Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007617.1 Hibiscus syriacus cultivar Beakdansim tig00022804_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: 87060
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Found at i:2163 original size:16 final size:18
Alignment explanation
Indices: 2142--2179 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2132 AGTTAGTGGT
2142 CAGCGTAGA-G-TAAAGG
1 CAGCGTAGAGGCTAAAGG
2158 CAGCGTAGAGGCTAAAGG
1 CAGCGTAGAGGCTAAAGG
2176 CAGC
1 CAGC
2180 TGTTGAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 10 0.50
ACGTcount: A:0.34, C:0.18, G:0.37, T:0.11
Consensus pattern (18 bp):
CAGCGTAGAGGCTAAAGG
Found at i:13700 original size:20 final size:20
Alignment explanation
Indices: 13675--13714 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13665 GACTTCTTTC
13675 TATACGAAAATAGAAATTAG
1 TATACGAAAATAGAAATTAG
13695 TATACGAAAATAGAAATTAG
1 TATACGAAAATAGAAATTAG
13715 AAAGAGGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (20 bp):
TATACGAAAATAGAAATTAG
Found at i:17771 original size:27 final size:27
Alignment explanation
Indices: 17740--17812 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
17730 TCCGTTAGGA
17740 CTGGTTTTTCAAAGCCAGGAAGCGTAG
1 CTGGTTTTTCAAAGCCAGGAAGCGTAG
17767 CTGGTTTTTCAAAGCCAGGAAGCGTAG
1 CTGGTTTTTCAAAGCCAGGAAGCGTAG
*
17794 CTGGTTTTTCAACGCCAGG
1 CTGGTTTTTCAAAGCCAGG
17813 TGCCTACGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (27 bp):
CTGGTTTTTCAAAGCCAGGAAGCGTAG
Found at i:20902 original size:17 final size:19
Alignment explanation
Indices: 20863--20902 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
20853 ATCGATTGAA
20863 CTCTTTGCTAGAAATTCCT
1 CTCTTTGCTAGAAATTCCT
20882 CTCTTTGCTAGAAATTCCT
1 CTCTTTGCTAGAAATTCCT
20901 CT
1 CT
20903 TCTCTGTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42
Consensus pattern (19 bp):
CTCTTTGCTAGAAATTCCT
Found at i:22881 original size:15 final size:15
Alignment explanation
Indices: 22861--22892 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
22851 AGCCTTTTTT
22861 TAATGATTTACGAAA
1 TAATGATTTACGAAA
22876 TAATGATTTACGAAA
1 TAATGATTTACGAAA
22891 TA
1 TA
22893 TGGCTGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (15 bp):
TAATGATTTACGAAA
Found at i:35730 original size:28 final size:28
Alignment explanation
Indices: 35681--35753 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
35671 TGATCGATTG
*
35681 AGATAGACTCCCCAAAGGGAGGAATTGGA
1 AGATAGACT-CGCAAAGGGAGGAATTGGA
35710 AGATAGACTCGCAAAGGGAGGAATTGGA
1 AGATAGACTCGCAAAGGGAGGAATTGGA
35738 AGATAGACTCGCAAAG
1 AGATAGACTCGCAAAG
35754 AAATGTAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 34 0.79
29 9 0.21
ACGTcount: A:0.40, C:0.15, G:0.32, T:0.14
Consensus pattern (28 bp):
AGATAGACTCGCAAAGGGAGGAATTGGA
Found at i:50043 original size:16 final size:18
Alignment explanation
Indices: 50022--50059 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
50012 AGTTAGTGGT
50022 CAGCGTAGA-G-TAAAGG
1 CAGCGTAGAGGCTAAAGG
50038 CAGCGTAGAGGCTAAAGG
1 CAGCGTAGAGGCTAAAGG
50056 CAGC
1 CAGC
50060 TGTTGAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 10 0.50
ACGTcount: A:0.34, C:0.18, G:0.37, T:0.11
Consensus pattern (18 bp):
CAGCGTAGAGGCTAAAGG
Found at i:61608 original size:20 final size:20
Alignment explanation
Indices: 61583--61622 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
61573 GACTTCTTTC
61583 TATACGAAAATAGAAATTAG
1 TATACGAAAATAGAAATTAG
61603 TATACGAAAATAGAAATTAG
1 TATACGAAAATAGAAATTAG
61623 AAAGAGGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (20 bp):
TATACGAAAATAGAAATTAG
Found at i:65683 original size:27 final size:27
Alignment explanation
Indices: 65652--65724 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
65642 TCCGTTAGGA
65652 CTGGTTTTTCAAAGCCAGGAAGCGTAG
1 CTGGTTTTTCAAAGCCAGGAAGCGTAG
65679 CTGGTTTTTCAAAGCCAGGAAGCGTAG
1 CTGGTTTTTCAAAGCCAGGAAGCGTAG
*
65706 CTGGTTTTTCAACGCCAGG
1 CTGGTTTTTCAAAGCCAGG
65725 TGCCTACGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (27 bp):
CTGGTTTTTCAAAGCCAGGAAGCGTAG
Found at i:68811 original size:17 final size:19
Alignment explanation
Indices: 68772--68811 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
68762 ATCGATTGAA
68772 CTCTTTGCTAGAAATTCCT
1 CTCTTTGCTAGAAATTCCT
68791 CTCTTTGCTAGAAATTCCT
1 CTCTTTGCTAGAAATTCCT
68810 CT
1 CT
68812 TCTCTGTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42
Consensus pattern (19 bp):
CTCTTTGCTAGAAATTCCT
Found at i:70790 original size:15 final size:15
Alignment explanation
Indices: 70770--70801 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
70760 AGCCTTTTTT
70770 TAATGATTTACGAAA
1 TAATGATTTACGAAA
70785 TAATGATTTACGAAA
1 TAATGATTTACGAAA
70800 TA
1 TA
70802 TGGCTGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (15 bp):
TAATGATTTACGAAA
Found at i:83634 original size:28 final size:28
Alignment explanation
Indices: 83585--83657 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
83575 TGATCGATTG
*
83585 AGATAGACTCCCCAAAGGGAGGAATTGGA
1 AGATAGACT-CGCAAAGGGAGGAATTGGA
83614 AGATAGACTCGCAAAGGGAGGAATTGGA
1 AGATAGACTCGCAAAGGGAGGAATTGGA
83642 AGATAGACTCGCAAAG
1 AGATAGACTCGCAAAG
83658 AAATGTAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 34 0.79
29 9 0.21
ACGTcount: A:0.40, C:0.15, G:0.32, T:0.14
Consensus pattern (28 bp):
AGATAGACTCGCAAAGGGAGGAATTGGA
Done.