Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002140.1 Hibiscus syriacus cultivar Beakdansim tig00004374_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: 43872
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:751 original size:12 final size:12
Alignment explanation
Indices: 734--767 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
724 AGATGAGCAT
*
734 GAGCAGCCCGAG
1 GAGCAGCACGAG
746 GAGCAGCACGAG
1 GAGCAGCACGAG
758 GAGCAAGCAC
1 GAGC-AGCAC
768 AACAAACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.32, C:0.29, G:0.38, T:0.00
Consensus pattern (12 bp):
GAGCAGCACGAG
Found at i:2720 original size:30 final size:30
Alignment explanation
Indices: 2686--2742 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
2676 AACTTTGAAT
2686 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
2716 AAATTCAATTCAAGTCCAAAAACATTT
1 AAATTCAATTCAAATCCAAAAACATTT
2743 GCCTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:4052 original size:19 final size:19
Alignment explanation
Indices: 4016--4061 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
4006 CTAAATCCTT
*
4016 TTTCAAAATTTCATTTTGGC
1 TTTCAAAATCTCATTTT-GC
*
4036 TTTCAAAATCT-ATTTTGT
1 TTTCAAAATCTCATTTTGC
4054 TTTCAAAA
1 TTTCAAAA
4062 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 10 0.42
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTCATTTTGC
Found at i:5551 original size:30 final size:30
Alignment explanation
Indices: 5515--5574 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5505 ACCTTTGAAT
5515 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
5545 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
5575 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:13785 original size:37 final size:37
Alignment explanation
Indices: 13709--13785 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
13699 TTTTTATATT
*
13709 TTTAATTTTGTAAAAAAAATTATATAAATATTCTGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTCTCAA
* * *
13746 TTTAATTTTTTAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTCT-CAA
13783 TTT
1 TTT
13786 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTCTCAA
Found at i:14689 original size:7 final size:7
Alignment explanation
Indices: 14679--14710 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
14669 ATAATTTATC
*
14679 TTTTAAG
1 TTTTGAG
14686 TTTTGAG
1 TTTTGAG
14693 TTTTGAG
1 TTTTGAG
14700 TTTTGAG
1 TTTTGAG
14707 TTTT
1 TTTT
14711 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.22, T:0.62
Consensus pattern (7 bp):
TTTTGAG
Found at i:26029 original size:20 final size:21
Alignment explanation
Indices: 25990--26030 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25980 TCAGGGTTCG
*
25990 AATATCAATATTGGGATGAAT
1 AATATCAATATTGAGATGAAT
*
26011 AATATCGATATT-AGATGAAT
1 AATATCAATATTGAGATGAAT
26031 TGGGGCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (21 bp):
AATATCAATATTGAGATGAAT
Found at i:26815 original size:21 final size:21
Alignment explanation
Indices: 26790--26853 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
26780 CCGTTAGACA
*
26790 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
* *
26811 GGGGGAATTTGTTCCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
26832 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
26853 G
1 G
26854 CAATCTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.12, C:0.27, G:0.41, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:29607 original size:16 final size:15
Alignment explanation
Indices: 29583--29618 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
29573 ATTATATAAA
*
29583 ATATAATGAATTATTT
1 ATATTATGAATTA-TT
29599 ATATTATGAATTATT
1 ATATTATGAATTATT
29614 ATATT
1 ATATT
29619 TTGTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
ATATTATGAATTATT
Found at i:30705 original size:20 final size:20
Alignment explanation
Indices: 30662--30763 Score: 134
Period size: 20 Copynumber: 5.1 Consensus size: 20
30652 CCGTTAGACA
*
30662 GGGGGAATCGGTACCCCTTGG
1 GGGGGAATCGGTACCCCCT-G
*
30683 GGGGGAATCGGTTCCCCCTG
1 GGGGGAATCGGTACCCCCTG
*
30703 GGGGGAATCAGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
* *
30723 GGGGGAATCTGTTCCCCCT-
1 GGGGGAATCGGTACCCCCTG
*
30742 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
30762 GG
1 GG
30764 TAATCTGATT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.25
20 38 0.52
21 17 0.23
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.20
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Done.