Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000227.1 Hibiscus syriacus cultivar Beakdansim tig00000397_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: 49827
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3881 original size:18 final size:19
Alignment explanation
Indices: 3842--3882 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
3832 TAACGGCGTT
*
3842 AAAACAAAACCGTTTTAGA
1 AAAACAAAACCGTTTTACA
*
3861 AAAACAAAA-C-TTTTACC
1 AAAACAAAACCGTTTTACA
3878 AAAAC
1 AAAAC
3883 GACATCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.20
Consensus pattern (19 bp):
AAAACAAAACCGTTTTACA
Found at i:4806 original size:14 final size:14
Alignment explanation
Indices: 4787--4834 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
4777 GCTTTAAAAT
*
4787 AAACAAACAAATAC
1 AAACAAACAAACAC
**
4801 AAACAAACGTACAC
1 AAACAAACAAACAC
4815 AAACAAACAGAAACAC
1 AAACAAAC--AAACAC
4831 AAAC
1 AAAC
4835 TTATTCGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 19 0.70
16 8 0.30
ACGTcount: A:0.67, C:0.25, G:0.04, T:0.04
Consensus pattern (14 bp):
AAACAAACAAACAC
Found at i:5412 original size:2 final size:2
Alignment explanation
Indices: 5405--5445 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5395 CCTCATGGCC
5405 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
5446 CAGGAAACTA
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:17837 original size:445 final size:445
Alignment explanation
Indices: 17008--17899 Score: 1649
Period size: 445 Copynumber: 2.0 Consensus size: 445
16998 CAAAGATAAA
* *
17008 TCATATTGACTCGAGATGAAAGAGAAACTAATGAGCGTAGATTGAAACTTATCAGACTAAGCATG
1 TCATATTGACTCGAGATGAAAGAGAAACTAATGAGCATAGATTGAAACTTATCAGACTAAGCACG
*
17073 TGGAGCCTGTTTTAAACCATAGAGTGACTTTTTTAGTTTACAAACATCAGAAGAGGCTATAGAAA
66 TGGAGCCTATTTTAAACCATAGAGTGACTTTTTTAGTTTACAAACATCAGAAGAGGCTATAGAAA
17138 ATAACCCTTGTAAAGGAGTCATATAAATTCCTTCCTTAATATCCCCATGCAAAAAGGCATTATTA
131 ATAACCCTTGTAAAGGAGTCATATAAATTCCTTCCTTAATATCCCCATGCAAAAAGGCATTATTA
*
17203 ACATCCATTTGTCGTAATGACCAGCCCTTGGAAGCAGCAATAGCAATAACAAGTCGCATTGTCAT
196 ACATCCATTTGTCGTAATGACCAGCCCTTGGAAGCAGCAATAGCAAGAACAAGTCGCATTGTCAT
* *
17268 CATTTTTGCCACTGGTACGAATATCTCCTCATAATCAACTCCATACTCTTGTTGATTTTTGAGGG
261 CATTTTTGCCACTGGTACAAATATCTCCTCATAATCAACTCCATACTCTTGTTGATTTTCGAGGG
*
17333 CCACCAACCTCGATTTGTATCAATCAAGTGACCCATCAGATCTTAGTTTAATGGAATATACCTAT
326 CCACCAACCTCGATTTGTATCAATCAAGTGACCCATCAGATCTTAGTTTAATGGAATATACCCAT
17398 TTACAACCAATGGGTTTAACACCAGTAGGACATGAAACAATATATCAAGTATGAT
391 TTACAACCAATGGGTTTAACACCAGTAGGACATGAAACAATATATCAAGTATGAT
17453 TCATATTGACTCGAGATGAAAGAGAAACTAATGAGCATAGATTGAAACTTATCAGACTAAGCACG
1 TCATATTGACTCGAGATGAAAGAGAAACTAATGAGCATAGATTGAAACTTATCAGACTAAGCACG
*
17518 TGGAGCCTATTTTAAACCATAGAGTGACTTTTTTAGTTTACAAACATCAGAAGAGGCTGTAGAAA
66 TGGAGCCTATTTTAAACCATAGAGTGACTTTTTTAGTTTACAAACATCAGAAGAGGCTATAGAAA
17583 ATAACCCTTGTAAAGGAGTCATATAAATTCCTTCCTTAATATCCCCATGCAAAAAGGCATTATTA
131 ATAACCCTTGTAAAGGAGTCATATAAATTCCTTCCTTAATATCCCCATGCAAAAAGGCATTATTA
*
17648 ACATCCATTTGTCGTAATGACCAGCCCTTGGAAGCAGCAATAGCTAGAACAAGTCGCATTGTCAT
196 ACATCCATTTGTCGTAATGACCAGCCCTTGGAAGCAGCAATAGCAAGAACAAGTCGCATTGTCAT
* *
17713 CATTTTTTCCACTGGTACAAATATCTCCTCATAATCAACTCCATACTCTTGTTGATTTTCGAGTG
261 CATTTTTGCCACTGGTACAAATATCTCCTCATAATCAACTCCATACTCTTGTTGATTTTCGAGGG
*
17778 CCACCAACCTCGATTTGTATCAGTCAAGTGACCCATCAGATCTTAGTTTAATGGAATATACCCAT
326 CCACCAACCTCGATTTGTATCAATCAAGTGACCCATCAGATCTTAGTTTAATGGAATATACCCAT
* * *
17843 TTACAACCAATGGGTTTAACACTAGTAGGACATGAAGCAATATCTCAAGTATGAT
391 TTACAACCAATGGGTTTAACACCAGTAGGACATGAAACAATATATCAAGTATGAT
17898 TC
1 TC
17900 CCAACATACA
Statistics
Matches: 432, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
445 432 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (445 bp):
TCATATTGACTCGAGATGAAAGAGAAACTAATGAGCATAGATTGAAACTTATCAGACTAAGCACG
TGGAGCCTATTTTAAACCATAGAGTGACTTTTTTAGTTTACAAACATCAGAAGAGGCTATAGAAA
ATAACCCTTGTAAAGGAGTCATATAAATTCCTTCCTTAATATCCCCATGCAAAAAGGCATTATTA
ACATCCATTTGTCGTAATGACCAGCCCTTGGAAGCAGCAATAGCAAGAACAAGTCGCATTGTCAT
CATTTTTGCCACTGGTACAAATATCTCCTCATAATCAACTCCATACTCTTGTTGATTTTCGAGGG
CCACCAACCTCGATTTGTATCAATCAAGTGACCCATCAGATCTTAGTTTAATGGAATATACCCAT
TTACAACCAATGGGTTTAACACCAGTAGGACATGAAACAATATATCAAGTATGAT
Found at i:22807 original size:53 final size:53
Alignment explanation
Indices: 22652--22807 Score: 208
Period size: 53 Copynumber: 2.9 Consensus size: 53
22642 CTTTAAATGA
* * *
22652 CGGGTCCGCTCCCTCTTG-TTCAGGGATTAAGGAACTCGAACAATCTTCTAAAAAT
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCT-GAAAT
* ***
22707 -GGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTT
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGAAAT
22759 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
22808 GTGTGATTCT
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
52 1 0.01
53 65 0.71
54 16 0.18
55 9 0.10
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (53 bp):
CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGAAAT
Found at i:23303 original size:93 final size:93
Alignment explanation
Indices: 23141--23324 Score: 298
Period size: 93 Copynumber: 2.0 Consensus size: 93
23131 TACTCGAAAG
* *
23141 ACTTATTGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTACCTGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTACCTGAAGGATTTAAG
23206 CATCATGCTCGAAAGACTTACTGATGAC
66 CATCATGCTCGAAAGACTTACTGATGAC
* * *
23234 ACTTACTGATGGGTTTGCTTCACTGCTCTTTTGTGAAGGCTTACAAATTACCCT-AAGGATTTAA
1 ACTTACTGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTA-CCTGAAGGATTTAA
*
23298 GCATCATGCTCGAAAGACTTATTGATG
65 GCATCATGCTCGAAAGACTTACTGATG
23325 GCCTGAAGGA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
93 81 0.96
94 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (93 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTACCTGAAGGATTTAAG
CATCATGCTCGAAAGACTTACTGATGAC
Found at i:29570 original size:6 final size:6
Alignment explanation
Indices: 29545--29580 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
29535 AGCTAATAAG
* *
29545 AATGCA AATGCG AATACA AATGCA AATGCA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA
29581 CAAGGTGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
AATGCA
Found at i:41698 original size:2 final size:2
Alignment explanation
Indices: 41691--41729 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41681 TAACTTTAAT
41691 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 T
41730 TTCTCTCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44273 original size:30 final size:30
Alignment explanation
Indices: 44209--44276 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
44199 GAGCCGAAGC
* **
44209 AGAAGCAGGAGTAGAGACAGGAGGAGGCGA
1 AGAAGCAGGAGTAGAGACAGAAGGACACGA
* * *
44239 AGAAGCAGGAGTATAGAGAGAAGGACACGG
1 AGAAGCAGGAGTAGAGACAGAAGGACACGA
44269 AGAAGCAG
1 AGAAGCAG
44277 AAGCAGGAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.43, T:0.04
Consensus pattern (30 bp):
AGAAGCAGGAGTAGAGACAGAAGGACACGA
Found at i:44316 original size:24 final size:24
Alignment explanation
Indices: 44282--44327 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
44272 AGCAGAAGCA
*
44282 GGAGTATGTCGCCGCGTAGAGATC
1 GGAGTAGGTCGCCGCGTAGAGATC
* *
44306 GGAGTAGGTCGCCTCGTCGAGA
1 GGAGTAGGTCGCCGCGTAGAGA
44328 AGGAAGTCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.22, G:0.39, T:0.20
Consensus pattern (24 bp):
GGAGTAGGTCGCCGCGTAGAGATC
Found at i:48811 original size:44 final size:44
Alignment explanation
Indices: 48762--48883 Score: 235
Period size: 44 Copynumber: 2.8 Consensus size: 44
48752 CATGTTTGAG
48762 AACCAAACAGAATATGAAATTGGATTCCAATTCCATTTCTTGCC
1 AACCAAACAGAATATGAAATTGGATTCCAATTCCATTTCTTGCC
48806 AACCAAACAGAATATGAAATTGGATTCCAATTCCATTTCTTGCC
1 AACCAAACAGAATATGAAATTGGATTCCAATTCCATTTCTTGCC
*
48850 AACCAAACAGAATATGGAATTGGATTCCAATTCC
1 AACCAAACAGAATATGAAATTGGATTCCAATTCC
48884 CTCATAAACA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 77 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (44 bp):
AACCAAACAGAATATGAAATTGGATTCCAATTCCATTTCTTGCC
Done.