Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005212.1 Hibiscus syriacus cultivar Beakdansim tig00011791_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: 72134
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:220 original size:22 final size:22
Alignment explanation
Indices: 144--220 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
134 TCAGAAGGTC
* *
144 TTAGCACTAATACTAAAGTGCC
1 TTAGCACTGATACTAAAGTGCA
* * *
166 TCT-GCACTTATA-TAGAATTGTA
1 T-TAGCACTGATACTA-AAGTGCA
188 TTCA-CACTGATACTAAAGTGCA
1 TT-AGCACTGATACTAAAGTGCA
210 TTAGCACTGAT
1 TTAGCACTGAT
221 GGATAATCTG
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
21 4 0.10
22 35 0.83
23 3 0.07
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32
Consensus pattern (22 bp):
TTAGCACTGATACTAAAGTGCA
Found at i:10921 original size:22 final size:22
Alignment explanation
Indices: 10863--10922 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
10853 AGTACCTTAG
* *
10863 CACTAATACTAAAGTTCCTCAT
1 CACTGATACTAAAGTGCCTCAT
*
10885 CACTGATAC-AGAAGTGCATTCAT
1 CACTGATACTA-AAGTGC-CTCAT
10908 -ACTGATACTAAAGTG
1 CACTGATACTAAAGTG
10923 ACTTAGCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 1 0.03
22 26 0.81
23 5 0.16
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (22 bp):
CACTGATACTAAAGTGCCTCAT
Found at i:37196 original size:2 final size:2
Alignment explanation
Indices: 37189--37220 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
37179 TTACAACCGC
37189 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
37221 CATTCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49219 original size:35 final size:35
Alignment explanation
Indices: 49162--49233 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
49152 TCGTAAGAAG
*
49162 TCTGATTGTGTGAAGTTTTTCTGAATATATTGAAT
1 TCTGATTGTGTGAAGTTCTTCTGAATATATTGAAT
49197 TCTGATTGTGT-AAGGTTCTTCTGAATATATTGAAT
1 TCTGATTGTGTGAA-GTTCTTCTGAATATATTGAAT
49232 TC
1 TC
49234 AACACTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (35 bp):
TCTGATTGTGTGAAGTTCTTCTGAATATATTGAAT
Found at i:65316 original size:85 final size:85
Alignment explanation
Indices: 65168--65344 Score: 320
Period size: 85 Copynumber: 2.1 Consensus size: 85
65158 AATTGAGCAG
* * *
65168 AATAT-GAAAAATCAGGGTAAGGGTATCGGTACTGGAAGAACAGTACCGATACTATAGGTTTAAA
1 AATATCGAAAAATCAGGGTAAGGGTATCGGTACTGAAAGAACAATACCGACACTATAGGTTTAAA
65232 TTTGAAGAAATACGATGAAC
66 TTTGAAGAAATACGATGAAC
65252 AATATCGAAAAATCAGGGTAAGGGTATCGGTACTGAAAGAACAATACCGACACTATAGGTTTAAA
1 AATATCGAAAAATCAGGGTAAGGGTATCGGTACTGAAAGAACAATACCGACACTATAGGTTTAAA
65317 TTTGAAGAAATACGATGAAC
66 TTTGAAGAAATACGATGAAC
65337 AATATCGA
1 AATATCGA
65345 CACTAATGCA
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
84 5 0.06
85 84 0.94
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (85 bp):
AATATCGAAAAATCAGGGTAAGGGTATCGGTACTGAAAGAACAATACCGACACTATAGGTTTAAA
TTTGAAGAAATACGATGAAC
Found at i:65891 original size:54 final size:54
Alignment explanation
Indices: 65799--66300 Score: 718
Period size: 54 Copynumber: 9.3 Consensus size: 54
65789 TTACAGAATG
* * * *
65799 GGCACTATATGTGCAACCTAAGAAATTCATATTTAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
65853 GGCAGTATCTGTGCAACATAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
65907 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
65961 GACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
66015 GGCACTATATGTGCAACCTAAGAAACTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
66069 GGCATTATGTGTGAAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
66123 GACACTATGTGTGCAACCTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
66177 GGCACTATGTGTGCAACCTAAGAAATTCATAATTAA-TTTATGAATTTCCATATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAA-TAAGTTTATGAATTTCCGTATT
* * * ** * * * * *
66231 GGCACTATGTGTGCACCCCACGGTATTCATAGTGAGTTTTTGAATTACCGTATC
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
66285 GGCACTACGTGTGCAA
1 GGCACTATGTGTGCAA
66301 AAACCATTGA
Statistics
Matches: 401, Mismatches: 45, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
53 2 0.00
54 396 0.99
55 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
Found at i:69916 original size:81 final size:81
Alignment explanation
Indices: 69398--69894 Score: 683
Period size: 81 Copynumber: 6.1 Consensus size: 81
69388 TTGTTTTAAA
* * * * * * *
69398 TAAAAGATTTATTTCCTAGATATGCATTTGTCAGAAATGTGTCAATTATGTTAA-TTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATG-CAAGTTAGATGAAA
69462 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * * *
69479 TAAAATATTAATTGCCTAGCTGTGCATCTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAG
*
69544 TTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
69560 TAAAAGATTAATTGCCTATCTGTGCATCTT-ACAGAAAGGTGTCAATTATGCTAGTTACATTAAA
1 TAAAAGATTAATTGCCTAGCTGTGCAT-TTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAA
69624 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * *
69641 TAAAAGATTAATTGCCTAGCCGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAG
*
69706 GTTAAATACCTTTAAG
66 GTTAAATACCTTTGAG
* * *
69722 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGGAAGGTGTCAATTATCCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAG
*
69787 GTTAAATACCTTCGAG
66 GTTAAATACCTTTGAG
* * *
69803 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAAAAAGGTGTCAATAATGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAG
* * *
69868 GCTAAATGCCTTTGGG
66 GTTAAATACCTTTGAG
*
69884 TAAAATATTAA
1 TAAAAGATTAA
69895 ATGCTTAACA
Statistics
Matches: 369, Mismatches: 44, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
80 3 0.01
81 365 0.99
82 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAG
GTTAAATACCTTTGAG
Done.