Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003922.1 Hibiscus syriacus cultivar Beakdansim tig00008480_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: 72755
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8956 original size:16 final size:15
Alignment explanation
Indices: 8895--8964 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 15
8885 TTTTGAAAAA
*
8895 ATATGTTTTAATCACTT
1 ATAT-TTTTAATTA-TT
* *
8912 ATGTTATTAATCTATT
1 ATATTTTTAAT-TATT
* *
8928 A-AATTTTAGTTATTT
1 ATATTTTTAATTA-TT
8943 ATATTTTTAATTATT
1 ATATTTTTAATTATT
8958 ATATTTT
1 ATATTTT
8965 AGTCATTGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
14 2 0.05
15 17 0.41
16 18 0.44
17 4 0.10
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (15 bp):
ATATTTTTAATTATT
Found at i:17895 original size:97 final size:97
Alignment explanation
Indices: 17784--17977 Score: 379
Period size: 97 Copynumber: 2.0 Consensus size: 97
17774 ACTGAATGAT
17784 ATGTATAGACAATCACTTTTGTTTCCACAAGATAACACTACGGTAAAACTGGCTTTTTACAGTGT
1 ATGTATAGACAATCACTTTTGTTTCCACAAGATAACACTACGGTAAAACTGGCTTTTTACAGTGT
17849 TTTTCTTGACTTATAGCAGCGTTTTTAAACGC
66 TTTTCTTGACTTATAGCAGCGTTTTTAAACGC
17881 ATGTATAGACAATCACTTTTGTTTCCACAAGATAACACTACGGTAAAACTGGCTTTTTACAGTGT
1 ATGTATAGACAATCACTTTTGTTTCCACAAGATAACACTACGGTAAAACTGGCTTTTTACAGTGT
*
17946 TTTTCTTGACTTATAGCGGCGTTTTTAAACGC
66 TTTTCTTGACTTATAGCAGCGTTTTTAAACGC
17978 CGCAAAAAAC
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (97 bp):
ATGTATAGACAATCACTTTTGTTTCCACAAGATAACACTACGGTAAAACTGGCTTTTTACAGTGT
TTTTCTTGACTTATAGCAGCGTTTTTAAACGC
Found at i:18251 original size:85 final size:85
Alignment explanation
Indices: 18137--18292 Score: 233
Period size: 85 Copynumber: 1.8 Consensus size: 85
18127 TGATATTTTT
* * **
18137 ACAAACGCCGCAATAGGTGTTGATGTTTAGCGGTGTTTTCCCCACAAATGCCGCAATAGATGTTG
1 ACAAACACCGCAATAAGTGTTGATGTTTAGCGGCATTTTCCCCACAAATGCCGCAATAGATGTTG
18202 AGATTTAGCGCGTTTTTATC
66 AGATTTAGCGCGTTTTTATC
* * *
18222 ACAAACACCGCAATAAGTGTTGA-GATTTAGCGGCATTTTTCTCACAAATGCCGCAATAGGTGTT
1 ACAAACACCGCAATAAGTGTTGATG-TTTAGCGGCATTTTCCCCACAAATGCCGCAATAGATGTT
18286 GAGATTT
65 GAGATTT
18293 CACGGCCTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
84 1 0.02
85 62 0.98
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (85 bp):
ACAAACACCGCAATAAGTGTTGATGTTTAGCGGCATTTTCCCCACAAATGCCGCAATAGATGTTG
AGATTTAGCGCGTTTTTATC
Found at i:18304 original size:43 final size:43
Alignment explanation
Indices: 18137--18292 Score: 199
Period size: 43 Copynumber: 3.7 Consensus size: 43
18127 TGATATTTTT
* * *
18137 ACAAACGCCGCAATAGGTGTTGATG-TTTAGCGGTGTTTTCCCC
1 ACAAACGCCGCAATAGGTGTTGA-GATTTAGCGGCGTTTTTCTC
* * *
18180 ACAAATGCCGCAATAGATGTTGAGATTTAGC-GCGTTTTTATC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTC
* * *
18222 ACAAACACCGCAATAAGTGTTGAGATTTAGCGGCATTTTTCTC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTC
*
18265 ACAAATGCCGCAATAGGTGTTGAGATTT
1 ACAAACGCCGCAATAGGTGTTGAGATTT
18293 CACGGCCTTT
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
42 35 0.36
43 61 0.64
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTC
Found at i:18348 original size:44 final size:44
Alignment explanation
Indices: 18307--18454 Score: 192
Period size: 44 Copynumber: 3.4 Consensus size: 44
18297 GCCTTTTTTT
* * * *
18307 GATACAAACGTCGCCAAAGGTCTAGTATATAGCGACATTTTTAG
1 GATACAAACGCCGCTAAAGGTATGGTATATAGCGACATTTTTAG
* *
18351 GATACAAACGCCGCTAAAGGTATGGTATATAGCGGCGTTTTTAG
1 GATACAAACGCCGCTAAAGGTATGGTATATAGCGACATTTTTAG
* * *
18395 GATACAAACGCCGCTAAATGAATGGTATATTGCGACATTTTT--
1 GATACAAACGCCGCTAAAGGTATGGTATATAGCGACATTTTTAG
*
18437 GTTACAAACGCCGCTAAA
1 GATACAAACGCCGCTAAA
18455 TAACACATAA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 17 0.18
44 75 0.82
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (44 bp):
GATACAAACGCCGCTAAAGGTATGGTATATAGCGACATTTTTAG
Found at i:18800 original size:21 final size:21
Alignment explanation
Indices: 18776--18823 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
18766 GATATGCAGT
* *
18776 TTCTCTCTGTGCTACCGCTGC
1 TTCTCTCTATACTACCGCTGC
*
18797 TTCTCTCTATACTGCCGCTGC
1 TTCTCTCTATACTACCGCTGC
*
18818 CTCTCT
1 TTCTCT
18824 GGCTGCTTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.06, C:0.40, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCTCTCTATACTACCGCTGC
Found at i:28000 original size:22 final size:22
Alignment explanation
Indices: 27952--28005 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
27942 TTCTTCATGT
* *
27952 TTTCAAAAGCTATTATTTTCCA
1 TTTCGAAACCTATTATTTTCCA
*
27974 TTTCGAAACCTATTATTTTTC-
1 TTTCGAAACCTATTATTTTCCA
27995 TATTCGAAACC
1 T-TTCGAAACC
28006 GGAAAAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (22 bp):
TTTCGAAACCTATTATTTTCCA
Found at i:42715 original size:44 final size:44
Alignment explanation
Indices: 42647--42745 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
42637 AGCTCCTTTT
* *
42647 TTTTATGACATATATAACATCCTCGACTCGTTCTATAATGAAAA
1 TTTTATGACATATATAACACCCTCGACTAGTTCTATAATGAAAA
* * *
42691 TTTTATGATATGTGTAACACCCTCGACTAGTTCTATAATGAAAA
1 TTTTATGACATATATAACACCCTCGACTAGTTCTATAATGAAAA
* *
42735 TTATATCACAT
1 TTTTATGACAT
42746 GTGTTATTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.37
Consensus pattern (44 bp):
TTTTATGACATATATAACACCCTCGACTAGTTCTATAATGAAAA
Found at i:44961 original size:40 final size:40
Alignment explanation
Indices: 44906--44987 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
44896 TTTAACTTCT
44906 TTTATAAATATTTCTAAAAATTTAAATACTCAATACATAG
1 TTTATAAATATTTCTAAAAATTTAAATACTCAATACATAG
44946 TTTATAAATATTTCTAAAAATTTAAATACTCAATACATAG
1 TTTATAAATATTTCTAAAAATTTAAATACTCAATACATAG
44986 TT
1 TT
44988 ACAATAATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (40 bp):
TTTATAAATATTTCTAAAAATTTAAATACTCAATACATAG
Found at i:48154 original size:24 final size:24
Alignment explanation
Indices: 48122--48175 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
48112 CACCTTTTAG
48122 ACACTTTAATGTTGTCGTGTTTTT
1 ACACTTTAATGTTGTCGTGTTTTT
48146 ACACTTTAATGTTGTCGTGTTTTT
1 ACACTTTAATGTTGTCGTGTTTTT
48170 ACACTT
1 ACACTT
48176 AAGTCACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.52
Consensus pattern (24 bp):
ACACTTTAATGTTGTCGTGTTTTT
Found at i:51095 original size:18 final size:18
Alignment explanation
Indices: 51052--51097 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
51042 TCAAGCCCAG
51052 ACCCAAAACCCAACCAAA
1 ACCCAAAACCCAACCAAA
** * *
51070 ACATAAAACCCAACTAGA
1 ACCCAAAACCCAACCAAA
51088 ACCCAAAACC
1 ACCCAAAACC
51098 TGACCCAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.54, C:0.39, G:0.02, T:0.04
Consensus pattern (18 bp):
ACCCAAAACCCAACCAAA
Found at i:52824 original size:13 final size:13
Alignment explanation
Indices: 52805--52841 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
52795 ATAAAATGCC
52805 CGATTACTCGAAT
1 CGATTACTCGAAT
*
52818 TGATTACTCGAAT
1 CGATTACTCGAAT
52831 CGATTACTCGA
1 CGATTACTCGA
52842 CCTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (13 bp):
CGATTACTCGAAT
Found at i:62529 original size:17 final size:17
Alignment explanation
Indices: 62490--62531 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
62480 CCCTTCCCTT
*
62490 TCTTT-GAGAAAAATTC
1 TCTTTCGAGAAAAACTC
62506 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
62523 -CTGTTCGAG
1 TCT-TTCGAG
62532 CAACAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Done.