Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008875.1 Hibiscus syriacus cultivar Beakdansim tig00112112_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: 33448
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:9879 original size:40 final size:40
Alignment explanation
Indices: 9835--9915 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
9825 ACAAAAGAGA
9835 AAGAATTAATTTCTCAAAACAATTCATCATGTTTAAAAAT
1 AAGAATTAATTTCTCAAAACAATTCATCATGTTTAAAAAT
9875 AAGAATTAATTTCTCAAAACAATTCATCATGTTTAAAAAT
1 AAGAATTAATTTCTCAAAACAATTCATCATGTTTAAAAAT
9915 A
1 A
9916 GAAAAATGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (40 bp):
AAGAATTAATTTCTCAAAACAATTCATCATGTTTAAAAAT
Found at i:10640 original size:15 final size:16
Alignment explanation
Indices: 10614--10643 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10604 TTCAATAGTA
10614 TTCAAGAGTCAAATTT
1 TTCAAGAGTCAAATTT
10630 TTCAA-AGTCAAATT
1 TTCAAGAGTCAAATT
10644 ATTTTTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (16 bp):
TTCAAGAGTCAAATTT
Found at i:18431 original size:13 final size:13
Alignment explanation
Indices: 18413--18440 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18403 AAATGACCCT
18413 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
18426 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
18439 TT
1 TT
18441 CTAACCACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTCTTTC
Found at i:25476 original size:9 final size:9
Alignment explanation
Indices: 25462--25560 Score: 99
Period size: 10 Copynumber: 10.3 Consensus size: 9
25452 GCTGCTGGAA
25462 ACCGGTTTG
1 ACCGGTTTG
*
25471 ACCGGTTTTCA
1 ACCGG-TTT-G
25482 ACCGGTTCTG
1 ACCGGTT-TG
25492 ACCGGTTTG
1 ACCGGTTTG
*
25501 ACCGGTTTCA
1 ACCGGTTT-G
25511 ACCGGTTTG
1 ACCGGTTTG
25520 AACCGGTTTG
1 -ACCGGTTTG
*
25530 ACCGGTCTG
1 ACCGGTTTG
*
25539 AATCGGTTTG
1 -ACCGGTTTG
*
25549 ACCGGTCTG
1 ACCGGTTTG
25558 ACC
1 ACC
25561 CGACCCGATC
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
9 33 0.44
10 36 0.48
11 6 0.08
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:25506 original size:19 final size:18
Alignment explanation
Indices: 25462--25560 Score: 99
Period size: 19 Copynumber: 5.2 Consensus size: 18
25452 GCTGCTGGAA
*
25462 ACCGGTTTGACCGGTTTTCA
1 ACCGGTTTGACCGG-TTT-G
25482 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTTTG
*
25501 ACCGGTTTCAACCGGTTTG
1 ACCGGTTT-GACCGGTTTG
*
25520 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTTTG
* *
25539 AATCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTTTG
25558 ACC
1 ACC
25561 CGACCCGATC
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.04
19 42 0.60
20 18 0.26
21 7 0.10
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (18 bp):
ACCGGTTTGACCGGTTTG
Found at i:25524 original size:29 final size:28
Alignment explanation
Indices: 25462--25560 Score: 135
Period size: 29 Copynumber: 3.4 Consensus size: 28
25452 GCTGCTGGAA
25462 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTT-TG
25492 ACCGGTTTGACCGGTTTCAACCGGTTTG
1 ACCGGTTTGACCGGTTTCAACCGGTTTG
* * *
25520 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTTG
*
25549 ACCGGTCTGACC
1 ACCGGTTTGACC
25561 CGACCCGATC
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
28 13 0.20
29 37 0.58
30 14 0.22
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTTG
Found at i:25578 original size:17 final size:17
Alignment explanation
Indices: 25556--25628 Score: 87
Period size: 17 Copynumber: 4.3 Consensus size: 17
25546 TTGACCGGTC
*
25556 TGACCCGACCCGATCGT
1 TGACCCGACCCGACCGT
*
25573 TGACCCGACCGTTGACC--
1 TGACCCGACC--CGACCGT
*
25590 CGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
25607 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
25624 TGACC
1 TGACC
25629 GTTGACCGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
15 4 0.09
17 40 0.85
19 3 0.06
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:25599 original size:22 final size:22
Alignment explanation
Indices: 25574--25635 Score: 97
Period size: 22 Copynumber: 2.7 Consensus size: 22
25564 CCCGATCGTT
25574 GACCCGACCGTTGACCCGACCC
1 GACCCGACCGTTGACCCGACCC
25596 GACCCGACCGTTGACCCGACCC
1 GACCCGACCGTTGACCCGACCC
*
25618 GACCGTTGACCGTTGACC
1 GACC--CGACCGTTGACC
25636 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
22 26 0.70
24 11 0.30
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (22 bp):
GACCCGACCGTTGACCCGACCC
Found at i:25628 original size:7 final size:7
Alignment explanation
Indices: 25618--25648 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
25608 GACCCGACCC
25618 GACCGTT
1 GACCGTT
25625 GACCGTT
1 GACCGTT
25632 GACCGTT
1 GACCGTT
25639 GACCGTT
1 GACCGTT
25646 GAC
1 GAC
25649 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:25628 original size:12 final size:12
Alignment explanation
Indices: 25562--25616 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
25552 GGTCTGACCC
*
25562 GACCCGATCGTT
1 GACCCGACCGTT
25574 GACCCGACCGTT
1 GACCCGACCGTT
*
25586 GACCCGACC--C
1 GACCCGACCGTT
25596 GACCCGACCGTT
1 GACCCGACCGTT
25608 GACCCGACC
1 GACCCGACC
25617 CGACCGTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 9 0.24
12 29 0.76
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:26600 original size:32 final size:31
Alignment explanation
Indices: 26517--26592 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
26507 CTAATGTGAC
* *
26517 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
* *
26548 TC-TCGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
26579 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
26593 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 22 0.58
31 6 0.16
32 10 0.26
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:32805 original size:9 final size:9
Alignment explanation
Indices: 32791--32830 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
32781 GCTGCTGGAA
32791 ACCGGTTTG
1 ACCGGTTTG
32800 ACCGGTTTG
1 ACCGGTTTG
*
32809 AATCGGTTTG
1 -ACCGGTTTG
*
32819 ACCGGTCTG
1 ACCGGTTTG
32828 ACC
1 ACC
32831 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.25, G:0.30, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:32848 original size:17 final size:17
Alignment explanation
Indices: 32826--32876 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
32816 TTGACCGGTC
32826 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
32843 T-----GACCCGACCGT
1 TGACCCGACCCGACCGT
32855 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
32872 TGACC
1 TGACC
32877 GTTGACCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 12 0.41
17 17 0.59
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.14
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:32860 original size:29 final size:30
Alignment explanation
Indices: 32826--32890 Score: 105
Period size: 29 Copynumber: 2.2 Consensus size: 30
32816 TTGACCGGTC
32826 TGACCCGACCCGACCGTTGACC-CGACCGT
1 TGACCCGACCCGACCGTTGACCGCGACCGT
*
32855 TGACCCGACCCGACCGTTGACCGTTGACCGT
1 TGACCCGACCCGACCGTTGACCG-CGACCGT
32886 TGACC
1 TGACC
32891 GTTGACCGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 22 0.67
31 11 0.33
ACGTcount: A:0.17, C:0.42, G:0.25, T:0.17
Consensus pattern (30 bp):
TGACCCGACCCGACCGTTGACCGCGACCGT
Found at i:32876 original size:7 final size:7
Alignment explanation
Indices: 32866--32903 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
32856 GACCCGACCC
32866 GACCGTT
1 GACCGTT
32873 GACCGTT
1 GACCGTT
32880 GACCGTT
1 GACCGTT
32887 GACCGTT
1 GACCGTT
32894 GACCGTT
1 GACCGTT
32901 GAC
1 GAC
32904 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:32876 original size:12 final size:12
Alignment explanation
Indices: 32832--32864 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
32822 GGTCTGACCC
32832 GACCCGACCGTT
1 GACCCGACCGTT
32844 GACCCGACCGTT
1 GACCCGACCGTT
32856 GACCCGACC
1 GACCCGACC
32865 CGACCGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.12
Consensus pattern (12 bp):
GACCCGACCGTT
Done.