Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000435.1 Hibiscus syriacus cultivar Beakdansim tig00000797_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: 41963
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:6566 original size:22 final size:21
Alignment explanation
Indices: 6540--6620 Score: 58
Period size: 23 Copynumber: 3.8 Consensus size: 21
6530 ATAGGACAGA
6540 GGGAATCGATACCCCCATGAAG
1 GGGAATCGATACCCCC-TGAAG
* *
6562 GGGAA-CTGATTCCCCCTTTGAAT
1 GGGAATC-GATACCCCC--TGAAG
* * *
6585 GGGAACCGATTCCCCCT-TAG
1 GGGAATCGATACCCCCTGAAG
*
6605 GGGAATTGATACCCCC
1 GGGAATCGATACCCCC
6621 CAAGGGTTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
20 14 0.29
21 2 0.04
22 13 0.27
23 18 0.38
24 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.21
Consensus pattern (21 bp):
GGGAATCGATACCCCCTGAAG
Found at i:6583 original size:23 final size:23
Alignment explanation
Indices: 6540--6602 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
6530 ATAGGACAGA
* * *
6540 GGGAATCGATACCCCC-ATGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
6562 GGGAACTGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAG
6585 GGGAACCGATTCCCCCTT
1 GGGAACCGATTCCCCCTT
6603 AGGGGAATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:9146 original size:22 final size:22
Alignment explanation
Indices: 9120--9172 Score: 99
Period size: 21 Copynumber: 2.5 Consensus size: 22
9110 AGAGGGAACC
9120 GATTCCCCCTTAAGGGGGTACT
1 GATTCCCCCTTAAGGGGGTACT
9142 GATTCCCCC-TAAGGGGGTACT
1 GATTCCCCCTTAAGGGGGTACT
9163 GATTCCCCCT
1 GATTCCCCCT
9173 GAATGGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.17, C:0.32, G:0.25, T:0.26
Consensus pattern (22 bp):
GATTCCCCCTTAAGGGGGTACT
Found at i:11108 original size:23 final size:23
Alignment explanation
Indices: 11082--11158 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
11072 GGTTCTACGC
* *
11082 GGTCCTTCTGGATAATTCTATAT
1 GGTCCTTCTGGACAATTCTACAT
11105 GGTCCTTCTGGACAATTCTACAT
1 GGTCCTTCTGGACAATTCTACAT
* **
11128 GGTCCTT-TGAGACATTTCTACGC
1 GGTCCTTCTG-GACAATTCTACAT
11151 GGTCCTTC
1 GGTCCTTC
11159 GGGAAAATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
22 2 0.04
23 45 0.96
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (23 bp):
GGTCCTTCTGGACAATTCTACAT
Found at i:11147 original size:46 final size:46
Alignment explanation
Indices: 11097--11194 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 46
11087 TTCTGGATAA
* * * * * *
11097 TTCTATATGGTCCTTCTGGACAATTCTACATGGTCCTTTGAGACAT
1 TTCTATACGGTCCTTCGGGAAAATACTACATGGTCATTCGAGACAT
** **
11143 TTCTACGCGGTCCTTCGGGAAAATACTATGTGGTCATTCGAGACAT
1 TTCTATACGGTCCTTCGGGAAAATACTACATGGTCATTCGAGACAT
11189 TTCTAT
1 TTCTAT
11195 GTGGCATTTC
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (46 bp):
TTCTATACGGTCCTTCGGGAAAATACTACATGGTCATTCGAGACAT
Found at i:11194 original size:23 final size:23
Alignment explanation
Indices: 11127--11202 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
11117 CAATTCTACA
* * *
11127 TGGTCCTTTGAGACATTTCTACG
1 TGGTCATTCGAGACATTTCTATG
* * * * * *
11150 CGGTCCTTCGGGAAAATACTATG
1 TGGTCATTCGAGACATTTCTATG
11173 TGGTCATTCGAGACATTTCTATG
1 TGGTCATTCGAGACATTTCTATG
11196 TGG-CATT
1 TGGTCATT
11203 TCAGTGTAAT
Statistics
Matches: 40, Mismatches: 13, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
22 4 0.10
23 36 0.90
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (23 bp):
TGGTCATTCGAGACATTTCTATG
Found at i:13006 original size:20 final size:20
Alignment explanation
Indices: 12981--13024 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
12971 ATTTTCTCTT
* *
12981 AAAAGCAAAATTAGATTTTG
1 AAAAGCAAAATGAAATTTTG
13001 AAAAGCAAAATGAAATTTTG
1 AAAAGCAAAATGAAATTTTG
13021 AAAA
1 AAAA
13025 ATGATTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.25
Consensus pattern (20 bp):
AAAAGCAAAATGAAATTTTG
Found at i:14137 original size:106 final size:108
Alignment explanation
Indices: 14019--14230 Score: 329
Period size: 106 Copynumber: 2.0 Consensus size: 108
14009 ATATGTTTGC
* * *
14019 AAAATTCAATTTCTCAATGAAAAAGGAGGAGCTTTAATATTTTTCAAATATTTCTCTTTTTCATG
1 AAAATTCAATTTCTCAATGAAAAAGGAGGAGCTTTAATATTTTCCAAATACTTCTCTTTTTAATG
*
14084 AAATATTTTATTAAGG-GG-GTTTTGCCAAAAATAAATTTTAA
66 AAATATTTTATTAAGGAGGAGTTTTGCCAAAAACAAATTTTAA
* * *
14125 AAAATTCAATTTCTCATTGAAGAATGAGGAGCTTTAATATTTTCCAAATACTTCTCTTTTTAATG
1 AAAATTCAATTTCTCAATGAAAAAGGAGGAGCTTTAATATTTTCCAAATACTTCTCTTTTTAATG
* *
14190 AAATATTTTATTATGGAGGAGTTTTGCTAAAAACAAATTTT
66 AAATATTTTATTAAGGAGGAGTTTTGCCAAAAACAAATTTT
14231 CAAATGTTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
106 74 0.78
107 2 0.02
108 19 0.20
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (108 bp):
AAAATTCAATTTCTCAATGAAAAAGGAGGAGCTTTAATATTTTCCAAATACTTCTCTTTTTAATG
AAATATTTTATTAAGGAGGAGTTTTGCCAAAAACAAATTTTAA
Found at i:15427 original size:75 final size:75
Alignment explanation
Indices: 15329--15652 Score: 407
Period size: 75 Copynumber: 4.3 Consensus size: 75
15319 CACAACAATT
* * * * * * * * *
15329 ATAGGTAGCACCCACTTTATTTTACCGTTTACATTATTATTAACATTTAAACAAACTGGTAGCTA
1 ATAGGTAGCGCCTATTTTATTTTACCATTTACATTATTAGTAACCTTTAAACAAACCGATAGGTA
*
15394 GTTTAATGTA
66 GTTTAACGTA
* * * *
15404 ATAAGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGATAGATA
1 ATAGGTAGCGCCTATTTTATTTTACCATTTACATTATTAGTAACCTTTAAACAAACCGATAGGTA
15469 GTTTAACGTA
66 GTTTAACGTA
* * *
15479 ATAGGTAGTGCCTATTTTATTTTACTATTTACATTATTAGTAACCTTTAAACAAACCAATAGGTA
1 ATAGGTAGCGCCTATTTTATTTTACCATTTACATTATTAGTAACCTTTAAACAAACCGATAGGTA
*
15544 TTTTAACGTA
66 GTTTAACGTA
* * * *
15554 ATATGTATCACCTA-TTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAACCGATAGGTA
1 ATAGGTAGCGCCTATTTTATTTTACCATTTACATTATTAGTAACCTTTAAACAAACCGATAGGTA
*
15618 GTTTAACATA
66 GTTTAACGTA
* *
15628 ATAGGTAGTGCATATTTTTATTTTA
1 ATAGGTAGCGCCTA-TTTTATTTTA
15653 ACCGATTAAC
Statistics
Matches: 216, Mismatches: 31, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
74 64 0.30
75 143 0.66
76 9 0.04
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (75 bp):
ATAGGTAGCGCCTATTTTATTTTACCATTTACATTATTAGTAACCTTTAAACAAACCGATAGGTA
GTTTAACGTA
Found at i:17040 original size:4 final size:4
Alignment explanation
Indices: 17031--17060 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
17021 AAAATAACAT
17031 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
17061 AAAAATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:27295 original size:2 final size:2
Alignment explanation
Indices: 27288--27312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27278 AAAAGCTCGG
27288 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
27313 GTGCCTGGCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:40089 original size:5 final size:5
Alignment explanation
Indices: 40074--40110 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
40064 GTAATTTTTG
*
40074 TAAAGA TAAAA TAAAA TAAAA TAAAA TAAAA CAAAA T
1 TAAA-A TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
40111 TAAAGTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (5 bp):
TAAAA
Done.