Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009499.1 Hibiscus syriacus cultivar Beakdansim tig00114999_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: 54648
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:1130 original size:2 final size:2
Alignment explanation
Indices: 1125--1153 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1115 AAAAATATCT
1125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1154 TTCCAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5450 original size:16 final size:17
Alignment explanation
Indices: 5429--5474 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
5419 ATTTTAATAA
5429 ATTATATTAATTTTTT-
1 ATTATATTAATTTTTTG
*
5445 ATTATAATAATATTTTTG
1 ATTATATTAAT-TTTTTG
*
5463 ATTATTTTAATT
1 ATTATATTAATT
5475 ACTGTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 10 0.40
17 6 0.24
18 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTATATTAATTTTTTG
Found at i:5663 original size:29 final size:30
Alignment explanation
Indices: 5630--5702 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
5620 TTGAAAAATC
*
5630 ATTATATATTATTA-AA-ATAAAAGTATAA
1 ATTATATATTATTATAATATAAAAGAATAA
* *
5658 TATTATATATCATTATAATATTAAAGAATAA
1 -ATTATATATTATTATAATATAAAAGAATAA
5689 A-TATCATATTATTA
1 ATTAT-ATATTATTA
5703 GAATTATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 16 0.43
30 11 0.30
31 10 0.27
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (30 bp):
ATTATATATTATTATAATATAAAAGAATAA
Found at i:9652 original size:21 final size:20
Alignment explanation
Indices: 9613--9650 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9603 TTAAGATTAT
9613 TAAATTTATTGAATTTTTAA
1 TAAATTTATTGAATTTTTAA
9633 TAAATTATATT-AATTTTT
1 TAAATT-TATTGAATTTTT
9651 TATTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TAAATTTATTGAATTTTTAA
Found at i:9827 original size:18 final size:19
Alignment explanation
Indices: 9804--9852 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
9794 AAGTTTTGTA
*
9804 ATTTATGAATAAT-AGTAT
1 ATTTATGAAAAATCAGTAT
*
9822 ATTTATTGAAAAATCATTAT
1 ATTTA-TGAAAAATCAGTAT
*
9842 ATTTATTAAAA
1 ATTTATGAAAA
9853 TAAAAGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 5 0.19
19 12 0.46
20 9 0.35
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (19 bp):
ATTTATGAAAAATCAGTAT
Found at i:9862 original size:20 final size:21
Alignment explanation
Indices: 9811--9862 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
9801 GTAATTTATG
*
9811 AATAATAGTATATTTATTGAA
1 AATAAAAGTATATTTATTGAA
** *
9832 AA-ATCATTATATTTATT-AA
1 AATAAAAGTATATTTATTGAA
9851 AATAAAAGTATA
1 AATAAAAGTATA
9863 ATATTATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.17
20 18 0.75
21 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (21 bp):
AATAAAAGTATATTTATTGAA
Found at i:12910 original size:19 final size:18
Alignment explanation
Indices: 12879--12914 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12869 AAGTTTGTAA
*
12879 TTTATGAATAATATTATT
1 TTTATGAAAAATATTATT
12897 TTTATTGAAAAATATTAT
1 TTTA-TGAAAAATATTAT
12915 ATTATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTATGAAAAATATTATT
Found at i:20544 original size:13 final size:13
Alignment explanation
Indices: 20525--20558 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
20515 ACCCGACCCG
20525 ACCCGACCCATTT
1 ACCCGACCCATTT
* *
20538 TCCCGACCCGTTT
1 ACCCGACCCATTT
20551 ACCCGACC
1 ACCCGACC
20559 AGAACCGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.18, C:0.50, G:0.12, T:0.21
Consensus pattern (13 bp):
ACCCGACCCATTT
Found at i:20582 original size:15 final size:16
Alignment explanation
Indices: 20562--20596 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
20552 CCCGACCAGA
20562 ACCGTTGACC-CGTTG
1 ACCGTTGACCGCGTTG
20577 ACCGTTGACCGGCGTTG
1 ACCGTTGACC-GCGTTG
20594 ACC
1 ACC
20597 ACTGTTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
17 8 0.44
ACGTcount: A:0.14, C:0.34, G:0.29, T:0.23
Consensus pattern (16 bp):
ACCGTTGACCGCGTTG
Found at i:23092 original size:12 final size:12
Alignment explanation
Indices: 23072--23140 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
23062 GATACATTAC
*
23072 CTGAATTCTGTT
1 CTGATTTCTGTT
*
23084 CTGATTTCTGAT
1 CTGATTTCTGTT
23096 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
23108 CTGATATCTGAT
1 CTGATTTCTGTT
* *
23120 ATGAATTCTGTT
1 CTGATTTCTGTT
23132 -TGATTTCTG
1 CTGATTTCTG
23141 ATATCTCCGT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
11 10 0.22
12 33 0.73
13 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.49
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:23103 original size:24 final size:24
Alignment explanation
Indices: 23073--23144 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
23063 ATACATTACC
*
23073 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATA
* *
23097 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
23121 TGAATTCTGTT-TGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
23144 T
1 T
23145 CTCCGTTTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 12 0.28
24 31 0.72
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:23113 original size:48 final size:49
Alignment explanation
Indices: 23035--23142 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 49
23025 AAATATTTTA
* *
23035 TCTGATTTCTGA-CTTGAATTATGTTATGATA-CATTACCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTATGTTATGATATC-TGACATGAATTCTGT
* * * *
23083 TCTGATTTCTGATC-TGGATTCTGTTCTGATATCTGATATGAATTCTGT
1 TCTGATTTCTGATCTTGAATTATGTTATGATATCTGACATGAATTCTGT
23131 T-TGATTTCTGAT
1 TCTGATTTCTGAT
23143 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
47 11 0.21
48 39 0.75
49 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTATGTTATGATATCTGACATGAATTCTGT
Found at i:27804 original size:24 final size:23
Alignment explanation
Indices: 27774--27846 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 23
27764 ATACATTACC
* *
27774 TGAATTCTGTTCTGACTTCTGATC
1 TGAATTCTGTTATGA-TTCTGATA
*
27798 TGGATTCTGTTATGATATCTGATA
1 TGAATTCTGTTATGAT-TCTGATA
*
27822 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGA-TTCTGATA
27846 T
1 T
27847 CTCCGTTTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 1 0.02
24 40 0.95
25 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (23 bp):
TGAATTCTGTTATGATTCTGATA
Found at i:28737 original size:15 final size:15
Alignment explanation
Indices: 28717--28768 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
28707 AAAATAAAAG
28717 TATAATATATATGAT
1 TATAATATATATGAT
* *
28732 TATAATAT-TAAAGAA
1 TATAATATAT-ATGAT
*
28747 TATAATATCATATTAT
1 TATAATAT-ATATGAT
28763 TATAAT
1 TATAAT
28769 TATGAGTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 1 0.03
15 19 0.66
16 8 0.28
17 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (15 bp):
TATAATATATATGAT
Found at i:28744 original size:28 final size:29
Alignment explanation
Indices: 28696--28768 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 29
28686 GAAAAATCAT
28696 TATATATTATTA-AA-ATAAAAG-TATAA
1 TATATATTATTATAATATAAAAGATATAA
* *
28722 TATATATGATTATAATATTAAAGAATATAA
1 TATATATTATTATAATATAAAAG-ATATAA
28752 TATCATATTATTATAAT
1 TAT-ATATTATTATAAT
28769 TATGAGTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 11 0.28
27 2 0.05
28 6 0.15
30 8 0.21
31 12 0.31
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (29 bp):
TATATATTATTATAATATAAAAGATATAA
Found at i:29194 original size:2 final size:2
Alignment explanation
Indices: 29177--29227 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
29167 TTAATTCTTG
* *
29177 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29219 AT AT AT AT A
1 AT AT AT AT A
29228 AAATATTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:32472 original size:18 final size:19
Alignment explanation
Indices: 32433--32474 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
32423 ATATATATAT
*
32433 ATATATATTTTTCTGAAAA
1 ATATATATTTTTATGAAAA
32452 ATAT-TATTTTTAT-AAATA
1 ATATATATTTTTATGAAA-A
32470 ATATA
1 ATATA
32475 AAAGTCCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 3 0.15
18 13 0.65
19 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATATATTTTTATGAAAA
Found at i:35938 original size:26 final size:25
Alignment explanation
Indices: 35888--35958 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
35878 TTTATTGAAA
*
35888 AATA-ATTATATTATTAAAATAAAAG
1 AATATATTATA-TATTATAATAAAAG
* *
35913 TATAATATTATATATTATAATTAAAG
1 AAT-ATATTATATATTATAATAAAAG
*
35939 AATATAATATCATATTATAA
1 AATATATTAT-ATATTATAA
35959 GAATTATGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
25 8 0.21
26 24 0.63
27 6 0.16
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (25 bp):
AATATATTATATATTATAATAAAAG
Found at i:36425 original size:18 final size:18
Alignment explanation
Indices: 36387--36426 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
36377 ATATATATAT
*
36387 ATATTATTTTTCTGAAAA
1 ATATTATTTTTATGAAAA
36405 ATATTATTTTTAT-AAATA
1 ATATTATTTTTATGAAA-A
36423 ATAT
1 ATAT
36427 AAAAGTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATATTATTTTTATGAAAA
Found at i:46368 original size:10 final size:10
Alignment explanation
Indices: 46355--46408 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
46345 CGGGTCGGAT
*
46355 CGGTTCAGAC
1 CGGTTCAAAC
*
46365 CGGTTGAAAC
1 CGGTTCAAAC
46375 CGGTTTC-AAC
1 CGG-TTCAAAC
46385 CGGTTCAAAC
1 CGGTTCAAAC
*
46395 C-GATCAAAC
1 CGGTTCAAAC
46404 CGGTT
1 CGGTT
46409 TTCAACCACT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
9 11 0.31
10 23 0.64
11 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (10 bp):
CGGTTCAAAC
Found at i:47265 original size:2 final size:2
Alignment explanation
Indices: 47255--47297 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
47245 AGAAAAAATA
47255 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47296 AT
1 AT
47298 CAAGAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47765 original size:18 final size:18
Alignment explanation
Indices: 47724--47778 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
47714 ATATATATTC
47724 TTTAATATTATAATGATA
1 TTTAATATTATAATGATA
* * **
47742 TATAATATTATACTTTTA
1 TTTAATATTATAATGATA
47760 TTTAATAATATATAATGAT
1 TTTAAT-AT-TATAATGAT
47779 TTTTCAATAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
18 19 0.70
19 2 0.07
20 6 0.22
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (18 bp):
TTTAATATTATAATGATA
Found at i:47815 original size:24 final size:24
Alignment explanation
Indices: 47788--47834 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
47778 TTTTTCAATA
*
47788 AAAATAGTATTATTCATAAATTAC
1 AAAACAGTATTATTCATAAATTAC
* **
47812 AAAACATTATTATTTTTAAATTA
1 AAAACAGTATTATTCATAAATTA
47835 TTTAATATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (24 bp):
AAAACAGTATTATTCATAAATTAC
Found at i:49799 original size:16 final size:18
Alignment explanation
Indices: 49755--49800 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
49745 TTTCAATAGT
*
49755 AATTAAAATAATCAAGAA
1 AATTAATATAATCAAGAA
* *
49773 TATTTATATAAT-AA-AA
1 AATTAATATAATCAAGAA
49789 AATTAATATAAT
1 AATTAATATAAT
49801 TTATTAAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
16 12 0.52
17 2 0.09
18 9 0.39
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
AATTAATATAATCAAGAA
Found at i:53167 original size:2 final size:2
Alignment explanation
Indices: 53160--53194 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53150 TTTCTTGGAA
53160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53195 AGATATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54459 original size:26 final size:25
Alignment explanation
Indices: 54408--54459 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
54398 CATAATTCTA
*
54408 ATAATGATATTATATTCTTTAATATT
1 ATAATGATATTATATACTTT-ATATT
54434 ATAATGATATATAATATACTTT-TATT
1 ATAATGATAT-T-ATATACTTTATATT
54460 TTAAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 14 0.61
27 1 0.04
28 8 0.35
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (25 bp):
ATAATGATATTATATACTTTATATT
Done.