Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003275.1 Hibiscus syriacus cultivar Beakdansim tig00006886_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: 74467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:5821 original size:26 final size:26
Alignment explanation
Indices: 5739--5841 Score: 152
Period size: 26 Copynumber: 4.0 Consensus size: 26
5729 ACTAAGTTTA
*
5739 TATGGTGGGCACGACCTTATATGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
* * *
5765 TATGATGGGAACAACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
*
5791 TATGGTGAGCACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
*
5817 TATGGGGGGCACGACCTTATGTGTA
1 TATGGTGGGCACGACCTTATGTGTA
5842 AGCACTACGG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTATGTGTAT
Found at i:6942 original size:103 final size:103
Alignment explanation
Indices: 6760--6962 Score: 291
Period size: 103 Copynumber: 2.0 Consensus size: 103
6750 AATATTTCTA
* * * *
6760 TGATTGCCTCACTAAATGTATACTTAGCGTGTGATGATTTTCACTCGTAGGTAAAATATAACGAA
1 TGATTGCCTCACTAAATGTATACTTAGCGTGTGATGATTTTCACGCCTAGGTAAAAGAAAACGAA
6825 TGGAGTAAGAAGCTGAGCTTAGCATCAATCATCAAAGG
66 TGGAGTAAGAAGCTGAGCTTAGCATCAATCATCAAAGG
* *
6863 TGATTGCCTCACTAAGTGTATACTTAGTGTGTGATGATTTTCACGCCTAGGTAAAAGAAAACGAA
1 TGATTGCCTCACTAAATGTATACTTAGCGTGTGATGATTTTCACGCCTAGGTAAAAGAAAACG-A
* * * * *
6928 AT-GAGTATGGAGCTGAGTTTGGCATCAATCGTCAA
65 ATGGAGTAAGAAGCTGAGCTTAGCATCAATCATCAA
6963 GGAATATCAT
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
103 85 0.97
104 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (103 bp):
TGATTGCCTCACTAAATGTATACTTAGCGTGTGATGATTTTCACGCCTAGGTAAAAGAAAACGAA
TGGAGTAAGAAGCTGAGCTTAGCATCAATCATCAAAGG
Found at i:7039 original size:22 final size:23
Alignment explanation
Indices: 7013--7063 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
7003 AAGTATAGTA
*
7013 TTAAAT-ATTAATTAATTGGATT
1 TTAAATAATAAATTAATTGGATT
**
7035 TTAAATAATAAATTAATTTTATT
1 TTAAATAATAAATTAATTGGATT
7058 TTAAAT
1 TTAAAT
7064 TAGTTAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TTAAATAATAAATTAATTGGATT
Found at i:11220 original size:2 final size:2
Alignment explanation
Indices: 11213--11305 Score: 170
Period size: 2 Copynumber: 47.0 Consensus size: 2
11203 ATGTTCTTCA
11213 AT AT AT 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
*
11255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11297 AT AT A- AT AT
1 AT AT AT AT AT
11306 CATTTAAAAT
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 87 0.99
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15811 original size:59 final size:60
Alignment explanation
Indices: 15714--15832 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 60
15704 ATTCATATAA
15714 TGTTAATATTAGTAGCATGATTGAAAATACAAGTAAAGTGGTCATAATGGATTGAATACT
1 TGTTAATATTAGTAGCATGATTGAAAATACAAGTAAAGTGGTCATAATGGATTGAATACT
*
15774 TGTT-ATATTAGTAGCATGATTTAAAATACAAGTAAAGTGGTCATAATGGATTGAATACT
1 TGTTAATATTAGTAGCATGATTGAAAATACAAGTAAAGTGGTCATAATGGATTGAATACT
15833 ATTATTGTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 54 0.93
60 4 0.07
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.34
Consensus pattern (60 bp):
TGTTAATATTAGTAGCATGATTGAAAATACAAGTAAAGTGGTCATAATGGATTGAATACT
Found at i:15831 original size:29 final size:29
Alignment explanation
Indices: 15739--15831 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
15729 CATGATTGAA
15739 AATACAAGTAAAGTGGTCATAATGGATTG
1 AATACAAGTAAAGTGGTCATAATGGATTG
** * * * ** *
15768 AATACTTGTTATATTAGT-AGCAT-GATTTAA
1 AATACAAG-TAAAGTGGTCATAATGGA-TT-G
15798 AATACAAGTAAAGTGGTCATAATGGATTG
1 AATACAAGTAAAGTGGTCATAATGGATTG
15827 AATAC
1 AATAC
15832 TATTATTGTT
Statistics
Matches: 43, Mismatches: 16, Indels: 10
0.62 0.23 0.14
Matches are distributed among these distances:
28 2 0.05
29 22 0.51
30 17 0.40
31 2 0.05
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (29 bp):
AATACAAGTAAAGTGGTCATAATGGATTG
Found at i:18182 original size:54 final size:54
Alignment explanation
Indices: 18100--18630 Score: 692
Period size: 54 Copynumber: 9.8 Consensus size: 54
18090 TTACCAAATG
*
18100 GGCACTATGTTTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* *
18154 GGCACTATTTGTGCAACTTAAGAAATTCAAAATAAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* * * * *
18208 GCCACTATATGTACAACTTAAGAAATTCATAATAAGTTTATGAATTACCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
*
18262 GGCACTATGCGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTT-TCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCT-GTATT
**
18316 GGCACTATCCGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTT-TCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCT-GTATT
* * * *
18370 GGCACTGTGCGTGCAACTTAATAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* * *
18424 GCCACTATGTGGGCAACTTAAGAAATTCATAATAAGTTTATGAATTTATGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* *
18478 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTT-GGTGTT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* * * * * ** *
18531 GGCACTGTGTGTGCAACTTCACGTAATTCATAATGAGTTTGTGAATCACTGTATC
1 GGCACTATGTGTGCAACTT-AAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* * ** * *
18586 GACACTAAGTGTGCAACCCACA-AAATTCATAATGAGCTTATGAAT
1 GGCACTATGTGTGCAACTTA-AGAAATTCATAATAAGTTTATGAAT
18631 GACCGTATCG
Statistics
Matches: 422, Mismatches: 50, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
53 22 0.05
54 383 0.91
55 17 0.04
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (54 bp):
GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
Found at i:23604 original size:54 final size:54
Alignment explanation
Indices: 23522--24024 Score: 776
Period size: 54 Copynumber: 9.3 Consensus size: 54
23512 TTACCAAATA
* *
23522 GGCACTATGTTTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* * *
23576 GGCACTAT-TAGTGTAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTGTGT-GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* *
23630 GGCACTGTGTGTGTAACTTAAGAAATTCCTAATAAGTTTATGAATTT-TCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCT-GTATT
23684 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
*
23738 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* *
23792 GGCAGTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* * *
23846 GACACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAGTTTTTGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* * * *
23900 GCCACTGTGTATGCAACATAAGAAATTCATAATAAGTTTATGAGTTTCTGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* *
23954 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCGGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* * *
24008 AGCATTGTTTGTGCAAC
1 GGCACTGTGTGTGCAAC
24025 CCCACGTAAT
Statistics
Matches: 416, Mismatches: 29, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
53 1 0.00
54 413 0.99
55 2 0.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.39
Consensus pattern (54 bp):
GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
Found at i:28783 original size:21 final size:22
Alignment explanation
Indices: 28739--28788 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
28729 TATTAGTTTT
**
28739 AATTGATTTTTAAAATATTTAA
1 AATTGATTTTTAAAATATGAAA
28761 AATTGATTTTTAAAA-ATGAAA
1 AATTGATTTTTAAAATATGAAA
28782 AATTGAT
1 AATTGAT
28789 ACTTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (22 bp):
AATTGATTTTTAAAATATGAAA
Found at i:29571 original size:22 final size:23
Alignment explanation
Indices: 29546--29588 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
29536 TTTTATTAAG
29546 TTTGGAC-TTTTAACGAAATGCT
1 TTTGGACATTTTAACGAAATGCT
**
29568 TTTGTTCATTTTAACGAAATG
1 TTTGGACATTTTAACGAAATG
29589 ATTTCTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (23 bp):
TTTGGACATTTTAACGAAATGCT
Found at i:30631 original size:13 final size:13
Alignment explanation
Indices: 30589--30636 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
30579 TCAATGAACG
* *
30589 TCATAAATTAGCA
1 TCATAAATGAGTA
*
30602 TCATAAATGTGTA
1 TCATAAATGAGTA
*
30615 TCATAAATGAGTG
1 TCATAAATGAGTA
30628 TCATAAATG
1 TCATAAATG
30637 CGCGTCATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (13 bp):
TCATAAATGAGTA
Found at i:30643 original size:13 final size:13
Alignment explanation
Indices: 30581--30645 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
30571 AATGACGCTC
*
30581 AATGAACGTCATA
1 AATGAGCGTCATA
* *
30594 AATTAGCATCATA
1 AATGAGCGTCATA
* **
30607 AATGTGTATCATA
1 AATGAGCGTCATA
*
30620 AATGAGTGTCATA
1 AATGAGCGTCATA
*
30633 AATGCGCGTCATA
1 AATGAGCGTCATA
30646 GATTTATGAC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (13 bp):
AATGAGCGTCATA
Found at i:30644 original size:26 final size:26
Alignment explanation
Indices: 30587--30645 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
30577 GCTCAATGAA
* *
30587 CGTCATAAATTAGCATCATAAATGTG
1 CGTCATAAATGAGCATCATAAATGCG
** **
30613 TATCATAAATGAGTGTCATAAATGCG
1 CGTCATAAATGAGCATCATAAATGCG
30639 CGTCATA
1 CGTCATA
30646 GATTTATGAC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (26 bp):
CGTCATAAATGAGCATCATAAATGCG
Found at i:35694 original size:27 final size:28
Alignment explanation
Indices: 35640--35708 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
35630 GTTTAACTTC
35640 ATTTATTTAATTTTTTTTTATTTCATAA-
1 ATTTATTT-ATTTTTTTTTATTTCATAAT
*
35668 ATTTATTTATTTTTTATTTGTTT-ATAAT
1 ATTTATTTATTTTTT-TTTATTTCATAAT
*
35696 AATT-TTTATTTTT
1 ATTTATTTATTTTT
35709 AAATATTCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (28 bp):
ATTTATTTATTTTTTTTTATTTCATAAT
Found at i:37703 original size:22 final size:22
Alignment explanation
Indices: 37676--37723 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
37666 TTCTATATAT
*
37676 TATAATATAT-TAGATTATTATC
1 TATAATAT-TCTAAATTATTATC
37698 TATAATATTCTAAATTATTATC
1 TATAATATTCTAAATTATTATC
37720 TATA
1 TATA
37724 TAAATGACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (22 bp):
TATAATATTCTAAATTATTATC
Found at i:45556 original size:21 final size:21
Alignment explanation
Indices: 45530--45569 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45520 CCCCCTTTGA
*
45530 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
45551 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
45570 TGGGGCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:46016 original size:19 final size:19
Alignment explanation
Indices: 45985--46025 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
45975 GTTATTTTTC
45985 AAATTATTGTGTT-TTGATT
1 AAATTATTGTGTTGTTG-TT
46004 AAATTA-TGTTGTTGTTGTT
1 AAATTATTG-TGTTGTTGTT
46023 AAA
1 AAA
46026 AACTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.10
19 15 0.75
20 3 0.15
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (19 bp):
AAATTATTGTGTTGTTGTT
Found at i:52103 original size:19 final size:19
Alignment explanation
Indices: 52081--52120 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
52071 TCTATTAGAA
52081 ATTTTTATATCTTGTTTGT
1 ATTTTTATATCTTGTTTGT
52100 ATTTTTATATCTTGTTTGT
1 ATTTTTATATCTTGTTTGT
52119 AT
1 AT
52121 ATATATTGGA
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:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (19 bp):
ATTTTTATATCTTGTTTGT
Found at i:52548 original size:12 final size:11
Alignment explanation
Indices: 52533--52566 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
52523 ATTATTTAAT
52533 ATTAAATAATAA
1 ATTAAATAA-AA
52545 ATTAAATAAAA
1 ATTAAATAAAA
*
52556 ATGAAATAAAA
1 ATTAAATAAAA
52567 TTGGGTCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
ATTAAATAAAA
Done.