Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006902.1 Hibiscus syriacus cultivar Beakdansim tig00017627_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: 195944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:165266 original size:26 final size:26
Alignment explanation
Indices: 165237--165318 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 26
165227 TTGTTAAGAC
*
165237 TTGATACTCTTGTGTGATATTTTATT
1 TTGATACTCTTGTGTAATATTTTATT
* * **
165263 TTGA-ACATCTTGTGTTA-ATTTGAGAC
1 TTGATAC-TCTTGTGTAATATTTTA-TT
*
165289 TTGATACTCTTATGTAATATTTTTATT
1 TTGATACTCTTGTGTAATA-TTTTATT
165316 TTG
1 TTG
165319 CACATCTTGT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
25 7 0.17
26 25 0.60
27 6 0.14
28 4 0.10
ACGTcount: A:0.23, C:0.09, G:0.15, T:0.54
Consensus pattern (26 bp):
TTGATACTCTTGTGTAATATTTTATT
Found at i:165799 original size:59 final size:61
Alignment explanation
Indices: 165727--165858 Score: 155
Period size: 59 Copynumber: 2.2 Consensus size: 61
165717 TAGGGTAAAA
*
165727 TACACAAATGGTCCCCT-AACTATAAGATA-CTACTTTGATGAGTCATT-GGCTATTAAAAGT
1 TACA-AAATGGTCCCCTCAACTATAAGA-AGCTACTTTGATGAGTCATTCGACTATTAAAAGT
* * * ** *
165787 TATAAAATGGT-CCCTCGACTATAAGAAGTTGTTTTGTTGAGTCATTCGACTATTAAAAGT
1 TACAAAATGGTCCCCTCAACTATAAGAAGCTACTTTGATGAGTCATTCGACTATTAAAAGT
165847 TACAAAATGGTC
1 TACAAAATGGTC
165859 ACCCGTATGT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
58 5 0.08
59 30 0.50
60 25 0.42
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (61 bp):
TACAAAATGGTCCCCTCAACTATAAGAAGCTACTTTGATGAGTCATTCGACTATTAAAAGT
Found at i:167529 original size:2 final size:2
Alignment explanation
Indices: 167522--167563 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
167512 TATTTGTAGG
167522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
167564 TATCGTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:171094 original size:25 final size:25
Alignment explanation
Indices: 171066--171142 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
171056 GCAATGAAAC
171066 CTTGATATCCTTGTAACAATAATTT
1 CTTGATATCCTTGTAACAATAATTT
* * * **
171091 CTTG--GTCACAT-TAGCAATGAA-AC
1 CTTGATATC-CTTGTAACAAT-AATTT
171114 CTTGATATCCTTGTAACAATAATTT
1 CTTGATATCCTTGTAACAATAATTT
171139 CTTG
1 CTTG
171143 GCCGACATTA
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
23 12 0.33
24 8 0.22
25 16 0.44
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (25 bp):
CTTGATATCCTTGTAACAATAATTT
Found at i:171104 original size:48 final size:48
Alignment explanation
Indices: 171048--171152 Score: 192
Period size: 48 Copynumber: 2.2 Consensus size: 48
171038 TGAGTATCAA
171048 TCACATTAGCAATGAAACCTTGATATCCTTGTAACAATAATTTCTTGG
1 TCACATTAGCAATGAAACCTTGATATCCTTGTAACAATAATTTCTTGG
171096 TCACATTAGCAATGAAACCTTGATATCCTTGTAACAATAATTTCTTGG
1 TCACATTAGCAATGAAACCTTGATATCCTTGTAACAATAATTTCTTGG
*
171144 CCGACATTA
1 TC-ACATTA
171153 CTGATATTAC
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 49 0.89
49 6 0.11
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.34
Consensus pattern (48 bp):
TCACATTAGCAATGAAACCTTGATATCCTTGTAACAATAATTTCTTGG
Found at i:172084 original size:22 final size:21
Alignment explanation
Indices: 172059--172100 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
172049 CCGAAGTGCC
172059 ACATAGAATGTCCCGAAGGACT
1 ACATA-AATGTCCCGAAGGACT
*
172081 ACATATATGTCCCGAAGGAC
1 ACATAAATGTCCCGAAGGAC
172101 CGAGTAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (21 bp):
ACATAAATGTCCCGAAGGACT
Found at i:172152 original size:23 final size:23
Alignment explanation
Indices: 172087--172155 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
172077 GACTACATAT
*
172087 ATGTCCCGAAGGACCGAGTAGAA
1 ATGTCCCGAAGGACCGCGTAGAA
* ** *
172110 ATGTCCCAAAATACCACGTAGAA
1 ATGTCCCGAAGGACCGCGTAGAA
*
172133 TTGTCCCGAAGGACCGCGTAGAA
1 ATGTCCCGAAGGACCGCGTAGAA
172156 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.16
Consensus pattern (23 bp):
ATGTCCCGAAGGACCGCGTAGAA
Found at i:173263 original size:23 final size:23
Alignment explanation
Indices: 173198--173266 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
173188 GAGTCGAGGG
* *
173198 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACTCGGTCCTTCGGGACAT
** *
173221 TTCTACGT-GGTATTTTGGGACAT
1 TTCTAC-TCGGTCCTTCGGGACAT
173244 TTCTACTCGGTCCTTCGGGACAT
1 TTCTACTCGGTCCTTCGGGACAT
173267 ATATGTAGTC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.35
Consensus pattern (23 bp):
TTCTACTCGGTCCTTCGGGACAT
Found at i:180085 original size:64 final size:65
Alignment explanation
Indices: 180017--180177 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 65
180007 GTGCACCAAG
* * *
180017 TGTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCCTAAGTGCATCGATGCATGGTC
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAGCCTAAGTGAATCGATGCATGGAC
* * * * *
180081 TGTGCATCAATGCATAAAATGCATTCGATGTTTTCATAAAATCCTGAGTGAATCGATGTATGGAG
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAGCCTAAGTGAATCGATGCATGGAC
* * *
180146 AGTGCGTCGATGTATAAAATGCATTCGATGTT
1 TGTGCATCGATGCATAAAATGCATTCGATGTT
180178 CAATTTATTC
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 34 0.40
65 50 0.60
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (65 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAGCCTAAGTGAATCGATGCATGGAC
Found at i:180213 original size:20 final size:20
Alignment explanation
Indices: 180188--180225 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
180178 CAATTTATTC
*
180188 ATTGGTGCATCGATGCATAG
1 ATTGGTACATCGATGCATAG
*
180208 ATTGGTACATCGGTGCAT
1 ATTGGTACATCGATGCAT
180226 GCCTTTGAAA
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:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
ATTGGTACATCGATGCATAG
Found at i:182874 original size:23 final size:22
Alignment explanation
Indices: 182844--182925 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
182834 GCATGGCCTT
182844 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
182866 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
182888 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
182911 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
182926 TGTTAAGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 19 0.40
24 12 0.25
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:182936 original size:44 final size:44
Alignment explanation
Indices: 182848--182944 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
182838 GGCCTTGTGC
* *
182848 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATAGTGT
*
182892 ATCGATGCACATTCAAAGG-GATGCATCGATGCA-CTGTTA-AGTGT
1 ATCGATGCACATTC-AAGGCG-TGCATCGATGCACCT-TCATAGTGT
182936 ATCGATGCA
1 ATCGATGCA
182945 TGAAGCACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 30 0.64
45 17 0.36
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATAGTGT
Found at i:188644 original size:60 final size:63
Alignment explanation
Indices: 188580--188735 Score: 212
Period size: 64 Copynumber: 2.5 Consensus size: 63
188570 GTGCACCAAG
* *
188580 TGTGCATCGATGCAT-AAATGCATTCGATGTTT-T-GAAGCCTGAGTGCATCGATGCATGGTC
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTATAAAAGCCTGAGTGCATCGATGCATGGAC
* *
188640 TGTGCATCGATGCATAAAATGC-TTCGATGTTTTCATAAAATCCTGAGTGCATCGATGCATGGAG
1 TGTGCATCGATGCATAAAATGCATTCGATG-TTT-ATAAAAGCCTGAGTGCATCGATGCATGGAC
**
188704 AATGCATCGATGCATAAAATGCATTCGATGTT
1 TGTGCATCGATGCATAAAATGCATTCGATGTT
188736 CAATTTATTC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
60 22 0.26
61 9 0.11
63 1 0.01
64 45 0.54
65 7 0.08
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (63 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTATAAAAGCCTGAGTGCATCGATGCATGGAC
Found at i:188772 original size:20 final size:20
Alignment explanation
Indices: 188747--188784 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
188737 AATTTATTCG
188747 TTGGTGAATCGATGCATGGA
1 TTGGTGAATCGATGCATGGA
* *
188767 TTGGTGCATCGGTGCATG
1 TTGGTGAATCGATGCATG
188785 CCTTTGAAAA
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:0.18, C:0.13, G:0.37, T:0.32
Consensus pattern (20 bp):
TTGGTGAATCGATGCATGGA
Found at i:192723 original size:22 final size:21
Alignment explanation
Indices: 192676--192723 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
192666 AAAATTGATC
* **
192676 ATTTTATTTTAGTTTTCTAAT
1 ATTTTATATTAGTTTTAAAAT
*
192697 TTTTTATCATTAGTTTTAAAAT
1 ATTTTAT-ATTAGTTTTAAAAT
192719 ATTTT
1 ATTTT
192724 GTTTTAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (21 bp):
ATTTTATATTAGTTTTAAAAT
Done.