Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000736.1 Hibiscus syriacus cultivar Beakdansim tig00001426_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: 58736
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:5754 original size:36 final size:35
Alignment explanation
Indices: 5692--5759 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 35
5682 TTTTTATATT
*
5692 TTTAATTTTGTAAAAAATTATATAAATATTTTGAA
1 TTTAATTTTGTAAAAAAATATATAAATATTTTGAA
*
5727 TTTAATTTTTTAAAGAAAATATATAAATATTTT
1 TTTAATTTTGTAAA-AAAATATATAAATATTTT
5760 ACAATTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (35 bp):
TTTAATTTTGTAAAAAAATATATAAATATTTTGAA
Found at i:5948 original size:20 final size:20
Alignment explanation
Indices: 5912--5949 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5902 ATCCTATTCC
**
5912 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
5932 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
5950 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:13222 original size:13 final size:13
Alignment explanation
Indices: 13204--13228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13194 TTATACCTTC
13204 ATATGTTATTATT
1 ATATGTTATTATT
13217 ATATGTTATTAT
1 ATATGTTATTAT
13229 CATACATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
ATATGTTATTATT
Found at i:17781 original size:22 final size:22
Alignment explanation
Indices: 17756--17802 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
17746 CTAAAATACA
*
17756 AACTGCTTCTAACTGATTCTCT
1 AACTGCTTCTAACTAATTCTCT
*
17778 AACTGCTTCTAACTAATTTTCT
1 AACTGCTTCTAACTAATTCTCT
17800 AAC
1 AAC
17803 AACCTAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (22 bp):
AACTGCTTCTAACTAATTCTCT
Found at i:22610 original size:22 final size:22
Alignment explanation
Indices: 22585--22631 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
22575 CTAAAATACA
*
22585 AACTACTTCTAACTGATTCTCT
1 AACTACTTCTAACTAATTCTCT
* *
22607 AACTGCTTCTAACTAATTTTCT
1 AACTACTTCTAACTAATTCTCT
22629 AAC
1 AAC
22632 AACCTAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (22 bp):
AACTACTTCTAACTAATTCTCT
Found at i:34599 original size:10 final size:10
Alignment explanation
Indices: 34584--34619 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
34574 ATTTCCCTTT
34584 AAGAGAAGAA
1 AAGAGAAGAA
*
34594 AAGAGAAGAG
1 AAGAGAAGAA
*
34604 AAGAGGAGAA
1 AAGAGAAGAA
34614 AAGAGA
1 AAGAGA
34620 TTCTGGATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (10 bp):
AAGAGAAGAA
Found at i:42707 original size:20 final size:20
Alignment explanation
Indices: 42682--42725 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
42672 GAGTCGTGCT
*
42682 TTTAGAAAAGTAATAGCGAA
1 TTTAGAAAAGTAACAGCGAA
*
42702 TTTAGAAAAGTAGCAGCGAA
1 TTTAGAAAAGTAACAGCGAA
42722 TTTA
1 TTTA
42726 CGATACGCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.27
Consensus pattern (20 bp):
TTTAGAAAAGTAACAGCGAA
Found at i:51501 original size:60 final size:60
Alignment explanation
Indices: 51391--51555 Score: 197
Period size: 60 Copynumber: 2.8 Consensus size: 60
51381 TATTTGGATA
* * * * *
51391 AATTTGAAGATGAAATTGAGA-GATTCAAAAGTTTGAGGACCAATTTAGAATAAGGATCAT
1 AATTTGAGGATGAAATTGAAATG-TTCAAAAGTTTAAGGACCAATTAAGAATAAGAATCAT
* * * * *
51451 AGTTTGGGGATGAAATTGACATGTTCAAAAGTTTAAGGACAAATTAAGAATGAGAATCAT
1 AATTTGAGGATGAAATTGAAATGTTCAAAAGTTTAAGGACCAATTAAGAATAAGAATCAT
* * *
51511 AATTTGAGGATGAAATTAAAATATTGAAAAGTTTAAGGACCAATT
1 AATTTGAGGATGAAATTGAAATGTTCAAAAGTTTAAGGACCAATT
51556 TAAATTGAAA
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 87 0.99
61 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (60 bp):
AATTTGAGGATGAAATTGAAATGTTCAAAAGTTTAAGGACCAATTAAGAATAAGAATCAT
Done.