATT
* * *
42194 CGTTTGTTGAAGATCGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGAT
1 CGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGAT
* *
42259 TGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
66 TGAGTCCTATACTCTCTGAATGAATAGAGAACGGACA
* * ** *
42296 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGA
1 CGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA
* * *
42361 TTGTTCGAGTTCTGTACTCTCTG-ATAGAATAGAGAACGGACC
65 ---TT-GAGTCCTATACTCTCTGAAT-GAATAGAGAACGGACA
* * **
42403 CGTTCGTTGAAGATTGTTTGAGT-C-ATGCTCTCTGAAGGAATAGGGAGCGGACATGTTTATTGA
1 CGTTCGTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGA
* * * * * * *
42466 AGATCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
62 AGATTGAGTCCTATACTCTCTGAATGAATAGAGAACGGACA
* * * *
42507 CGTTTGTTGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAG
1 CGTTCGTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAG
42556 AAGACACGTT
Statistics
Matches: 213, Mismatches: 34, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
102 46 0.22
103 10 0.05
104 47 0.22
105 2 0.01
106 24 0.11
107 40 0.19
108 10 0.05
109 27 0.13
110 1 0.00
111 6 0.03
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (102 bp):
CGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGAT
TGAGTCCTATACTCTCTGAATGAATAGAGAACGGACA
Found at i:42561 original size:55 final size:55
Alignment explanation
Indices: 42209--42611 Score: 347
Period size: 51 Copynumber: 7.6 Consensus size: 55
42199 GTTGAAGATC
* * *
42209 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA----TT
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTT
* * *
42260 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA----TT
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTT
* * * * *
42311 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACG-TTTGTTGAAGATTGTTT
* * * * *
42367 GAGT-TCTGTACTCTCTG-ATAGAATAGAGAACGGACCCGTTCGTTGAAGATTGTTT
1 GAGTCT-TATACTCTCTGAAT-GAATAGGGAGCGGACACGTTTGTTGAAGATTGTTT
* * * * *
42422 GAGTC--ATGCTCTCTGAAGGAATAGGGAGCGGACATGTTTATTGAAGA----TC
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTT
* * *
42471 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTT
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTT
* ** ** *
42526 GAGTCTTATACTCCCTGAATGAATAGGGAGAAGACACGTTTG-CCAAGGATTGTTC
1 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTTTGTTGAA-GATTGTTT
* *
42581 AAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCTTATACTCT-CTGAATGAATAGGGAGC
42612 AGGCTCGTCA
Statistics
Matches: 297, Mismatches: 38, Indels: 30
0.81 0.10 0.08
Matches are distributed among these distances:
49 6 0.02
51 121 0.41
52 10 0.03
53 31 0.10
54 3 0.01
55 94 0.32
56 32 0.11
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTT
Found at i:47028 original size:14 final size:16
Alignment explanation
Indices: 46999--47030 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
46989 TAAAAATGGT
46999 ATTTTTTAATTGTATA
1 ATTTTTTAATTGTATA
*
47015 ATTTTTTAATTATATA
1 ATTTTTTAATTGTATA
47031 GTTTCTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTTTTTAATTGTATA
Found at i:52852 original size:20 final size:20
Alignment explanation
Indices: 52816--52853 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52806 ATCCTATTCC
**
52816 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
52836 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
52854 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:53972 original size:2 final size:2
Alignment explanation
Indices: 53967--53992 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53957 AGGGGGGGGG
53967 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
53993 ACCCTGGAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:59139 original size:37 final size:38
Alignment explanation
Indices: 59079--59151 Score: 121
Period size: 37 Copynumber: 1.9 Consensus size: 38
59069 GCAACAAGTC
*
59079 AAATAGTAACCGAGGGATGAACATAATTTAGAGCACAA
1 AAATAGTAACCGAGGGATCAACATAATTTAGAGCACAA
*
59117 AAAT-GTAACTGAGGGATCAACATAATTTAGAGCAC
1 AAATAGTAACCGAGGGATCAACATAATTTAGAGCAC
59152 TACGATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (38 bp):
AAATAGTAACCGAGGGATCAACATAATTTAGAGCACAA
Found at i:59709 original size:25 final size:24
Alignment explanation
Indices: 59663--59709 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
59653 ATTTATCAAT
59663 ATATAAAAAATAAATAAAAATACG
1 ATATAAAAAATAAATAAAAATACG
59687 ATATAAAATAA-ACAATAAAAATA
1 ATATAAAA-AATA-AATAAAAATA
59710 ATAAACAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (24 bp):
ATATAAAAAATAAATAAAAATACG
Found at i:61704 original size:2 final size:2
Alignment explanation
Indices: 61697--61722 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61687 AATAAAAATA
61697 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
61723 TCAAATTAGT
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:65640 original size:35 final size:35
Alignment explanation
Indices: 65600--65670 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
65590 ATTCATCAAT
65600 TTCTAAACCCCAAATTCTAAAATACTTCAATTACA
1 TTCTAAACCCCAAATTCTAAAATACTTCAATTACA
* ** *
65635 TTCTAAACCTCAGTTTTTAAAATACTTCAATTACA
1 TTCTAAACCCCAAATTCTAAAATACTTCAATTACA
65670 T
1 T
65671 GACCAACCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.23, G:0.01, T:0.37
Consensus pattern (35 bp):
TTCTAAACCCCAAATTCTAAAATACTTCAATTACA
Found at i:68678 original size:17 final size:17
Alignment explanation
Indices: 68653--68691 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
68643 TCTGTGAAGA
* *
68653 AATTAAAATATGTCAGG
1 AATTGAAATATATCAGG
*
68670 AATTGAAATCTATCAGG
1 AATTGAAATATATCAGG
68687 AATTG
1 AATTG
68692 GAATCTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (17 bp):
AATTGAAATATATCAGG
Found at i:68696 original size:17 final size:17
Alignment explanation
Indices: 68665--68698 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
68655 TTAAAATATG
68665 TCAGGAATTGAAATCTA
1 TCAGGAATTGAAATCTA
*
68682 TCAGGAATTGGAATCTA
1 TCAGGAATTGAAATCTA
68699 ATTCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (17 bp):
TCAGGAATTGAAATCTA
Found at i:69112 original size:2 final size:2
Alignment explanation
Indices: 69105--69143 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
69095 ACTTAATTGG
69105 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69144 GAGGGGGGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:69734 original size:24 final size:24
Alignment explanation
Indices: 69702--69747 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
69692 GCCAACCAAA
69702 TGCCACCTTAAAAAATCAAATCAT
1 TGCCACCTTAAAAAATCAAATCAT
69726 TGCCACCTTAAAAAATCAAATC
1 TGCCACCTTAAAAAATCAAATC
69748 CATCCATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.26, G:0.04, T:0.24
Consensus pattern (24 bp):
TGCCACCTTAAAAAATCAAATCAT
Done.