Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007475.1 Hibiscus syriacus cultivar Beakdansim tig00020550_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: 249424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:205718 original size:22 final size:21
Alignment explanation
Indices: 205676--205715 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
205666 GAGTTTGTTT
*
205676 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
205697 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
205716 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:207753 original size:75 final size:76
Alignment explanation
Indices: 207660--207838 Score: 225
Period size: 75 Copynumber: 2.3 Consensus size: 76
207650 ACCCCCTTGG
* * ** * *
207660 GGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAATGTTTAGGGGGGAATCG
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCA
207725 GTTCCTCCTAT
66 GTTCCTCCTAT
* * * *
207736 -GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCAAACCATTCAGGGGGGAATCA
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCA
207800 GTTCCTCCTAT
66 GTTCCTCCTAT
*
207811 GGGGGGGGGAATCGGTTCCCTCTGAGCA
1 ---GGGGGGAATCGGTTCCCTCCGAGCA
207839 ATCTGTAATT
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
75 65 0.74
79 23 0.26
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (76 bp):
GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCAGGGGGGAATCA
GTTCCTCCTAT
Found at i:213081 original size:2 final size:2
Alignment explanation
Indices: 213074--213104 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
213064 TTTTATCTGA
213074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
213105 GATTAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:213813 original size:2 final size:2
Alignment explanation
Indices: 213808--213848 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
213798 TAGAATTAGG
213808 TA TA TA TA 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 TA TA TA TA T
213849 TCAAGGATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:222950 original size:22 final size:22
Alignment explanation
Indices: 222908--222951 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
222898 TAGGTATTCG
*
222908 ATAAAAGGTTAAGATTGTTTTA
1 ATAAAAGGTTAAAATTGTTTTA
* *
222930 ATAAAATGTTAGAAATTTTTTT
1 ATAAAAGGTTA-AAATTGTTTT
222952 TAGTTATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (22 bp):
ATAAAAGGTTAAAATTGTTTTA
Found at i:230849 original size:91 final size:91
Alignment explanation
Indices: 230738--230906 Score: 266
Period size: 91 Copynumber: 1.9 Consensus size: 91
230728 TTAATTATCA
* * * * *
230738 ATTTTTTAATTAAATGTGTTTGGTCACTTACGTTATTAATTGGGTAAACTAAATTTTTGACCTTT
1 ATTTTTAAATTAAATATGTTTGGTCACTCACGTTATTAATTGGGCAAACTAAATTTTCGACCTTT
230803 GCAAAAAAAAAAATCTTTAATCACCC
66 GCAAAAAAAAAAATCTTTAATCACCC
* * *
230829 ATTTTTAAATTAAGTATGTTTGTTCTCTCACGTTATTAATTGGGCAAACTAAATTTTCGACCTTT
1 ATTTTTAAATTAAATATGTTTGGTCACTCACGTTATTAATTGGGCAAACTAAATTTTCGACCTTT
230894 GCAAAAAAAAAAA
66 GCAAAAAAAAAAA
230907 AAACTTTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 70 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (91 bp):
ATTTTTAAATTAAATATGTTTGGTCACTCACGTTATTAATTGGGCAAACTAAATTTTCGACCTTT
GCAAAAAAAAAAATCTTTAATCACCC
Found at i:231008 original size:45 final size:44
Alignment explanation
Indices: 230945--231034 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 44
230935 CAGAAGTTGA
*
230945 ATACATAAAGTATTTGGAAGATACCCATTTTCTTGATATTTGTG
1 ATACATAAAGTATTTGGAAGATACCCATTTCCTTGATATTTGTG
230989 ATACATTAAAGTATTTGGAAGATACCCATTTCCTTGATATTTGTG
1 ATACA-TAAAGTATTTGGAAGATACCCATTTCCTTGATATTTGTG
231034 A
1 A
231035 GTTATAAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 5 0.11
45 39 0.89
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (44 bp):
ATACATAAAGTATTTGGAAGATACCCATTTCCTTGATATTTGTG
Found at i:232985 original size:17 final size:17
Alignment explanation
Indices: 232959--232991 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
232949 TTTTATTTTT
232959 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
232977 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
232992 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:232993 original size:17 final size:17
Alignment explanation
Indices: 232932--232993 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
232922 TTAAGATATA
* * *
232932 TTTTATTATATTAAATA
1 TTTTAATATTTTAAATT
232949 TTTT-AT-TTTT-AATT
1 TTTTAATATTTTAAATT
232963 TATTTAAGTA-TTTAAATT
1 T-TTTAA-TATTTTAAATT
232981 TTTTAATATTTTA
1 TTTTAATATTTTA
232994 TTTAATTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
14 4 0.11
15 6 0.17
16 4 0.11
17 17 0.47
18 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTAATATTTTAAATT
Found at i:234754 original size:33 final size:33
Alignment explanation
Indices: 234715--234789 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
234705 CATATGTGAT
*
234715 GCCGCCACCGCCGTTCCCTTACCCGATGCCGCC
1 GCCGCCACCGCCGTTCCCTTACCCGATGCCACC
234748 GCCGCCACCGCCGTTCCCTTACCCGATGCCACC
1 GCCGCCACCGCCGTTCCCTTACCCGATGCCACC
234781 GCCGCCACC
1 GCCGCCACC
234790 TGGTTTTATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.11, C:0.56, G:0.20, T:0.13
Consensus pattern (33 bp):
GCCGCCACCGCCGTTCCCTTACCCGATGCCACC
Found at i:235349 original size:33 final size:33
Alignment explanation
Indices: 235311--235384 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 33
235301 TAATACTTAC
235311 TTTATTTCATAAATTTGGTTGGA-TTTATT-TTAA
1 TTTATTTCATAAATTT-GTTGGACTTT-TTGTTAA
**
235344 TTTATTTTGTTAAATTTGTTGGACTTTTTGTTAA
1 TTTA-TTTCATAAATTTGTTGGACTTTTTGTTAA
*
235378 TGTATTT
1 TTTATTT
235385 TGGTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
33 15 0.43
34 20 0.57
ACGTcount: A:0.23, C:0.03, G:0.14, T:0.61
Consensus pattern (33 bp):
TTTATTTCATAAATTTGTTGGACTTTTTGTTAA
Found at i:235360 original size:34 final size:36
Alignment explanation
Indices: 235320--235396 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 36
235310 CTTTATTTCA
*
235320 TAAATTTGGTTGGA-TTTATT-TTAATTTATTTT-GT
1 TAAATTTGGTTGGACTTT-TTGTTAATGTATTTTGGT
235354 TAAATTT-GTTGGACTTTTTGTTAATGTATTTTGGT
1 TAAATTTGGTTGGACTTTTTGTTAATGTATTTTGGT
*
235389 TAATTTTG
1 TAAATTTG
235397 TTTATTACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
33 8 0.22
34 21 0.57
35 8 0.22
ACGTcount: A:0.22, C:0.01, G:0.17, T:0.60
Consensus pattern (36 bp):
TAAATTTGGTTGGACTTTTTGTTAATGTATTTTGGT
Found at i:235428 original size:35 final size:32
Alignment explanation
Indices: 235393--235473 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 32
235383 TTTGGTTAAT
235393 TTTGTT-TATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTATATTACCATTTAATAT---TTATTGTAA
235427 TTTGTTTATCATTTACCATTTAATATTTATTGTAA
1 TTTG-TTAT-A-TTACCATTTAATATTTATTGTAA
*
235462 GTTTGTTGTATT
1 -TTTGTTATATT
235474 TAAAATTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
33 2 0.05
34 5 0.12
35 14 0.34
36 5 0.12
37 1 0.02
38 14 0.34
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (32 bp):
TTTGTTATATTACCATTTAATATTTATTGTAA
Found at i:237446 original size:11 final size:11
Alignment explanation
Indices: 237430--237454 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
237420 AAATACTTTG
237430 TAAAATTATTT
1 TAAAATTATTT
237441 TAAAATTATTT
1 TAAAATTATTT
237452 TAA
1 TAA
237455 TTTTAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:237459 original size:17 final size:19
Alignment explanation
Indices: 237437--237472 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
237427 TTGTAAAATT
237437 ATTTTAAAA-TT-ATTTTA
1 ATTTTAAAACTTAATTTTA
237454 ATTTTAAAACTTAATTTTA
1 ATTTTAAAACTTAATTTTA
237473 CACTTTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTAAAACTTAATTTTA
Found at i:240038 original size:21 final size:21
Alignment explanation
Indices: 240012--240051 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
240002 AGAACCCCAG
*
240012 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
240033 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
240052 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:240060 original size:23 final size:21
Alignment explanation
Indices: 240034--240092 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
240024 TTCCCCTGTG
240034 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
*
240057 GGGGGAATTGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
* *
240077 GGGGGGATCGATTCCC
1 GGGGGAATCGGTTCCC
240093 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 12 0.39
21 4 0.13
22 3 0.10
23 12 0.39
ACGTcount: A:0.19, C:0.24, G:0.36, T:0.22
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:240081 original size:21 final size:23
Alignment explanation
Indices: 240033--240092 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
240023 ATTCCCCTGT
240033 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
240056 AGGGGGAATTGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
240077 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
240093 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 5 0.16
21 11 0.35
22 3 0.10
23 12 0.39
ACGTcount: A:0.18, C:0.23, G:0.37, T:0.22
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Done.