Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007690.1 Hibiscus syriacus cultivar Beakdansim tig00109876_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: 39431
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:9218 original size:47 final size:47
Alignment explanation
Indices: 9122--9220 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 47
9112 TCGAATAAAT
* * * **
9122 GCATGCGAACTAGATATCATGCGGTTAGGTTTATTTTTCTCGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAAGATTATTTGTCAAGAACAA
* * *
9169 GCATGCGAATTAGATATCATGCGGTTAAGATT-TTTGTGAATAACAAA
1 GCATGCGAACTAGATATCATGCGGTTAAGATTATTTGTCAAGAAC-AA
9216 GCATG
1 GCATG
9221 GGGTAGATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 7 0.16
47 36 0.84
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAAGATTATTTGTCAAGAACAA
Found at i:16200 original size:41 final size:42
Alignment explanation
Indices: 16098--16204 Score: 144
Period size: 42 Copynumber: 2.6 Consensus size: 42
16088 TTCACAATTT
* * * *
16098 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
* * *
16140 TTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
16181 ATAAGTCCTTCGGGCCATCTGTAA
1 ATAAGTCCTTCGGGCCATCTGTAA
16205 AACCTTCGGG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 21 0.38
42 34 0.62
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (42 bp):
ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
Found at i:16220 original size:41 final size:42
Alignment explanation
Indices: 16098--16221 Score: 117
Period size: 42 Copynumber: 3.0 Consensus size: 42
16088 TTCACAATTT
* ** * *
16098 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCGGGCCATCTGTAAAACCTTCGAGCAAGATGC
* * * * *
16140 TTAAATCCTTCGGGTCATCTGT-AAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGCCATCTGTAAAACC-TTCGAGCAAGATGC
* *
16181 ATAAGTCCTTCGGGCCATCTGTAAAACCTTCGGGTAAGATG
1 ATAAGTCCTTCGGGCCATCTGTAAAACCTTCGAGCAAGATG
16222 TTTTCAAAAG
Statistics
Matches: 64, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
41 31 0.48
42 33 0.52
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (42 bp):
ATAAGTCCTTCGGGCCATCTGTAAAACCTTCGAGCAAGATGC
Found at i:16361 original size:214 final size:214
Alignment explanation
Indices: 15981--16516 Score: 896
Period size: 214 Copynumber: 2.5 Consensus size: 214
15971 GTGAAGCAAA
* *
15981 CCATCCATAAGACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAATGATGTTTTAA
1 CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAA
*
16046 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
66 GAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
*
16111 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
131 GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
16176 AGATGATAAGTCCTTCGGG
196 AGATGATAAGTCCTTCGGG
** *
16195 CCATCTGTAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTGA
1 CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAA
* * *
16260 GAAGATGAAATTTTTGAAAACAAATAATGGGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
66 GAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
16325 GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
131 GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
16390 AGATGATAAGTCCTTCGGG
196 AGATGATAAGTCCTTCGGG
* * * * * *
16409 CCATCCATAAAACCTTCGGGTAGGATGTTTTTACATGAATTTGAAAAT--GAAACTTATGTTTTA
1 CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAAC-GATGTTTTA
*
16472 AGAAGATGAAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTT
65 AGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTT
16517 TATAATCAGT
Statistics
Matches: 299, Mismatches: 22, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
212 4 0.01
213 49 0.16
214 246 0.82
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.32
Consensus pattern (214 bp):
CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAA
GAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
AGATGATAAGTCCTTCGGG
Found at i:16389 original size:42 final size:41
Alignment explanation
Indices: 16312--16418 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
16302 TTCACAATTT
* * * *
16312 ATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAATAAGCCTTTAGAGCAAGATG
* * **
16353 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAATAAGCCTTTAGAGCAAGATG
* *
16395 ATAAGTCCTTCGGGCCATCCATAA
1 ATAAATCCTTCGGGCCATCAATAA
16419 AACCTTCGGG
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
41 19 0.37
42 33 0.63
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAATAAGCCTTTAGAGCAAGATG
Found at i:17064 original size:53 final size:53
Alignment explanation
Indices: 17001--17451 Score: 543
Period size: 53 Copynumber: 8.5 Consensus size: 53
16991 ATCAAACCAT
*
17001 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
17054 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGACAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
17107 AAGACTGTTTGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* **
17160 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCAAAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
17213 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCG-A-CCATAGACAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * **
17264 AATATTGTTCAAGTTTTACTCCATGAAGCAAGAGGGAGCGAACTTGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * *
17317 AAGACTGTTCAAGTTCTACTCCCTTAAGCAAGAGGGAGCGAACCCGCT-GATC-G
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAG-GCAG
* * * ** **
17370 AAGATTGTTCGAGTTCTACTCCCTGAAACAATAGGGAG-AAGACCCGTTTGTTG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGA-ACCCGTAGGCAG
*
17423 AAGATTGTTCGAGTCCTATACTCCCTGAA
1 AAGATTGTTCGAGT--TCTACTCCCTGAA
17452 CGAATAGGTA
Statistics
Matches: 344, Mismatches: 45, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
51 43 0.12
52 4 0.01
53 283 0.82
54 2 0.01
55 12 0.03
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:17375 original size:210 final size:212
Alignment explanation
Indices: 17001--17407 Score: 599
Period size: 210 Copynumber: 1.9 Consensus size: 212
16991 ATCAAACCAT
* * * * *
17001 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTTCGA
1 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGACAGAAGATTGTTCAA
* **
17066 GTTTTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGACAGAAGACTGTTTGAGTTCTACTCCTT
66 GTTTTACTCCATGAAGCAAGAGGGAGCAAACCCGTAGACAGAAGACTGTTCAAGTTCTACTCCTT
* *
17131 GAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGG
131 GAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTTCGAGTTCTACTCCCTGAAACAAGAGGG
17196 AGCGAACCCAAAGGCAG
196 AGCGAACCCAAAGGCAG
*
17213 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCG-A-CCATAGACAGAATATTGTTCAA
1 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGACAGAAGATTGTTCAA
* ** *
17276 GTTTTACTCCATGAAGCAAGAGGGAGCGAACTTGTAGGCAGAAGACTGTTCAAGTTCTACTCCCT
66 GTTTTACTCCATGAAGCAAGAGGGAGCAAACCCGTAGACAGAAGACTGTTCAAGTTCTACT-CCT
* *
17341 T-AAGCAAGAGGGAGCGAACCCGCT-GATC-GAAGATTGTTCGAGTTCTACTCCCTGAAACAATA
130 TGAAGCAAGAGGGAGCGAACCCG-TAG-GCAGAAGATTGTTCGAGTTCTACTCCCTGAAACAAGA
17403 GGGAG
193 GGGAG
17408 AAGACCCGTT
Statistics
Matches: 175, Mismatches: 17, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
210 130 0.74
211 7 0.04
212 38 0.22
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (212 bp):
AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGACAGAAGATTGTTCAA
GTTTTACTCCATGAAGCAAGAGGGAGCAAACCCGTAGACAGAAGACTGTTCAAGTTCTACTCCTT
GAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTTCGAGTTCTACTCCCTGAAACAAGAGGG
AGCGAACCCAAAGGCAG
Found at i:20582 original size:47 final size:46
Alignment explanation
Indices: 20491--20582 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 46
20481 GTGGAACCTC
* *
20491 TAATTTTAAAATCCTATGTCACAAGTTACACATGCAAATTTGCTAAT
1 TAATTTTAAAATACTATGTCACAAGTTACACATG-AAATGTGCTAAT
20538 TAATTTTAAAATACTATGTCACAAGTTACACTTATG-AATGTGCTA
1 TAATTTTAAAATACTATGTCACAAGTTACAC--ATGAAATGTGCTA
20583 CTGCTAGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
47 38 0.93
49 3 0.07
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (46 bp):
TAATTTTAAAATACTATGTCACAAGTTACACATGAAATGTGCTAAT
Done.