Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009519.1 Hibiscus syriacus cultivar Beakdansim tig00115776_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: 12024
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Found at i:4509 original size:32 final size:31
Alignment explanation
Indices: 4469--4671 Score: 128
Period size: 32 Copynumber: 6.6 Consensus size: 31
4459 CCAATGGCCC
*
4469 GGGTTGCCGATGGTGACCGA-GACACCCGTCT
1 GGGTTGCCGATGGTGACCGAGGACACCC-CCT
*
4500 GGGTTTGCCGATGGTGACCGAGGCCACCCCCT
1 GGG-TTGCCGATGGTGACCGAGGACACCCCCT
*
4532 GGGTTGCCGA---T----G-GG--ACCCGCT
1 GGGTTGCCGATGGTGACCGAGGACACCCCCT
* * *
4553 GGG-GGCCGATGGTGACCGAGGCTCCCGCACCACCCG
1 GGGTTGCCGATGGTGACCGAGG-----ACACC-CCCT
*
4589 GGGTTGCCGATGGTGACCGA-GACACCCGTCT
1 GGGTTGCCGATGGTGACCGAGGACACCC-CCT
*
4620 GGGTTTGCCGATGGTGACCGA-GCCACCCGCCT
1 GGG-TTGCCGATGGTGACCGAGGACACCC-CCT
4652 GGGATTGCCGATGGTGACCG
1 GGG-TTGCCGATGGTGACCG
4672 GCTCACGCAC
Statistics
Matches: 138, Mismatches: 13, Indels: 41
0.72 0.07 0.21
Matches are distributed among these distances:
20 5 0.04
21 9 0.07
23 3 0.02
24 1 0.01
27 1 0.01
28 3 0.02
30 1 0.01
31 18 0.13
32 67 0.49
33 6 0.04
35 3 0.02
36 6 0.04
37 15 0.11
ACGTcount: A:0.14, C:0.32, G:0.37, T:0.17
Consensus pattern (31 bp):
GGGTTGCCGATGGTGACCGAGGACACCCCCT
Found at i:4549 original size:21 final size:21
Alignment explanation
Indices: 4525--4569 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4515 GACCGAGGCC
*
4525 ACCCCCTGGGTTGCCGATGG-G
1 ACCCCCTGGG-GGCCGATGGTG
*
4546 ACCCGCTGGGGGCCGATGGTG
1 ACCCCCTGGGGGCCGATGGTG
4567 ACC
1 ACC
4570 GAGGCTCCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.11, C:0.33, G:0.40, T:0.16
Consensus pattern (21 bp):
ACCCCCTGGGGGCCGATGGTG
Found at i:4785 original size:31 final size:30
Alignment explanation
Indices: 4750--4831 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 30
4740 CAATGGCCCG
*
4750 GGGTTGCCGATGGTGACCGAGACACCCGTCT
1 GGGTTGCCGATGGTGACCGAGACACCCG-CC
*
4781 GGGTTGCCGATGGTGACCGAGGCCACCCGCC
1 GGGTTGCCGATGGTGACCGA-GACACCCGCC
* *
4812 CGGATGCCGATGGTG-CCGAG
1 GGGTTGCCGATGGTGACCGAG
4832 GCTCACCACA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 1 0.02
30 4 0.09
31 34 0.74
32 7 0.15
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (30 bp):
GGGTTGCCGATGGTGACCGAGACACCCGCC
Found at i:4808 original size:161 final size:162
Alignment explanation
Indices: 4585--5129 Score: 726
Period size: 161 Copynumber: 3.4 Consensus size: 162
4575 TCCCGCACCA
4585 CCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGA-GCCACCCG
1 CCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCG
* * *
4649 CCTGGGATTGCCGATGGTGACCGGCTCACGCACAACCTGATGGGGACCGAGACCCCGCACCAACG
66 CCTCGGATTGCCGATGGTGACCGGCTCACGCACAACCTGATGGTGACCGAGGCCCCGCACCAACG
4714 CTCGGTTCTGTGCGGCACTCCCGCACCAATGG
131 CTCGGTTCTGTGCGGCACTCCCGCACCAATGG
4746 CCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGG-TTGCCGATGGTGACCGAGGCCACCCG
1 CCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCG
*
4810 CC-CGGA-TGCCGATGGTG-CCGAGGCTCAC-CACACGGGGCCTGATGGTGACCGAGGCCCCGCA
66 CCTCGGATTGCCGATGGTGACC--GGCTCACGCACA----ACCTGATGGTGACCGAGGCCCCGCA
* *
4871 CCAAAGCTCGGTACTGTGCGGCACTCCCGCACCAATGG
125 CCAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGG
4909 -CC-GGGTTGCCGATGGTG-CCGAGACAAGACCCCGTCTGGGTTTGCCGATGGTGACCGAGGCCA
1 CCCGGGGTTGCCGATGGTGACCGAGAC---A-CCCGTCTGGGTTTGCCGATGGTGACCGAGGCCA
* * *
4971 CCCGCCTTGGATTACCGAT-GTGACCGAGC-CACGCAC-ACGGGGCCGATGGTGA-CGAGGCTCC
62 CCCGCCTCGGATTGCCGATGGTGACCG-GCTCACGCACAAC----CTGATGGTGACCGAGGC-CC
*
5032 CGC-CCAACGCTCGGTTCTGTGCGGCACTCCCTCACCAAT-G
121 CGCACCAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGG
* *
5072 CCCTGGGTTGCCGATGGTGACCGAGACACCCGTCT-GTTTTGCCGATGGTGACCGAGGC
1 CCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGC
5130 ACGCACACGG
Statistics
Matches: 345, Mismatches: 14, Indels: 50
0.84 0.03 0.12
Matches are distributed among these distances:
158 2 0.01
159 15 0.04
160 34 0.10
161 86 0.25
162 9 0.03
163 61 0.18
164 51 0.15
165 61 0.18
166 18 0.05
167 8 0.02
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.17
Consensus pattern (162 bp):
CCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCG
CCTCGGATTGCCGATGGTGACCGGCTCACGCACAACCTGATGGTGACCGAGGCCCCGCACCAACG
CTCGGTTCTGTGCGGCACTCCCGCACCAATGG
Found at i:4864 original size:31 final size:31
Alignment explanation
Indices: 4786--4865 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
4776 CGTCTGGGTT
* * *
4786 GCCGATGGTGACCGAGGCCACCCGCCCGGAT
1 GCCGATGGTGACCGAGGCCACCCACACGGAG
4817 GCCGATGGTG-CCGAGGCTCA-CCACACGG-G
1 GCCGATGGTGACCGAGGC-CACCCACACGGAG
4846 GCCTGATGGTGACCGAGGCC
1 GCC-GATGGTGACCGAGGCC
4866 CCGCACCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 3 0.07
30 21 0.49
31 19 0.44
ACGTcount: A:0.16, C:0.35, G:0.38, T:0.11
Consensus pattern (31 bp):
GCCGATGGTGACCGAGGCCACCCACACGGAG
Done.