Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007591.1 Hibiscus syriacus cultivar Beakdansim tig00021856_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: 17841
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:185 original size:48 final size:49
Alignment explanation
Indices: 89--199 Score: 215
Period size: 48 Copynumber: 2.3 Consensus size: 49
79 GTTCTGTTGA
89 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
138 ACAAAGAACTTGTTATCAGAGTTA-TCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
186 ACAAAGAACTTGTT
1 ACAAAGAACTTGTT
200 CTAACCGCTT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 38 0.61
49 24 0.39
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.26
Consensus pattern (49 bp):
ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
Found at i:2237 original size:20 final size:20
Alignment explanation
Indices: 2194--2241 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2184 CAAAGTGACC
*
2194 CAATTTC-ACATTCTAACAT
1 CAATTTCAACAATCTAACAT
*
2213 CAATTTCAACAATCTAATAT
1 CAATTTCAACAATCTAACAT
*
2233 TAATTTCAA
1 CAATTTCAA
2242 GCATAGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.38
Consensus pattern (20 bp):
CAATTTCAACAATCTAACAT
Found at i:4617 original size:16 final size:16
Alignment explanation
Indices: 4594--4626 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4584 AGAAAAAATG
*
4594 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
4609 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
4625 AG
1 AG
4627 GAAAGAGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:6310 original size:49 final size:49
Alignment explanation
Indices: 6253--6364 Score: 224
Period size: 49 Copynumber: 2.3 Consensus size: 49
6243 GTTCTGTTGA
6253 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
6302 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
6351 ACAAAGAACTTGTT
1 ACAAAGAACTTGTT
6365 CTAACCGCTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (49 bp):
ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
Found at i:8426 original size:20 final size:20
Alignment explanation
Indices: 8390--8437 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
8380 CAAAGTGACC
*
8390 CAATTTC-ACATTCTAACAT
1 CAATTTCAACAATCTAACAT
8409 CAATTTCAACAATCTAACAT
1 CAATTTCAACAATCTAACAT
*
8429 TAATTTCAA
1 CAATTTCAA
8438 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACAATCTAACAT
Found at i:10026 original size:16 final size:16
Alignment explanation
Indices: 10003--10039 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
9993 GAAAAAAATG
*
10003 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
10018 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
10034 AGAAAA
1 AGAAAA
10040 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:10260 original size:8 final size:9
Alignment explanation
Indices: 10248--10306 Score: 60
Period size: 8 Copynumber: 7.3 Consensus size: 9
10238 ATTAGGATAA
10248 ATATTATAT
1 ATATTATAT
10257 -TATTA-AT
1 ATATTATAT
*
10264 ATA-TATAC
1 ATATTATAT
10272 ATA-TATAT
1 ATATTATAT
10280 ATA-TATAT
1 ATATTATAT
10288 ATATTATAT
1 ATATTATAT
10297 -TATT-TAT
1 ATATTATAT
10304 ATA
1 ATA
10307 GATTTTTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
7 7 0.16
8 32 0.73
9 5 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (9 bp):
ATATTATAT
Found at i:10269 original size:2 final size:2
Alignment explanation
Indices: 10262--10306 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
10252 TATATTATTA
* *
10262 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10302 AT AT A
1 AT AT A
10307 GATTTTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:11703 original size:51 final size:49
Alignment explanation
Indices: 11626--11740 Score: 189
Period size: 49 Copynumber: 2.3 Consensus size: 49
11616 GTTCTTTTGA
11626 ACAAAGAACTTG-T-TATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTCTATCAGAGTTATTCTACCAATTCAAC-ACT-AGAGC
*
11675 ACAAAGAACTTGTTCTATCAGAGTTATTCTACCAATTCAACACTTGAGC
1 ACAAAGAACTTGTTCTATCAGAGTTATTCTACCAATTCAACACTAGAGC
11724 ACAAAGAACTTGTTCTA
1 ACAAAGAACTTGTTCTA
11741 ACCGCTTCTA
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
49 33 0.52
50 4 0.06
51 26 0.41
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (49 bp):
ACAAAGAACTTGTTCTATCAGAGTTATTCTACCAATTCAACACTAGAGC
Found at i:13786 original size:20 final size:20
Alignment explanation
Indices: 13743--13790 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
13733 CAAAGTGACC
*
13743 CAATTTC-ACATTCTAACAT
1 CAATTTCAACAATCTAACAT
*
13762 CAATTTCAACAATCTAATAT
1 CAATTTCAACAATCTAACAT
*
13782 TAATTTCAA
1 CAATTTCAA
13791 GCATAGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.38
Consensus pattern (20 bp):
CAATTTCAACAATCTAACAT
Found at i:16173 original size:16 final size:16
Alignment explanation
Indices: 16150--16186 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
16140 AAAAAAAATG
*
16150 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
16165 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
16181 AGAAAA
1 AGAAAA
16187 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Done.