Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007339.1 Hibiscus syriacus cultivar Beakdansim tig00019665_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: 70266
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:40016 original size:183 final size:183
Alignment explanation
Indices: 39706--40067 Score: 652
Period size: 183 Copynumber: 2.0 Consensus size: 183
39696 CGATGGATGA
*
39706 TGAAGTGTCTGATGAAATGTCGAGTGTGGATGAAACGGTGGCCGGAGTTGAAGAGGGTGAGTTCT
1 TGAAGTGTCTGATGAAATGTCGAGTGAGGATGAAACGGTGGCCGGAGTTGAAGAGGGTGAGTTCT
* * *
39771 CTGGTGTGGTTAAGGTTGCTGGTGGTGTTGAAAGTTCACCTAGATTAAAGGTGGCTTCGGGGGTT
66 CTGGTGTGGTTAACGTTGCTGGTAGTGTTGAAAGTTCACCTAGATTAAAGGTGGCCTCGGGGGTT
39836 GAAGACGAGGAGGTGTTGGAGGATTTTGTAGGTGAAGATAAGGGGTCTGATTT
131 GAAGACGAGGAGGTGTTGGAGGATTTTGTAGGTGAAGATAAGGGGTCTGATTT
* * * *
39889 TGAAGTGTTTGATGAAATGTCGAGTGAGGATGAAACGGTGGGCGGAGTTGAAGATGGTGGGTTCT
1 TGAAGTGTCTGATGAAATGTCGAGTGAGGATGAAACGGTGGCCGGAGTTGAAGAGGGTGAGTTCT
39954 CTGGTGTGGTTAACGTTGCTGGTAGTGTTGAAAGTTCACCTAGATTAAAGGTGGCCTCGGGGGTT
66 CTGGTGTGGTTAACGTTGCTGGTAGTGTTGAAAGTTCACCTAGATTAAAGGTGGCCTCGGGGGTT
40019 GAAGACGAGGAGGTGTTGGAGGATTTTGTAGGTGAAGATAAGGGGTCTG
131 GAAGACGAGGAGGTGTTGGAGGATTTTGTAGGTGAAGATAAGGGGTCTG
40068 GTTTGGAAAG
Statistics
Matches: 171, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 171 1.00
ACGTcount: A:0.23, C:0.08, G:0.40, T:0.29
Consensus pattern (183 bp):
TGAAGTGTCTGATGAAATGTCGAGTGAGGATGAAACGGTGGCCGGAGTTGAAGAGGGTGAGTTCT
CTGGTGTGGTTAACGTTGCTGGTAGTGTTGAAAGTTCACCTAGATTAAAGGTGGCCTCGGGGGTT
GAAGACGAGGAGGTGTTGGAGGATTTTGTAGGTGAAGATAAGGGGTCTGATTT
Found at i:40903 original size:90 final size:90
Alignment explanation
Indices: 40750--40931 Score: 258
Period size: 90 Copynumber: 2.0 Consensus size: 90
40740 TCGTAGACTC
* * *
40750 TGATGAAGAAGCTGAAGCTGAGAGGGAATATGAAGCTAAAGAGCTACAAGATTCTGCTGCATTGA
1 TGATGAAGAAGCGGAAGCTGAGAGGGAATATCAAGCGAAAGAGCTACAAGATTCTGCTGCATTGA
40815 CTGCTCTTTTGAAAGCTGCAGCAAG
66 CTGCTCTTTTGAAAGCTGCAGCAAG
* * * *
40840 TGATGAAGAAGCGGAAGTTGAGAGGGAATATCAAGCGGAAGAGCTACTTA-CTTCTGCTGCATTG
1 TGATGAAGAAGCGGAAGCTGAGAGGGAATATCAAGCGAAAGAGCTAC-AAGATTCTGCTGCATTG
* * *
40904 GCTGCTCTTTTGAAGGCTGCAGCCAG
65 ACTGCTCTTTTGAAAGCTGCAGCAAG
40930 TG
1 TG
40932 GCGAATCAGA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
90 80 0.99
91 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (90 bp):
TGATGAAGAAGCGGAAGCTGAGAGGGAATATCAAGCGAAAGAGCTACAAGATTCTGCTGCATTGA
CTGCTCTTTTGAAAGCTGCAGCAAG
Found at i:45156 original size:28 final size:27
Alignment explanation
Indices: 45124--45181 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
45114 CCCAAATTTA
45124 TATATA-TAATTATGAGTTCGAGTAGTAT
1 TATATAGTAATT-TGAGTTCGAGTA-TAT
*
45152 TATATAGTGATTTGAGTTCGAGTATAT
1 TATATAGTAATTTGAGTTCGAGTATAT
45179 TAT
1 TAT
45182 TTAGAGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 6 0.21
28 18 0.64
29 4 0.14
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (27 bp):
TATATAGTAATTTGAGTTCGAGTATAT
Found at i:49855 original size:162 final size:164
Alignment explanation
Indices: 49581--49892 Score: 445
Period size: 162 Copynumber: 1.9 Consensus size: 164
49571 CATTTTATCA
* * *
49581 AACGAACAATAACAAACTAAATTTCTTAATGAACGAACATGAATAAGAAATTTGTTTGTTTCATT
1 AACGAACAATAACAAACTAAATTTCTTAATGAACAAACATGAATAAAAAATTTATTTGTTTCATT
* * *
49646 GTTCGTGTTCGTTCGTTCGTTTGATTAAAGTTAAACAAACGAACATGAACATATACTCATTCGTG
66 GTTCG-GTTCGTTCATTCGTTTGATTAAAGTTAAACAAACGAACATGAACATACACTCATTCGTA
* *
49711 TTCGTTCTGTTCGATAACATACCTATGTTTTAACG
130 TTCGTTCGGTTCAATAACATACCTATGTTTTAACG
** *
49746 AACGAACACA-AACAAGTTAAATTTCTTAATGGACAAACATGAATAAAAAAGTTTATTTGTTT-A
1 AACGAACA-ATAACAAACTAAATTTCTTAATGAACAAACATGAATAAAAAA-TTTATTTGTTTCA
*
49809 GTTGTTC-G-T-GTTCATTCGTTTGATTAAAGTTAAACAAACGAACATGAACATACACTTATTCG
64 -TTGTTCGGTTCGTTCATTCGTTTGATTAAAGTTAAACAAACGAACATGAACATACACTCATTCG
49871 TATTCGTTCGGTTCAATAACAT
128 TATTCGTTCGGTTCAATAACAT
49893 GCCTGCCTAT
Statistics
Matches: 132, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
162 69 0.52
163 1 0.01
164 1 0.01
165 44 0.33
166 17 0.13
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (164 bp):
AACGAACAATAACAAACTAAATTTCTTAATGAACAAACATGAATAAAAAATTTATTTGTTTCATT
GTTCGGTTCGTTCATTCGTTTGATTAAAGTTAAACAAACGAACATGAACATACACTCATTCGTAT
TCGTTCGGTTCAATAACATACCTATGTTTTAACG
Found at i:50770 original size:2 final size:2
Alignment explanation
Indices: 50763--50796 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
50753 TTACACATAC
50763 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
50797 TTAATACCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51512 original size:30 final size:30
Alignment explanation
Indices: 51441--51514 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
51431 CCCGGGAGGA
* *
51441 GGATACCCATAACCGGGCTGCGGCGGCGGC
1 GGATACCCATACCCCGGCTGCGGCGGCGGC
* *
51471 GGATACCCATACCCCGGCTGCTGTGGCGGC
1 GGATACCCATACCCCGGCTGCGGCGGCGGC
51501 GGATACCCATACCC
1 GGATACCCATACCC
51515 TGGTGGAGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.18, C:0.36, G:0.32, T:0.14
Consensus pattern (30 bp):
GGATACCCATACCCCGGCTGCGGCGGCGGC
Found at i:56393 original size:22 final size:22
Alignment explanation
Indices: 56336--56396 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
56326 ACATAAAAAC
* * *
56336 ACATGTCACAAAGACATAGATA
1 ACATGTCACAAAAATATAGAGA
** *
56358 A-ATGTGTCATAAATATAGAGA
1 ACATGTCACAAAAATATAGAGA
56379 ACATGTCACAAAAATATA
1 ACATGTCACAAAAATATA
56397 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (22 bp):
ACATGTCACAAAAATATAGAGA
Found at i:57811 original size:15 final size:15
Alignment explanation
Indices: 57791--57823 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
57781 CCACATCATT
57791 TTTTATTTT-TAATTA
1 TTTTATTTTAT-ATTA
57806 TTTTATTTTATATTA
1 TTTTATTTTATATTA
57821 TTT
1 TTT
57824 CTGCAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTTTATATTA
Found at i:66508 original size:12 final size:12
Alignment explanation
Indices: 66491--66515 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66481 TAACTATAGG
66491 TGTCTAATATTT
1 TGTCTAATATTT
66503 TGTCTAATATTT
1 TGTCTAATATTT
66515 T
1 T
66516 TTCAGTTACA
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:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TGTCTAATATTT
Found at i:66605 original size:32 final size:31
Alignment explanation
Indices: 66546--66607 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
66536 TTATCATTAT
* *
66546 ATTTTTTTAAAAAAAATTAATAATAAAAATA
1 ATTTTTTTAAAAAAAATAAAAAATAAAAATA
66577 ATTTTTTTAAAAAAGAA-AAAAAATTAAAAAT
1 ATTTTTTTAAAAAA-AATAAAAAA-TAAAAAT
66608 CAAACCCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (31 bp):
ATTTTTTTAAAAAAAATAAAAAATAAAAATA
Done.