Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004946.1 Hibiscus syriacus cultivar Beakdansim tig00011119_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: 99126
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:82957 original size:2 final size:2
Alignment explanation
Indices: 82950--83004 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
82940 AGGTAATTAA
82950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82992 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
83005 GACCGAAACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:85015 original size:116 final size:111
Alignment explanation
Indices: 84811--85043 Score: 260
Period size: 112 Copynumber: 2.0 Consensus size: 111
84801 GGATCCCCAA
* * * *
84811 TTTTTATATTATAATTAGGGCCCCTAATTTTATAATTTCATAATTTTTTTTAGTTTTGAGCATCT
1 TTTTTATATTATAATTAGGGCCCCTAATTTTATAATTTCATAA-TATGTTTAATTTTGACCATCT
84876 TTTTCTATTTCTCTTATTAATTCATTCAATTTTGAATTAAATTTAACCAT-
65 TTTTCTATTTCTC---TT-ATTCATTCAATTTTGAATTAAATTTAACCATG
* * *
84926 TTTTTATACTTATAATTAGGGCCCCTAATTTTTTATATTTTCA-AA-ATGTTTAATTTTTACCCT
1 TTTTTATA-TTATAATTAGGGCCCCTAA--TTTTATAATTTCATAATATGTTTAATTTTGACCAT
*
84989 -TTTTTCGT-TTCTCTTCTTATTCATTCAATTTTGAATTAAATTTAATCATG
63 CTTTTTC-TATT-TC-TCTTATTCATTCAATTTTGAATTAAATTTAACCATG
85039 TTTTT
1 TTTTT
85044 CTTATTTTTT
Statistics
Matches: 103, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
112 30 0.29
113 7 0.07
114 8 0.08
115 23 0.22
116 21 0.20
117 2 0.02
118 12 0.12
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (111 bp):
TTTTTATATTATAATTAGGGCCCCTAATTTTATAATTTCATAATATGTTTAATTTTGACCATCTT
TTTCTATTTCTCTTATTCATTCAATTTTGAATTAAATTTAACCATG
Found at i:88881 original size:18 final size:19
Alignment explanation
Indices: 88858--88894 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
88848 TCATTTCAAA
88858 GTTGGTTAT-GTTGTTAAG
1 GTTGGTTATGGTTGTTAAG
*
88876 GTTGGTTTTGGTTGTTAAG
1 GTTGGTTATGGTTGTTAAG
88895 CCTGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.14, C:0.00, G:0.35, T:0.51
Consensus pattern (19 bp):
GTTGGTTATGGTTGTTAAG
Found at i:94908 original size:8 final size:8
Alignment explanation
Indices: 94867--94908 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
94857 CATGCATGCA
94867 TATGCATG
1 TATGCATG
*
94875 TATGAATG
1 TATGCATG
*
94883 TATGAATG
1 TATGCATG
94891 TATGCA--
1 TATGCATG
94897 TATGCATG
1 TATGCATG
94905 TATG
1 TATG
94909 TATTGGTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
8 24 0.80
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (8 bp):
TATGCATG
Found at i:95501 original size:21 final size:21
Alignment explanation
Indices: 95468--95557 Score: 157
Period size: 21 Copynumber: 4.4 Consensus size: 21
95458 TCTTTTAGCT
95468 AATGAAA--ATAACGCTTCAA
1 AATGAAACCATAACGCTTCAA
95487 AATGAAACCATAACGCTTCAA
1 AATGAAACCATAACGCTTCAA
95508 AATGAAACCATAACGCTTCAA
1 AATGAAACCATAACGCTTCAA
95529 AATGAAACCATAACGCTTCAA
1 AATGAAACCATAACGCTTCAA
*
95550 AAAGAAAC
1 AATGAAAC
95558 ATCTATTCTT
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
19 7 0.10
21 61 0.90
ACGTcount: A:0.51, C:0.21, G:0.10, T:0.18
Consensus pattern (21 bp):
AATGAAACCATAACGCTTCAA
Found at i:96477 original size:43 final size:42
Alignment explanation
Indices: 96411--96632 Score: 179
Period size: 43 Copynumber: 5.4 Consensus size: 42
96401 GCGGTGTTTG
* * **
96411 AACGCCACTAAAGTATGAATCTTTAGTTGCGTTTGTAAATACA
1 AACGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTGTAAATA-A
* * * *
96454 AACGCCACTAAAGTAAGAGTCTTTAGCTGCATTTGTAAACACG
1 AACGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTGTAAATA-A
* *
96497 AACGCCACTACAGTACGAGTCTTTAGCGGCG-TT-T--ATAA
1 AACGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTGTAAATAA
* * *
96535 AAGCGCCACTAAAGTACGAGTCTATAGCAGCGTTTGT--ATAA
1 AA-CGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTGTAAATAA
** * * *
96576 AATACCACTAAAGTAAGAGTCTATAGTGGTC-TTTGTAAAAAA
1 AACGCCACTAAAGTAAGAGTCTTTAGCGG-CGTTTGTAAATAA
* *
96618 AATGCCGCTAAAGTA
1 AACGCCACTAAAGTA
96633 CTACTATTAC
Statistics
Matches: 150, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.01
39 28 0.19
40 29 0.19
41 9 0.06
42 18 0.12
43 64 0.43
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (42 bp):
AACGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTGTAAATAA
Found at i:96612 original size:40 final size:40
Alignment explanation
Indices: 96458--96601 Score: 119
Period size: 39 Copynumber: 3.5 Consensus size: 40
96448 AATACAAACG
* * * **
96458 CCACTAAAGTAAGAGTCTTTAGCTGCATTTGTAAACACGAACG
1 CCACTAAAGTAAGAGTCTATAGCAGCGTTTGTAAA-A--AATA
* * * * * ***
96501 CCACTACAGTACGAGTCTTTAGCGGCGTTTAT-AAAAGCG
1 CCACTAAAGTAAGAGTCTATAGCAGCGTTTGTAAAAAATA
* *
96540 CCACTAAAGTACGAGTCTATAGCAGCGTTTGTATAAAATA
1 CCACTAAAGTAAGAGTCTATAGCAGCGTTTGTAAAAAATA
96580 CCACTAAAGTAAGAGTCTATAG
1 CCACTAAAGTAAGAGTCTATAG
96602 TGGTCTTTGT
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
39 31 0.36
40 24 0.28
41 1 0.01
42 2 0.02
43 27 0.32
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (40 bp):
CCACTAAAGTAAGAGTCTATAGCAGCGTTTGTAAAAAATA
Found at i:96779 original size:80 final size:81
Alignment explanation
Indices: 96615--96882 Score: 287
Period size: 82 Copynumber: 3.3 Consensus size: 81
96605 TCTTTGTAAA
* **
96615 AAAAATGCCGCTAAAGTACTACTA--TT-ACGGCGTTTATTGAAAAAAAATCCACTATAGATAAA
1 AAAAACGCCGCTAAAGTA-TACTATGTTGA-GGCGTTTATTG-AAAAAACGCCACTATAGATAAA
*
96677 TCCTATTGCGTCGTTTGTAT
63 -CCTATTGCGGCGTTTGTAT
** * *
96697 AAAAACGCCGCTAAAGTATACTATGTT-ATGGC-TTT-TTGTTGAAAACGCCACTATAGATGACC
1 AAAAACGCCGCTAAAGTATACTATGTTGA-GGCGTTTATTG-AAAAAACGCCACTATAGATAAAC
*
96759 CTCTTGCGGCGTTTGTAT
64 CTATTGCGGCGTTTGTAT
* * *
96777 AAAAACGCCGCTAAAGTACCACTATGTTGAGGCGTTTATTGAAAAAATGCCACTATGGATAAACC
1 AAAAACGCCGCTAAAGTA-TACTATGTTGAGGCGTTTATTGAAAAAACGCCACTATAGATAAACC
* *
96842 TATTGCAGCATTTGTAT
65 TATTGCGGCGTTTGTAT
* *
96859 AAAAACGCCGTTGAAGTATACTAT
1 AAAAACGCCGCTAAAGTATACTAT
96883 ATTGCGGTGT
Statistics
Matches: 156, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
80 35 0.22
81 40 0.26
82 72 0.46
83 9 0.06
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (81 bp):
AAAAACGCCGCTAAAGTATACTATGTTGAGGCGTTTATTGAAAAAACGCCACTATAGATAAACCT
ATTGCGGCGTTTGTAT
Done.