Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006422.1 Hibiscus syriacus cultivar Beakdansim tig00015495_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: 49264
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:4497 original size:17 final size:18
Alignment explanation
Indices: 4475--4508 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4465 TATTACATTC
*
4475 AAAGTT-TTTAAGCAGTT
1 AAAGTTGTTTAAACAGTT
4492 AAAGTTGTTTAAACAGT
1 AAAGTTGTTTAAACAGT
4509 ATGAATCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (18 bp):
AAAGTTGTTTAAACAGTT
Found at i:6858 original size:17 final size:17
Alignment explanation
Indices: 6836--6868 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6826 AGTTAACGCT
6836 CCAAAATAGAAGTCTTC
1 CCAAAATAGAAGTCTTC
6853 CCAAAATAGAAGTCTT
1 CCAAAATAGAAGTCTT
6869 TTTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.24
Consensus pattern (17 bp):
CCAAAATAGAAGTCTTC
Found at i:9280 original size:23 final size:23
Alignment explanation
Indices: 9231--9280 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
9221 AACGACCGAA
*
9231 AAAGAAGACGAAAAACGTGTCAC
1 AAAGAAGACGAAAAACGTATCAC
* *
9254 AAAGACAGA-GAAAAATGTATCAT
1 AAAGA-AGACGAAAAACGTATCAC
9277 AAAG
1 AAAG
9281 GCATAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.56, C:0.12, G:0.20, T:0.12
Consensus pattern (23 bp):
AAAGAAGACGAAAAACGTATCAC
Found at i:9530 original size:2 final size:2
Alignment explanation
Indices: 9525--9573 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
9515 ATATAACATG
9525 AT AT AT AT AT 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 AT AT AT AT AT
9567 AT AT AT A
1 AT AT AT A
9574 CGAGTTAGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18958 original size:65 final size:65
Alignment explanation
Indices: 18854--18988 Score: 261
Period size: 65 Copynumber: 2.1 Consensus size: 65
18844 CTTGCAAAGC
18854 TTCAAAGCCACAACCATCGGAGTAGGAACAGAATGTGCACCTCACATACCCGTCCTATCAAGCAA
1 TTCAAAGCCACAACCATCGGAGTAGGAACAGAATGTGCACCTCACATACCCGTCCTATCAAGCAA
*
18919 TTCAAAGCCACAACCATCGGAGTAGGAACAGAATGTGCACCTCACATACCCGTCGTATCAAGCAA
1 TTCAAAGCCACAACCATCGGAGTAGGAACAGAATGTGCACCTCACATACCCGTCCTATCAAGCAA
18984 TTCAA
1 TTCAA
18989 GGATAAATTT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.18
Consensus pattern (65 bp):
TTCAAAGCCACAACCATCGGAGTAGGAACAGAATGTGCACCTCACATACCCGTCCTATCAAGCAA
Found at i:21830 original size:19 final size:19
Alignment explanation
Indices: 21806--21861 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
21796 GAACGCTGGA
21806 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
21825 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
21846 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
21862 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:21841 original size:11 final size:11
Alignment explanation
Indices: 21806--21854 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
21796 GAACGCTGGA
21806 AACCGGTTTTG
1 AACCGGTTTTG
21817 -ACCGG-TTT-
1 AACCGGTTTTG
21825 AACCGGTTTTG
1 AACCGGTTTTG
21836 AACCGGTTTTG
1 AACCGGTTTTG
21847 -ACCGGTTT
1 AACCGGTTT
21855 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:21857 original size:9 final size:10
Alignment explanation
Indices: 21807--21861 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
21797 AACGCTGGAA
21807 ACCGGTTTTG
1 ACCGGTTTTG
*
21817 ACCGG-TTTA
1 ACCGGTTTTG
21826 ACCGGTTTTG
1 ACCGGTTTTG
21836 AACCGGTTTTG
1 -ACCGGTTTTG
21847 ACCGG-TTTG
1 ACCGGTTTTG
21856 ACCGGT
1 ACCGGT
21862 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:21879 original size:8 final size:8
Alignment explanation
Indices: 21866--21894 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
21856 ACCGGTCACG
21866 ACCCGTTT
1 ACCCGTTT
21874 ACCCGTTT
1 ACCCGTTT
21882 ACCCGTTT
1 ACCCGTTT
21890 ACCCG
1 ACCCG
21895 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.14, C:0.41, G:0.14, T:0.31
Consensus pattern (8 bp):
ACCCGTTT
Found at i:21900 original size:13 final size:13
Alignment explanation
Indices: 21864--21924 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 13
21854 TGACCGGTCA
21864 CGACCCGTTTACC
1 CGACCCGTTTACC
21877 CGTTTACCCGTTTACC
1 CG---ACCCGTTTACC
*
21893 CGACCCGTTGACC
1 CGACCCGTTTACC
21906 CGACCCG---ACC
1 CGACCCGTTTACC
21916 CGACCCGTT
1 CGACCCGTT
21925 GACCGTTGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
10 10 0.24
13 19 0.45
16 13 0.31
ACGTcount: A:0.15, C:0.46, G:0.18, T:0.21
Consensus pattern (13 bp):
CGACCCGTTTACC
Found at i:26315 original size:60 final size:59
Alignment explanation
Indices: 26190--26338 Score: 185
Period size: 60 Copynumber: 2.5 Consensus size: 59
26180 GATGAATTTG
* * * *
26190 GGGATGAAATT-GTAATATTCAAAAGTTT-GGGATTAATTTAGAAAGAGGGTTATAGTTT
1 GGGATGAAATTAG-AATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTGATAGTTT
* *
26248 AGGGATGAAATTAGAATTTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTGATAGTTT
1 -GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTGATAGTTT
* *
26308 GGAGATGAAATTAAAATATTCAAAAATTTAA
1 GG-GATGAAATTAGAATATTCAAAAGTTTAA
26339 TAACCAAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 27 0.35
60 51 0.65
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.34
Consensus pattern (59 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGAGTGATAGTTT
Found at i:26355 original size:60 final size:60
Alignment explanation
Indices: 26241--26372 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 60
26231 AAAGAGGGTT
* * * * * * *
26241 ATAGTTTAGG-GATGAAATTAGAATTTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTG
1 ATAGTTT-GGAGATGAAATTAAAATATTCAAAAATTTAAGAACCAAATTAAAATGAGAGTG
* * *
26301 ATAGTTTGGAGATGAAATTAAAATATTCAAAAATTTAATAACCAAATTAAAATGAGGGTT
1 ATAGTTTGGAGATGAAATTAAAATATTCAAAAATTTAAGAACCAAATTAAAATGAGAGTG
*
26361 ATAGTTTAGAGA
1 ATAGTTTGGAGA
26373 CATATGATGC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 2 0.03
60 58 0.97
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.33
Consensus pattern (60 bp):
ATAGTTTGGAGATGAAATTAAAATATTCAAAAATTTAAGAACCAAATTAAAATGAGAGTG
Found at i:31825 original size:15 final size:15
Alignment explanation
Indices: 31807--31837 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31797 AAAAACTTGA
31807 ATTCAAAACATTTTT
1 ATTCAAAACATTTTT
31822 ATTCAAAACATTTTT
1 ATTCAAAACATTTTT
31837 A
1 A
31838 GACTTAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTCAAAACATTTTT
Found at i:44580 original size:15 final size:15
Alignment explanation
Indices: 44560--44589 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
44550 ATGATCCTTC
44560 AATTTATCAAAATTT
1 AATTTATCAAAATTT
44575 AATTTATCAAAATTT
1 AATTTATCAAAATTT
44590 TATTACTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTATCAAAATTT
Found at i:44649 original size:30 final size:28
Alignment explanation
Indices: 44615--44670 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 28
44605 ATAATAAGAA
44615 TATTTTGTAA-TAGTTTGACAAGTTTAATAT
1 TATTTTGTAACT--TTTGA-AAGTTTAATAT
44645 TATTTTGTAACTTTTGAAAGTTTAAT
1 TATTTTGTAACTTTTGAAAGTTTAAT
44671 GACAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 9 0.36
29 5 0.20
30 10 0.40
31 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (28 bp):
TATTTTGTAACTTTTGAAAGTTTAATAT
Done.