Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001624.1 Hibiscus syriacus cultivar Beakdansim tig00003230_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: 52228
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1806 original size:46 final size:47
Alignment explanation
Indices: 1753--1844 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 47
1743 TAGTCTGGTG
*
1753 ATATAGAGCTCACAAGTTTCTA-TGAAAACTTACAAGTTTCTTTAGC
1 ATATAGAGCTCACAAGTTTCTATTGAAAACTAACAAGTTTCTTTAGC
* * ** *
1799 ATATAGAGCTTACAGGTTTCTATTGGGAACTAACAAGTTTTTTTAG
1 ATATAGAGCTCACAAGTTTCTATTGAAAACTAACAAGTTTCTTTAG
1845 AATAAAAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 20 0.51
47 19 0.49
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (47 bp):
ATATAGAGCTCACAAGTTTCTATTGAAAACTAACAAGTTTCTTTAGC
Found at i:10245 original size:179 final size:179
Alignment explanation
Indices: 9945--10302 Score: 698
Period size: 179 Copynumber: 2.0 Consensus size: 179
9935 CAGAGAGACA
*
9945 TCTGATGGTCATGCAGCAGATTGATGAGGATCATACACTGACACAACTTGCAATTGCATGGTTGA
1 TCTGATGGTCATGCAGCAGATTGATGAGGATCATACACTGACACAACTTGCAAATGCATGGTTGA
10010 ATCTGGCCATGGTATGGGATACTTTTCATTTTAGTAGCACGATAAATGAGAAACAATGGATGGTA
66 ATCTGGCCATGGTATGGGATACTTTTCATTTTAGTAGCACGATAAATGAGAAACAATGGATGGTA
10075 TAATGACATTTTCTACCCTATCAGGGTGGTTCCAAGATACAAGAAGCCT
131 TAATGACATTTTCTACCCTATCAGGGTGGTTCCAAGATACAAGAAGCCT
10124 TCTGATGGTCATGCAGCAGATTGATGAGGATCATACACTGACACAACTTGCAAATGCATGGTTGA
1 TCTGATGGTCATGCAGCAGATTGATGAGGATCATACACTGACACAACTTGCAAATGCATGGTTGA
10189 ATCTGGCCATGGTATGGGATACTTTTCATTTTAGTAGCACGATAAATGAGAAACAATGGATGGTA
66 ATCTGGCCATGGTATGGGATACTTTTCATTTTAGTAGCACGATAAATGAGAAACAATGGATGGTA
*
10254 TAATGACATTTTCTACCCTATCAGGGTGGTTCCAAGATACAGGAAGCCT
131 TAATGACATTTTCTACCCTATCAGGGTGGTTCCAAGATACAAGAAGCCT
10303 ATATGATCGT
Statistics
Matches: 177, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 177 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (179 bp):
TCTGATGGTCATGCAGCAGATTGATGAGGATCATACACTGACACAACTTGCAAATGCATGGTTGA
ATCTGGCCATGGTATGGGATACTTTTCATTTTAGTAGCACGATAAATGAGAAACAATGGATGGTA
TAATGACATTTTCTACCCTATCAGGGTGGTTCCAAGATACAAGAAGCCT
Found at i:13064 original size:46 final size:49
Alignment explanation
Indices: 13014--13114 Score: 145
Period size: 46 Copynumber: 2.1 Consensus size: 49
13004 GAGTTTTCAG
* *
13014 AAAAATATTAAGACTTATAA-CACCCTAAATCAAT-A-AAAAAAACTCT
1 AAAAATACTAAGACTTATAAGCAACCTAAATCAATAATAAAAAAACTCT
* *
13060 AAAAATACTAAGACTTATAAGTAACCTAAATTAATAATAAAAAAACTCT
1 AAAAATACTAAGACTTATAAGCAACCTAAATCAATAATAAAAAAACTCT
13109 AAAAAT
1 AAAAAT
13115 GTAAGACGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
46 19 0.40
47 11 0.23
48 1 0.02
49 17 0.35
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (49 bp):
AAAAATACTAAGACTTATAAGCAACCTAAATCAATAATAAAAAAACTCT
Found at i:44769 original size:42 final size:41
Alignment explanation
Indices: 44718--44796 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 41
44708 AACTATCATT
* * * * *
44718 TTAAAAAGTAATACATGACTGATATATCTTTTGGGATGAGC
1 TTAAAAAGTAACACAGGACTAACATATCTTTTAGGATGAGC
44759 TTAATAAAGTAACACAGGACTAACATATCTTTTAGGAT
1 TTAA-AAAGTAACACAGGACTAACATATCTTTTAGGAT
44797 AAGCATGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 4 0.12
42 28 0.88
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.33
Consensus pattern (41 bp):
TTAAAAAGTAACACAGGACTAACATATCTTTTAGGATGAGC
Found at i:44930 original size:80 final size:80
Alignment explanation
Indices: 44816--44963 Score: 217
Period size: 80 Copynumber: 1.9 Consensus size: 80
44806 CAACATATGA
* * *
44816 CTTAAAATATAATTTTAAAATAGTTTGTTCATAATGATTAATAATTAAGATATCTCAAAATAAGA
1 CTTAAAATATAATTTTAAAATAGTTTATTCATAATGATTAATAATTAAAAGATCTCAAAATAAGA
44881 TGAATCAACGTGTGG
66 TGAATCAACGTGTGG
* * * *
44896 CTTAAAGTATAATTTTAAAATCA-TTTATTTATAATTATTAATAATTAAAAGATGTCAAAATAAG
1 CTTAAAATATAATTTTAAAAT-AGTTTATTCATAATGATTAATAATTAAAAGATCTCAAAATAAG
44960 ATGA
65 ATGA
44964 GACGATAACA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 59 0.98
81 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (80 bp):
CTTAAAATATAATTTTAAAATAGTTTATTCATAATGATTAATAATTAAAAGATCTCAAAATAAGA
TGAATCAACGTGTGG
Found at i:49105 original size:51 final size:51
Alignment explanation
Indices: 49029--49128 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
49019 TTGTAAACAA
*
49029 AGGAACTCGCTGGAGCAGCCTCGGTCTGACCAGTCACCTCAACAGGAACGG
1 AGGAACTCACTGGAGCAGCCTCGGTCTGACCAGTCACCTCAACAGGAACGG
*
49080 AGGAACTCACTGGAGCAGCCTCGGTCTGGCCAGTCACCTCAACAGGAAC
1 AGGAACTCACTGGAGCAGCCTCGGTCTGACCAGTCACCTCAACAGGAAC
49129 TCATTGGAGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (51 bp):
AGGAACTCACTGGAGCAGCCTCGGTCTGACCAGTCACCTCAACAGGAACGG
Found at i:49141 original size:43 final size:43
Alignment explanation
Indices: 49080--49161 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
49070 ACAGGAACGG
* *
49080 AGGAACTCACTGGAGCAGCCTCGGTCTGGCCAGTCACCTCAAC
1 AGGAACTCACTGGAGCAGCCTCGGCCTGGCCAGCCACCTCAAC
* *
49123 AGGAACTCATTGGAGCAGCCTCGGCCTGGTCAGCCACCT
1 AGGAACTCACTGGAGCAGCCTCGGCCTGGCCAGCCACCT
49162 TAATAGGGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.17
Consensus pattern (43 bp):
AGGAACTCACTGGAGCAGCCTCGGCCTGGCCAGCCACCTCAAC
Found at i:51196 original size:11 final size:11
Alignment explanation
Indices: 51180--51206 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
51170 CAGTGACAAC
51180 CAGCTTATACT
1 CAGCTTATACT
51191 CAGCTTATACT
1 CAGCTTATACT
51202 CAGCT
1 CAGCT
51207 GATAACCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (11 bp):
CAGCTTATACT
Done.