Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007981.1 Hibiscus syriacus cultivar Beakdansim tig00110422_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: 1405786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1372869 original size:108 final size:108
Alignment explanation
Indices: 1372675--1372897 Score: 297
Period size: 108 Copynumber: 2.1 Consensus size: 108
1372665 AGAGTTATCA
* * *
1372675 CCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTCTGGAAATAAAGTTTTGCCTCTTTAGAG
1 CCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTGAAAACAAAGTTTTGCCTCTTTAGAG
** *
1372740 ATAGTTTCCCTTGAAGTAAATTTCGTCTCCC-TTGAGACAGTTT
66 ATAGTTTCCCTTGAAACAAATTTCGTCTCCCATT-AGACAGTCT
* * * * *
1372783 CCTTGAAACAAATTTTATCTCCCTTTAGATAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTT-GA
1 CCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTGAAAACAAAGTTTTGCCTCT-TTAGA
*
1372847 GATAGTTTCCCTTGAAACAAATTTTGTCTCCCATTAGACAGTCT
65 GATAGTTTCCCTTGAAACAAATTTCGTCTCCCATTAGACAGTCT
1372891 CTCTTGA
1 C-CTTGA
1372898 GATAGTTTCC
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
108 91 0.91
109 9 0.09
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.38
Consensus pattern (108 bp):
CCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTGAAAACAAAGTTTTGCCTCTTTAGAG
ATAGTTTCCCTTGAAACAAATTTCGTCTCCCATTAGACAGTCT
Found at i:1372892 original size:51 final size:51
Alignment explanation
Indices: 1372836--1372948 Score: 174
Period size: 51 Copynumber: 2.2 Consensus size: 51
1372826 ACAAAGTTTT
*
1372836 GTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCATT-AGACA
1 GTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTACC-TTGAGACA
*
1372887 GTCTCTCTTGAGATAGTTTCCTTTGAAACAAATTTTGTCTACCTTGAGACA
1 GTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTACCTTGAGACA
* *
1372938 GTTTCCCTTGA
1 GTCTCTCTTGA
1372949 AACAAATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
50 2 0.04
51 55 0.96
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (51 bp):
GTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTACCTTGAGACA
Found at i:1372907 original size:123 final size:123
Alignment explanation
Indices: 1372764--1373020 Score: 365
Period size: 123 Copynumber: 2.1 Consensus size: 123
1372754 AGTAAATTTC
* * *
1372764 GTCTCCCTTGAGACAGTTTCC-TTGAAACAAATTTTATCTCCCTTTAGATAGTTTCCCTTAAAAC
1 GTCTCCCTTGAGACAGTTTCCTTTGAAACAAATTTTATCTACCTTGAGACAGTTTCCCTTAAAAC
* *
1372828 AAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCATTAGACA
66 AAA-TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCATTAGACA
* * * *
1372887 GTCTCTCTTGAGATAGTTTCCTTTGAAACAAATTTTGTCTACCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCCCTTGAGACAGTTTCCTTTGAAACAAATTTTATCTACCTTGAGACAGTTTCCCTTAAAAC
* * *
1372952 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTTAAATAAATTTTGTCTCTC-TTAAGACA
66 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCATT-AGACA
*
1373010 GTTTCCCTTGA
1 GTCTCCCTTGA
1373021 AACAACCTTA
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
122 2 0.02
123 75 0.64
124 41 0.35
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (123 bp):
GTCTCCCTTGAGACAGTTTCCTTTGAAACAAATTTTATCTACCTTGAGACAGTTTCCCTTAAAAC
AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCATTAGACA
Found at i:1372933 original size:21 final size:20
Alignment explanation
Indices: 1372909--1372969 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
1372899 ATAGTTTCCT
1372909 TTGAAACAAATTTTGTCTACC
1 TTGAAACAAATTTTGTCT-CC
* *
1372930 TTGAGAC--A-GTT-TC-CC
1 TTGAAACAAATTTTGTCTCC
1372945 TTGAAACAAATTTTGTCTCCC
1 TTGAAACAAATTTTGTCT-CC
1372966 TTGA
1 TTGA
1372970 GACAGTTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 8 0.27
17 3 0.10
18 4 0.13
19 3 0.10
21 12 0.40
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (20 bp):
TTGAAACAAATTTTGTCTCC
Found at i:1372933 original size:87 final size:88
Alignment explanation
Indices: 1372800--1372982 Score: 273
Period size: 87 Copynumber: 2.1 Consensus size: 88
1372790 ACAAATTTTA
* *
1372800 TCTCCCTTTAGATAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
1 TCTCCCTTGAGATAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1372865 AAATTTTGTCTCCCATT-AGACAG
66 AAATTTTGTCTCCC-TTGAGACAG
* * *
1372888 TCTCTCTTGAGATAGTTTCCTTTGAAACAAA-TTTTGTCTAC-CTTGAGACAGTTTCCCTTGAAA
1 TCTCCCTTGAGATAGTTTCCCTTAAAACAAAGTTTTGTCT-CTCTTGAGACAGTTTCCCTTGAAA
1372951 CAAATTTTGTCTCCCTTGAGACAG
65 CAAATTTTGTCTCCCTTGAGACAG
*
1372975 TTTCCCTT
1 TCTCCCTT
1372983 TAAATAAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
86 2 0.02
87 56 0.65
88 28 0.33
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (88 bp):
TCTCCCTTGAGATAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAATTTTGTCTCCCTTGAGACAG
Found at i:1372941 original size:36 final size:35
Alignment explanation
Indices: 1372887--1373025 Score: 197
Period size: 36 Copynumber: 3.9 Consensus size: 35
1372877 CCATTAGACA
* *
1372887 GTCTCTCTTGAGATAGTTTCCTTTGAAACAAATTTT
1 GTCTC-CTTGAGACAGTTTCCCTTGAAACAAATTTT
1372923 GTCTACCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCT-CCTTGAGACAGTTTCCCTTGAAACAAATTTT
* *
1372959 GTCTCCCTTGAGACAGTTTCCCTTTAAATAAATTTT
1 GTCT-CCTTGAGACAGTTTCCCTTGAAACAAATTTT
*
1372995 GTCTCTCTTAAGACAGTTTCCCTTGAAACAA
1 GTCTC-CTTGAGACAGTTTCCCTTGAAACAA
1373026 CCTTAGCTTG
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
35 1 0.01
36 91 0.98
37 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (35 bp):
GTCTCCTTGAGACAGTTTCCCTTGAAACAAATTTT
Found at i:1372995 original size:159 final size:159
Alignment explanation
Indices: 1372737--1373025 Score: 454
Period size: 159 Copynumber: 1.8 Consensus size: 159
1372727 TGCCTCTTTA
** *
1372737 GAGATAGTTTCCCTTGAAGTAAATTTCGTCTCCCTTGAGACAGTTTCCTTGAAACAAATTTTATC
1 GAGATAGTTTCCCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCTTGAAACAAATTTTATC
* * * *
1372802 TCCCTTTAGATAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
66 TCCCTTGAGACAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAA
1372867 ATTTTGTCTCCCATTAGACAGTCTCTCTT
131 ATTTTGTCTCCCATTAGACAGTCTCTCTT
* * *
1372896 GAGATAGTTTCCTTTGAAACAAATTTTGTCTACCTTGAGACAGTTTCCCTTGAAACAAATTTTGT
1 GAGATAGTTTCCCTTGAAACAAATTTCGTCTACCTTGAGACAGTTT-CCTTGAAACAAATTTTAT
* *
1372961 CTCCCTTGAGACAGTTTCCCTTTAAATAAA-TTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACA
65 CTCCCTTGAGACAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACA
1373025 A
130 A
1373026 CCTTAGCTTG
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
159 74 0.63
160 43 0.37
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (159 bp):
GAGATAGTTTCCCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCTTGAAACAAATTTTATC
TCCCTTGAGACAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAA
ATTTTGTCTCCCATTAGACAGTCTCTCTT
Found at i:1383772 original size:15 final size:16
Alignment explanation
Indices: 1383745--1383777 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1383735 TAATATAAAA
1383745 ATAAAATTTAAAAGTT
1 ATAAAATTTAAAAGTT
*
1383761 ATAAAA-TTAAAATTT
1 ATAAAATTTAAAAGTT
1383776 AT
1 AT
1383778 GTATGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
ATAAAATTTAAAAGTT
Found at i:1383992 original size:20 final size:20
Alignment explanation
Indices: 1383949--1383988 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1383939 AATAATAATA
1383949 TATATTTATTTTTAATATTT
1 TATATTTATTTTTAATATTT
1383969 TATATTTATTTTTAA-ATTT
1 TATATTTATTTTTAATATTT
1383988 T
1 T
1383989 TATAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATATTTATTTTTAATATTT
Found at i:1384017 original size:21 final size:21
Alignment explanation
Indices: 1383949--1384024 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
1383939 AATAATAATA
**
1383949 TATATTT-ATTTTTAATATTT
1 TATATTTAATTTAAAATATTT
* *
1383969 TATATTTATTTTTAAAT-TTT
1 TATATTTAATTTAAAATATTT
1383989 TATAATTTAAATTTAAAATATTT
1 TAT-ATTT-AATTTAAAATATTT
1384012 T-TATTT--TTTAAAA
1 TATATTTAATTTAAAA
1384025 AATAAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.15
20 13 0.27
21 15 0.31
22 9 0.19
23 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATATTTAATTTAAAATATTT
Found at i:1389062 original size:23 final size:23
Alignment explanation
Indices: 1389036--1389096 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 23
1389026 ACTTCTGTGC
*
1389036 TGAATCATTCAGCACTGTTTTGT
1 TGAATCAGTCAGCACTGTTTTGT
* *
1389059 TGAATCGGTCA-CATTGTTTTGT
1 TGAATCAGTCAGCACTGTTTTGT
1389081 TGAATCAGTCAGCACT
1 TGAATCAGTCAGCACT
1389097 TAATCATTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (23 bp):
TGAATCAGTCAGCACTGTTTTGT
Found at i:1389618 original size:2 final size:2
Alignment explanation
Indices: 1389611--1389635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1389601 CAGCAACAAA
1389611 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 A
1389636 AAAGGTGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1390508 original size:76 final size:77
Alignment explanation
Indices: 1390409--1390551 Score: 207
Period size: 76 Copynumber: 1.9 Consensus size: 77
1390399 CCTAATATGT
* * * * * *
1390409 CATGATTAACTAAGAAATATGTTGTGATTTGTAATGTTAATATTTTTATTAATAAAATAGGTTGT
1 CATGATTAACTAAGAAACATGTTGCGATATGGAATCTTAATATTTTTAATAATAAAATAGGTTGT
1390474 GCCGAAGAAAGC
66 GCCGAAGAAAGC
* *
1390486 CATGGTTAACTAA-AAACATGTTGCGATATGGAATCTTAATATTTTTAATAATAAAATGGGTTGT
1 CATGATTAACTAAGAAACATGTTGCGATATGGAATCTTAATATTTTTAATAATAAAATAGGTTGT
1390550 GC
66 GC
1390552 ATAAATGTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
76 46 0.79
77 12 0.21
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (77 bp):
CATGATTAACTAAGAAACATGTTGCGATATGGAATCTTAATATTTTTAATAATAAAATAGGTTGT
GCCGAAGAAAGC
Found at i:1392661 original size:24 final size:24
Alignment explanation
Indices: 1392628--1392674 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1392618 TTTATTAGTT
*
1392628 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTATTAA
* *
1392652 TAATTAAATATGTAATATTATTA
1 TAATTAAATATATAAAATTATTA
1392675 TATATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAATTAAATATATAAAATTATTAA
Found at i:1394211 original size:14 final size:15
Alignment explanation
Indices: 1394192--1394223 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1394182 GTTATAAAAT
1394192 TTTTTATTAT-ATTA
1 TTTTTATTATGATTA
1394206 TTTTTATTATGATTA
1 TTTTTATTATGATTA
1394221 TTT
1 TTT
1394224 GAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTTATTATGATTA
Found at i:1397678 original size:35 final size:34
Alignment explanation
Indices: 1397593--1397679 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1397583 AATATAATTT
*
1397593 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
1397627 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
1397665 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1397680 AACAAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1398277 original size:27 final size:27
Alignment explanation
Indices: 1398224--1398277 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1398214 TCCTCTAGGA
* * *
1398224 GGGTCATAAAACTCTGTGACGGTGGCG
1 GGGTCATAAAACTCGGTGAAGGCGGCG
1398251 GGGTCATAAAAC-CAGGTGAAGGCGGCG
1 GGGTCATAAAACTC-GGTGAAGGCGGCG
1398278 ACATCATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.26, C:0.19, G:0.39, T:0.17
Consensus pattern (27 bp):
GGGTCATAAAACTCGGTGAAGGCGGCG
Found at i:1400067 original size:19 final size:20
Alignment explanation
Indices: 1400030--1400068 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1400020 AAACAGTTAT
*
1400030 AAGAGATATAAGAGTATTTG
1 AAGAGATATAAGAGGATTTG
*
1400050 AAGAGA-ATGAGAGGATTTG
1 AAGAGATATAAGAGGATTTG
1400069 TGTGATGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.26
Consensus pattern (20 bp):
AAGAGATATAAGAGGATTTG
Found at i:1402820 original size:47 final size:49
Alignment explanation
Indices: 1402693--1402822 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 49
1402683 ATATAAATTT
* *
1402693 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA--TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* ** *
1402739 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* **
1402789 CTTGCCA-TT-ATTCTGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
1402823 GTATGGTTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
46 6 0.09
47 25 0.36
48 20 0.29
49 2 0.03
50 17 0.24
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (49 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
Done.