Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006635.1 Hibiscus syriacus cultivar Beakdansim tig00016323_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: 68859
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Found at i:5920 original size:17 final size:17
Alignment explanation
Indices: 5883--5917 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5873 TTTGAGTTAC
5883 TTAATATTTACTAGACT
1 TTAATATTTACTAGACT
*
5900 TTAATATTTTCTAG-CT
1 TTAATATTTACTAGACT
5916 TT
1 TT
5918 TAACACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAATATTTACTAGACT
Found at i:7295 original size:28 final size:28
Alignment explanation
Indices: 7263--7354 Score: 184
Period size: 28 Copynumber: 3.3 Consensus size: 28
7253 TTATTTCCAC
7263 AATTTGTGAAACTTGATAATTCATTCAG
1 AATTTGTGAAACTTGATAATTCATTCAG
7291 AATTTGTGAAACTTGATAATTCATTCAG
1 AATTTGTGAAACTTGATAATTCATTCAG
7319 AATTTGTGAAACTTGATAATTCATTCAG
1 AATTTGTGAAACTTGATAATTCATTCAG
7347 AATTTGTG
1 AATTTGTG
7355 TTAAAATGAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (28 bp):
AATTTGTGAAACTTGATAATTCATTCAG
Found at i:9960 original size:17 final size:18
Alignment explanation
Indices: 9938--9975 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
9928 AATTCTACAT
9938 TAGGGCTTAG-CCAAAAC
1 TAGGGCTTAGACCAAAAC
*
9955 TAGGGCTTAGACCAAACC
1 TAGGGCTTAGACCAAAAC
9973 TAG
1 TAG
9976 AATTTGAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (18 bp):
TAGGGCTTAGACCAAAAC
Found at i:14505 original size:17 final size:17
Alignment explanation
Indices: 14483--14518 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
14473 TTTTTTCTAC
14483 ACTAGGGCTTAGACCAA
1 ACTAGGGCTTAGACCAA
14500 ACTAGGGCTTAGACCAA
1 ACTAGGGCTTAGACCAA
14517 AC
1 AC
14519 CTAGAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (17 bp):
ACTAGGGCTTAGACCAA
Found at i:23430 original size:17 final size:17
Alignment explanation
Indices: 23404--23444 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
23394 TTATTTCTAC
23404 ACTAGAGCTTAGACCAA
1 ACTAGAGCTTAGACCAA
*
23421 ACTAGGGCTTAGACCAA
1 ACTAGAGCTTAGACCAA
23438 ACCTAGA
1 A-CTAGA
23445 ATTTGAGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (17 bp):
ACTAGAGCTTAGACCAA
Found at i:26451 original size:17 final size:17
Alignment explanation
Indices: 26425--26465 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
26415 TTATTTCTAC
26425 ACTAGAGCTTAGACCAA
1 ACTAGAGCTTAGACCAA
*
26442 ACTAGGGCTTAGACCAA
1 ACTAGAGCTTAGACCAA
26459 ACCTAGA
1 A-CTAGA
26466 ATTTGAGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (17 bp):
ACTAGAGCTTAGACCAA
Found at i:31041 original size:17 final size:17
Alignment explanation
Indices: 31015--31055 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
31005 TTATTTCTAC
31015 ACTAGAGCTTAGACCAA
1 ACTAGAGCTTAGACCAA
*
31032 ACTAGGGCTTAGACCAA
1 ACTAGAGCTTAGACCAA
31049 ACCTAGA
1 A-CTAGA
31056 ATTTGAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (17 bp):
ACTAGAGCTTAGACCAA
Found at i:55614 original size:17 final size:18
Alignment explanation
Indices: 55575--55616 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
55565 ATCATCTTCT
55575 AAAATTCAATGATGAATTCC
1 AAAATTCAATGATGAA-T-C
55595 AAAATTCAATGATGAA-C
1 AAAATTCAATGATGAATC
55612 AAAAT
1 AAAAT
55617 AATTTACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.27
20 16 0.73
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (18 bp):
AAAATTCAATGATGAATC
Found at i:57026 original size:23 final size:22
Alignment explanation
Indices: 56999--57073 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
56989 TGATATATGA
56999 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
57022 ATATG-ATATGAAATGACATATG
1 ATATGAATACGTGAT-ACATGTG
*
57044 AATATGTAATACGTGATACGTGTG
1 -ATATG-AATACGTGATACATGTG
57068 ATATGA
1 ATATGA
57074 TATGAAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.18
23 15 0.38
24 5 0.13
25 6 0.15
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:57032 original size:46 final size:46
Alignment explanation
Indices: 56973--57085 Score: 178
Period size: 46 Copynumber: 2.5 Consensus size: 46
56963 GACATGACCA
*
56973 ATGTGA-AT-ATATGAAATGATATATGAATATGCAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
*
57017 ATGTGATATGATATGAAATGACATATGAATATGTAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
*
57063 GTGTGATATGATATGAAAT-ACAT
1 ATGTGATATGATATGAAATGACAT
57086 GGTTACACAT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
44 6 0.09
45 6 0.09
46 52 0.81
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (46 bp):
ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
Found at i:57293 original size:38 final size:38
Alignment explanation
Indices: 57239--57329 Score: 128
Period size: 38 Copynumber: 2.4 Consensus size: 38
57229 GACATATAAT
* * * *
57239 AGGTCCTACGGAACACAGATTACATCCTTCAGGATGGC
1 AGGTCCTTCGGGACACAGATGACATCCTTCAGGATGAC
* *
57277 AGGTCCTTCGGGACACAGATGACATCCTTCGGGATGAT
1 AGGTCCTTCGGGACACAGATGACATCCTTCAGGATGAC
57315 AGGTCCTTCGGGACA
1 AGGTCCTTCGGGACA
57330 TTTGTACGAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.22
Consensus pattern (38 bp):
AGGTCCTTCGGGACACAGATGACATCCTTCAGGATGAC
Found at i:57519 original size:20 final size:21
Alignment explanation
Indices: 57483--57524 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
57473 TGACATGATT
*
57483 TATATATATGTCATATTGAAA
1 TATATACATGTCATATTGAAA
57504 TATATACATG-CATATTGAAA
1 TATATACATGTCATATTGAAA
57524 T
1 T
57525 GTTATGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
TATATACATGTCATATTGAAA
Done.