Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002250.1 Hibiscus syriacus cultivar Beakdansim tig00004572_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: 91704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:371 original size:20 final size:20
Alignment explanation
Indices: 346--384 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
336 TTTGAATTTA
346 ATGAAGGTGTAC-GATACCCT
1 ATGAAGG-GTACTGATACCCT
366 ATGAAGGGTACTGATACCC
1 ATGAAGGGTACTGATACCC
385 CATGTTATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (20 bp):
ATGAAGGGTACTGATACCCT
Found at i:6062 original size:20 final size:20
Alignment explanation
Indices: 6026--6080 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
6016 ATTTTTATTG
6026 TTAAA-ATTATAAA-ATATCA
1 TTAAATATTATAAATAT-TCA
6045 TTAAATTATTATAAATATTCA
1 TTAAA-TATTATAAATATTCA
**
6066 TTTTATATTATAAAT
1 TTAAATATTATAAAT
6081 TAATTATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 5 0.16
20 10 0.32
21 14 0.45
22 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAATATTATAAATATTCA
Found at i:19175 original size:48 final size:45
Alignment explanation
Indices: 19137--19269 Score: 221
Period size: 45 Copynumber: 3.0 Consensus size: 45
19127 GTTTTATCCC
* *
19137 AAGGAATTATTTCGACCATGTCATCATCCATGCCTTCTGCACTAA
1 AAGGAATTATTCCGACCATGTCATCATCCATGCCTTCTGCATTAA
*
19182 AAGGAATTATTCCGACCATGTCATCATCCATGCCTTATGCATTAA
1 AAGGAATTATTCCGACCATGTCATCATCCATGCCTTCTGCATTAA
* *
19227 AAGGAATTATTCCGACCATGTTATCATCCATGCCTTCTTCATT
1 AAGGAATTATTCCGACCATGTCATCATCCATGCCTTCTGCATT
19270 TTAGTTTATA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (45 bp):
AAGGAATTATTCCGACCATGTCATCATCCATGCCTTCTGCATTAA
Found at i:32716 original size:2 final size:2
Alignment explanation
Indices: 32709--32769 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
32699 TTGTTTTTAA
32709 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
32751 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
32770 AAGCTTGCAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38194 original size:17 final size:17
Alignment explanation
Indices: 38172--38209 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
38162 AAAATAATTT
*
38172 ATTATAATA-AAAAAAGC
1 ATTATAA-ACAAAAAAGA
38189 ATTATAAACAAAAAAGA
1 ATTATAAACAAAAAAGA
38206 ATTA
1 ATTA
38210 ATACACAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (17 bp):
ATTATAAACAAAAAAGA
Found at i:64892 original size:22 final size:22
Alignment explanation
Indices: 64864--64908 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
64854 CATATAAATT
64864 ATATATATACAATATAAAAGAA
1 ATATATATACAATATAAAAGAA
64886 ATATATATACAATATAAAAGAA
1 ATATATATACAATATAAAAGAA
64908 A
1 A
64909 ACAAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (22 bp):
ATATATATACAATATAAAAGAA
Found at i:66129 original size:18 final size:18
Alignment explanation
Indices: 66104--66145 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
66094 ACTCTAGTAG
*
66104 AGAGATGGATGAAGATGA
1 AGAGATGGATAAAGATGA
*
66122 ATAGATGGATAAAGATGA
1 AGAGATGGATAAAGATGA
66140 AGAGAT
1 AGAGAT
66146 TGACAAGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (18 bp):
AGAGATGGATAAAGATGA
Found at i:69594 original size:16 final size:17
Alignment explanation
Indices: 69566--69597 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
69556 ATGTGTTTGT
69566 TATGAGTTATATGTGTA
1 TATGAGTTATATGTGTA
69583 TATGAG-TATATGTGT
1 TATGAGTTATATGTGT
69598 TGACTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (17 bp):
TATGAGTTATATGTGTA
Found at i:71489 original size:2 final size:2
Alignment explanation
Indices: 71482--71517 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
71472 AATAATAATG
71482 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
71518 TTCAAAGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71992 original size:30 final size:30
Alignment explanation
Indices: 71956--72017 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
71946 AGAGTCGAGG
*
71956 GTTACCTATGTCCTTTGGGACATATGGATA
1 GTTACCTATGTCCTTTGGAACATATGGATA
*
71986 GTTACCTATGTTCTTTGGAACATATGGATA
1 GTTACCTATGTCCTTTGGAACATATGGATA
72016 GT
1 GT
72018 GGTCCTTCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.39
Consensus pattern (30 bp):
GTTACCTATGTCCTTTGGAACATATGGATA
Found at i:72042 original size:22 final size:21
Alignment explanation
Indices: 72015--72078 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 21
72005 ACATATGGAT
*
72015 AGTGGTCCTTCGAGACATATAC
1 AGTGGTCATTCG-GACATATAC
*
72037 AGTGGTCTTTCGGGACATATAC
1 AGTGGTCATTC-GGACATATAC
72059 AGTGGTCATTCGGAACATAT
1 AGTGGTCATTCGG-ACATAT
72079 TTCACATGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.05
22 35 0.92
23 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (21 bp):
AGTGGTCATTCGGACATATAC
Found at i:75389 original size:23 final size:23
Alignment explanation
Indices: 75363--75431 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
75353 CACCACAACT
*
75363 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
75386 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
75409 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
75432 TATATAAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:84210 original size:12 final size:12
Alignment explanation
Indices: 84193--84217 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84183 ATAAAAATAA
84193 TAATTTTATTAT
1 TAATTTTATTAT
84205 TAATTTTATTAT
1 TAATTTTATTAT
84217 T
1 T
84218 TAAATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATTTTATTAT
Done.