Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002706.1 Hibiscus syriacus cultivar Beakdansim tig00005583_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: 72628
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:21842 original size:29 final size:31
Alignment explanation
Indices: 21770--21857 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 31
21760 TAAGTGTGAT
*
21770 ATTT-GGG-TCGGGTCGGGGTTTTTTTCAAAAA
1 ATTTCGGGATCGGGTC-GAGTTTTTTT-AAAAA
*
21801 ATTTTGGGATCGGGTCGA-TTTTTTTAAAAA
1 ATTTCGGGATCGGGTCGAGTTTTTTTAAAAA
* *
21831 A-TTCGGGTTCGGGTCGAGGTTTTTTAA
1 ATTTCGGGATCGGGTCGAGTTTTTTTAA
21858 GTTTGATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
29 14 0.28
30 14 0.28
31 11 0.22
32 4 0.08
33 7 0.14
ACGTcount: A:0.20, C:0.09, G:0.30, T:0.41
Consensus pattern (31 bp):
ATTTCGGGATCGGGTCGAGTTTTTTTAAAAA
Found at i:21883 original size:31 final size:32
Alignment explanation
Indices: 21831--21950 Score: 134
Period size: 39 Copynumber: 3.5 Consensus size: 32
21821 TTTTTAAAAA
*
21831 ATTCGGGTTCGGGTCGAGGTTTTTTAAGTTTGAT
1 ATTCGGG-TCGGGTCG-GGTTTTTTAAGTGTGAT
21865 ATTCGGGTC-GGTCGGGTTTTTTAAGTGTGAT
1 ATTCGGGTCGGGTCGGGTTTTTTAAGTGTGAT
*
21896 ATTCGGGTCGGGTTCGGGTTGGGTTTTTTTAAGTGTAAT
1 ATTCGGGTCGGG-TC-----GGG-TTTTTTAAGTGTGAT
21935 ATTCGGGTCGGGTCGG
1 ATTCGGGTCGGGTCGG
21951 ATCTCGGGTG
Statistics
Matches: 76, Mismatches: 2, Indels: 17
0.80 0.02 0.18
Matches are distributed among these distances:
31 25 0.33
32 7 0.09
33 6 0.08
34 7 0.09
38 5 0.07
39 26 0.34
ACGTcount: A:0.12, C:0.10, G:0.37, T:0.41
Consensus pattern (32 bp):
ATTCGGGTCGGGTCGGGTTTTTTAAGTGTGAT
Found at i:28794 original size:11 final size:12
Alignment explanation
Indices: 28766--28793 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28756 AACTTTTAAA
28766 TTTTTATGTATT
1 TTTTTATGTATT
28778 TTTTTATGTATT
1 TTTTTATGTATT
28790 TTTT
1 TTTT
28794 AAAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTATGTATT
Found at i:29200 original size:36 final size:36
Alignment explanation
Indices: 29154--29224 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
29144 TAAAGTCTAG
29154 TTTTTGTTTCATTCAGTATTCCATTCAAAATTTGAT
1 TTTTTGTTTCATTCAGTATTCCATTCAAAATTTGAT
**
29190 TTTTTGTTTCATTCAGTATTCTGTTCAAAATTTGA
1 TTTTTGTTTCATTCAGTATTCCATTCAAAATTTGA
29225 CATTAACTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.54
Consensus pattern (36 bp):
TTTTTGTTTCATTCAGTATTCCATTCAAAATTTGAT
Found at i:32679 original size:3 final size:3
Alignment explanation
Indices: 32671--32706 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
32661 TTTATGTTTG
32671 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
32707 TTGTTGCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:34510 original size:12 final size:12
Alignment explanation
Indices: 34493--34517 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34483 ACAAAGCACC
34493 ATTTGGTGCCTA
1 ATTTGGTGCCTA
34505 ATTTGGTGCCTA
1 ATTTGGTGCCTA
34517 A
1 A
34518 ATTAATTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:41791 original size:15 final size:15
Alignment explanation
Indices: 41767--41818 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
41757 TGAAACATTA
41767 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
41782 CCCGCTCCGCATCCG
1 CCCGCCCCGCATCCG
* * *
41797 TCCACCCCACATCCG
1 CCCGCCCCGCATCCG
*
41812 TCCGCCC
1 CCCGCCC
41819 AGCTAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.10, C:0.63, G:0.15, T:0.12
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:49577 original size:9 final size:9
Alignment explanation
Indices: 49565--49604 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
49555 TGTTGATGTT
49565 GATGATGAG
1 GATGATGAG
49574 GATGATGAG
1 GATGATGAG
* *
49583 GATGGTGAT
1 GATGATGAG
*
49592 GATGATGGG
1 GATGATGAG
49601 GATG
1 GATG
49605 TTGGTTCGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.47, T:0.25
Consensus pattern (9 bp):
GATGATGAG
Found at i:56559 original size:38 final size:39
Alignment explanation
Indices: 56484--56561 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
56474 AAAGTAAGAG
56484 CAAATATGAGGTCAAAACAGACCAAAAGATTGAGATTAC
1 CAAATATGAGGTCAAAACAGACCAAAAGATTGAGATTAC
56523 CAAATATGAGGTCAAAACAGACC-AAAGATTGAGATTAC
1 CAAATATGAGGTCAAAACAGACCAAAAGATTGAGATTAC
56561 C
1 C
56562 TGTGCAGCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 16 0.41
39 23 0.59
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.18
Consensus pattern (39 bp):
CAAATATGAGGTCAAAACAGACCAAAAGATTGAGATTAC
Found at i:64049 original size:2 final size:2
Alignment explanation
Indices: 64042--64074 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
64032 ATAGTCCTTT
64042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64075 GCATGTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71532 original size:29 final size:29
Alignment explanation
Indices: 71473--71611 Score: 110
Period size: 29 Copynumber: 4.9 Consensus size: 29
71463 ACCGTTGACC
* **
71473 GGTGTTATTCTGGGAATTAATTC-AGTTTT
1 GGTGCTATTCTGGGAATTAATTCGA-AATT
*
71502 GGTGCTATTCTGGAAATTAATTCGAAATT
1 GGTGCTATTCTGGGAATTAATTCGAAATT
* * **
71531 GGTGCTATTTTGGTAATATTTTTCG-----
1 GGTGCTATTCTGGGAAT-TAATTCGAAATT
* * *
71556 GGTGATATTATGGGTATTAATTCGAAATT
1 GGTGCTATTCTGGGAATTAATTCGAAATT
*
71585 GGTGCTATTTTGGGAATTAATTCGAAA
1 GGTGCTATTCTGGGAATTAATTCGAAA
71612 ATGATACTAT
Statistics
Matches: 86, Mismatches: 17, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
24 5 0.06
25 13 0.15
29 62 0.72
30 6 0.07
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATT
Found at i:71621 original size:29 final size:29
Alignment explanation
Indices: 71561--71632 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
71551 TTTCGGGTGA
* * * * *
71561 TATTATGGGTATTAATTCGAAATTGGTGC
1 TATTTTGGGAATTAATTCGAAAATGATAC
71590 TATTTTGGGAATTAATTCGAAAATGATAC
1 TATTTTGGGAATTAATTCGAAAATGATAC
*
71619 TATTTTGGTAATTA
1 TATTTTGGGAATTA
71633 TTTTAAAAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (29 bp):
TATTTTGGGAATTAATTCGAAAATGATAC
Found at i:71650 original size:29 final size:29
Alignment explanation
Indices: 71555--71652 Score: 79
Period size: 29 Copynumber: 3.4 Consensus size: 29
71545 AATATTTTTC
* * * * *
71555 GGGTGATATTATGGGTATTAATTCGAAAT
1 GGGTGCTATTTTGGGAATTAATTCAAAAA
* *
71584 TGGTGCTATTTTGGGAATTAATTCGAAAA
1 GGGTGCTATTTTGGGAATTAATTCAAAAA
* * * * * *
71613 TGATACTATTTTGGTAATTATTTTAAAAA
1 GGGTGCTATTTTGGGAATTAATTCAAAAA
71642 GGGTGCTATTT
1 GGGTGCTATTT
71653 GTGTAAAATA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.42
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTAATTCAAAAA
Done.