Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007570.1 Hibiscus syriacus cultivar Beakdansim tig00021542_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: 59525
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:231 original size:32 final size:31
Alignment explanation
Indices: 195--271 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
185 TGGGGCCACG
* *
195 GGGCCTACCTAAGAACACATCTTAGGGCCGTA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
227 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
258 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
272 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:5877 original size:32 final size:31
Alignment explanation
Indices: 5840--5916 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
5830 CGAGGCCACG
* *
5840 GGGCCTACCTAAGAAT-ACTTCTTAGGGCCGTA
1 GGGCCTACCTAAGAATGA--TCTCAGGGCCGCA
*
5872 GGGCCTACCTGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAATGATCTCAGGGCCGCA
*
5903 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
5917 GTCACATTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 23 0.59
32 15 0.38
33 1 0.03
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.19
Consensus pattern (31 bp):
GGGCCTACCTAAGAATGATCTCAGGGCCGCA
Found at i:10930 original size:20 final size:20
Alignment explanation
Indices: 10858--10930 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
10848 CCAGAACCCC
* * *
10858 ATGGGGGTATCGATTCCCCT
1 ATGGGGGAATCGGTTCCCTT
**
10878 ACAGGGGAATC-GTTCCCATT
1 ATGGGGGAATCGGTTCCC-TT
*
10898 CAAGGGGGAATCGGTTCCCTT
1 -ATGGGGGAATCGGTTCCCTT
*
10919 ATGGGGGTATCG
1 ATGGGGGAATCG
10931 ATTACTTCTG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 5 0.12
20 19 0.46
21 11 0.27
22 6 0.15
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.26
Consensus pattern (20 bp):
ATGGGGGAATCGGTTCCCTT
Found at i:19880 original size:21 final size:19
Alignment explanation
Indices: 19842--19886 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
19832 TTAGTTGTAC
19842 TTTTATATTTTTATTTTAT
1 TTTTATATTTTTATTTTAT
*
19861 TTTTATCTTTTTAAATTTTAT
1 TTTTATATTTTT--ATTTTAT
19882 TTTTA
1 TTTTA
19887 GATTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
21 12 0.52
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATATTTTTATTTTAT
Found at i:30128 original size:13 final size:13
Alignment explanation
Indices: 30110--30134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30100 GTCAACGGTC
30110 AACGGGTCGGGTT
1 AACGGGTCGGGTT
30123 AACGGGTCGGGT
1 AACGGGTCGGGT
30135 CGGTCAACGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.48, T:0.20
Consensus pattern (13 bp):
AACGGGTCGGGTT
Found at i:30145 original size:17 final size:17
Alignment explanation
Indices: 30105--30153 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
30095 ACCCGGTCAA
30105 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
30122 ---T-AACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
*
30135 CGGTCAACGGGTCAGGT
1 CGGTCAACGGGTCGGGT
30152 CG
1 CG
30154 TAACCGGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
13 12 0.44
14 1 0.04
16 1 0.04
17 13 0.48
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.18
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:41338 original size:9 final size:9
Alignment explanation
Indices: 41324--41359 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
41314 ATTGGAAACC
41324 TAATATAAA
1 TAATATAAA
41333 TAATATAAA
1 TAATATAAA
41342 TAATATTTAAA
1 TAATA--TAAA
41353 TAATATA
1 TAATATA
41360 CGAAAACCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 16 0.64
11 9 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TAATATAAA
Found at i:41973 original size:7 final size:7
Alignment explanation
Indices: 41961--41988 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
41951 AAATGTCACC
41961 CGGTCAA
1 CGGTCAA
41968 CGGTCAA
1 CGGTCAA
41975 CGGTCAA
1 CGGTCAA
41982 CGGTCAA
1 CGGTCAA
41989 AGGGTCAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (7 bp):
CGGTCAA
Found at i:42024 original size:22 final size:23
Alignment explanation
Indices: 41990--42035 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
41980 AACGGTCAAA
41990 GGGTCAGGTCAACGGGTCGAGTC
1 GGGTCAGGTCAACGGGTCGAGTC
*
42013 GGGTC-GGTCAACGGGTCGGGTC
1 GGGTCAGGTCAACGGGTCGAGTC
42035 G
1 G
42036 TAACCGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.13, C:0.22, G:0.48, T:0.17
Consensus pattern (23 bp):
GGGTCAGGTCAACGGGTCGAGTC
Found at i:46957 original size:31 final size:31
Alignment explanation
Indices: 46921--47018 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
46911 TTAAAAAATA
*
46921 AAAATAAGTATTAAATTTATTAATTGATTAT
1 AAAATAATTATTAAATTTATTAATTGATTAT
* * * *
46952 AAAATAATTATCATACTTATTAAATT-ACTAT
1 AAAATAATTATTAAATTTATT-AATTGATTAT
* *
46983 AAAATAATTATTAAATTTATTCATTG-TCAT
1 AAAATAATTATTAAATTTATTAATTGATTAT
47013 AAAATA
1 AAAATA
47019 GTCATAATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
30 11 0.20
31 39 0.72
32 4 0.07
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (31 bp):
AAAATAATTATTAAATTTATTAATTGATTAT
Found at i:47075 original size:76 final size:76
Alignment explanation
Indices: 46984--47142 Score: 284
Period size: 76 Copynumber: 2.1 Consensus size: 76
46974 AATTACTATA
* *
46984 AAATAATTATTAAATTTATTCATTGTCATAAAATAGTCATAATATTTATATTTTTCACG-AAGCT
1 AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTTATATTTTTCACGAAAG-T
47048 TTTTTTATTGAG
65 TTTTTTATTGAG
47060 AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTTATATTTTTCACGAAAGTT
1 AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTTATATTTTTCACGAAAGTT
47125 TTTTTATTGAG
66 TTTTTATTGAG
47136 AAATATT
1 AAATATT
47143 GCTTCCAGCT
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
76 77 0.96
77 3 0.04
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (76 bp):
AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTTATATTTTTCACGAAAGTT
TTTTTATTGAG
Found at i:52788 original size:19 final size:19
Alignment explanation
Indices: 52764--52814 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
52754 ATGTAATTAA
*
52764 TGTACCGATGTACCCCTAG
1 TGTACCGATGCACCCCTAG
52783 TGTACCGATGCACCCCTAG
1 TGTACCGATGCACCCCTAG
*
52802 TGTACTGATGCAC
1 TGTACCGATGCAC
52815 TAAGTCTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (19 bp):
TGTACCGATGCACCCCTAG
Found at i:57213 original size:128 final size:128
Alignment explanation
Indices: 56985--57240 Score: 424
Period size: 128 Copynumber: 2.0 Consensus size: 128
56975 GATGATCGTC
* *
56985 GTCTTCTTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCATTTGG
1 GTCTTATTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCATTTGA
* *
57050 AATGATCTCTCCATATGATTTGAGACCATTGACAATCGTAGAAAATCTATCCGTCATAGCTTT
66 AATGATCTCTCCATATGATTTGAGACCATTGACAATCGTAGAAAATATATCCGTCATAACTTT
* * *
57113 GTCTTATTTGATTGCCAAGATTTTGGAAGA-AAGTAAACTAACTTCCTCATAAGCTTCTCGTTTG
1 GTCTTATTTGATTGCCAAGATTTTGGAAGAGAA-TAAACTAACTTCCTCACAAGCTTCCCATTTG
*
57177 AAATGATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATATATCCGTCATAACTTT
65 AAATGATCTCTCCATATGATTTGAGACCATTGACAATCGTAGAAAATATATCCGTCATAACTTT
57241 AATATCTTCA
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
127 2 0.02
128 117 0.98
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (128 bp):
GTCTTATTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCATTTGA
AATGATCTCTCCATATGATTTGAGACCATTGACAATCGTAGAAAATATATCCGTCATAACTTT
Done.