Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005244.1 Hibiscus syriacus cultivar Beakdansim tig00011867_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: 58225
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:6464 original size:17 final size:18
Alignment explanation
Indices: 6441--6480 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
6431 ATTTGGAAGG
6441 CTCTTCATC-TTTTCTTTT
1 CTCTTCA-CATTTTCTTTT
6459 -TCTTCACATTTTCTTTT
1 CTCTTCACATTTTCTTTT
6476 CTCTT
1 CTCTT
6481 TTCTTGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.05
17 15 0.75
18 4 0.20
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (18 bp):
CTCTTCACATTTTCTTTT
Found at i:7408 original size:20 final size:23
Alignment explanation
Indices: 7358--7416 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
7348 GATACTTGAG
*
7358 GAAGTATCGATACCCTAGGAGAT
1 GAAGTATCGATACCCTAAGAGAT
7381 GAAGTATCGATACCC-AAGA-AT
1 GAAGTATCGATACCCTAAGAGAT
*
7402 G-AGTATCGGTACCCT
1 GAAGTATCGATACCCT
7417 CTTGAATCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.36
21 3 0.09
22 3 0.09
23 15 0.45
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (23 bp):
GAAGTATCGATACCCTAAGAGAT
Found at i:8566 original size:20 final size:20
Alignment explanation
Indices: 8539--8588 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
8529 CAAAGTGTAT
*
8539 CCATGCACTCTGCAATGCAT
1 CCATGCACTCTGCAATGCAC
* * *
8559 CGATGCACCCTGTAATGCAC
1 CCATGCACTCTGCAATGCAC
8579 CCATGCACTC
1 CCATGCACTC
8589 AAACACTGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (20 bp):
CCATGCACTCTGCAATGCAC
Found at i:8632 original size:20 final size:20
Alignment explanation
Indices: 8607--8644 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
8597 AATGTAATTA
*
8607 GTGCATCGATGTACCCTGCT
1 GTGCATCGATGCACCCTGCT
8627 GTGCATCGATGCACCCTG
1 GTGCATCGATGCACCCTG
8645 GCTGCAACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.32, G:0.26, T:0.26
Consensus pattern (20 bp):
GTGCATCGATGCACCCTGCT
Found at i:11068 original size:21 final size:19
Alignment explanation
Indices: 11027--11084 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
11017 CAACAATTGG
11027 TAACAATTGATAT-TTTTT
1 TAACAATTGATATATTTTT
11045 TAACAATTGATATCATTTTGT
1 TAACAATTGATAT-ATTTT-T
*
11066 TAACAATTGGTATATTTTT
1 TAACAATTGATATATTTTT
11085 CATTAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 13 0.36
19 1 0.03
20 9 0.25
21 13 0.36
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (19 bp):
TAACAATTGATATATTTTT
Found at i:11337 original size:20 final size:20
Alignment explanation
Indices: 11309--11349 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
11299 AGGGTGTCAA
*
11309 AGTGTATCCATGCATTGTGC
1 AGTGCATCCATGCATTGTGC
11329 AGTGCATCCATGCATTGTGC
1 AGTGCATCCATGCATTGTGC
11349 A
1 A
11350 TCGATTCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTGCATCCATGCATTGTGC
Found at i:11424 original size:20 final size:20
Alignment explanation
Indices: 11399--11436 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11389 AATGCAATTA
*
11399 GTGCATCGATGCACCCTGTT
1 GTGCATCCATGCACCCTGTT
11419 GTGCATCCATGCACCCTG
1 GTGCATCCATGCACCCTG
11437 GCTGCAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.34, G:0.24, T:0.26
Consensus pattern (20 bp):
GTGCATCCATGCACCCTGTT
Found at i:11562 original size:20 final size:22
Alignment explanation
Indices: 11524--11563 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
11514 TATTGCAGGA
11524 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
11546 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
11564 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:12358 original size:2 final size:2
Alignment explanation
Indices: 12351--12378 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12341 ATTTCTAATT
12351 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12379 ATAAAATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14893 original size:15 final size:15
Alignment explanation
Indices: 14867--14899 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
14857 ATATTATGTT
14867 TATTATGATTACGAA
1 TATTATGATTACGAA
14882 TATTATGATTACGAA
1 TATTATGATTACGAA
14897 TAT
1 TAT
14900 AATAACGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (15 bp):
TATTATGATTACGAA
Found at i:15869 original size:33 final size:33
Alignment explanation
Indices: 15832--15899 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
15822 GAAAAACTTG
15832 AAACTTTAAGTATTAAAACAGACAAAAATTGAT
1 AAACTTTAAGTATTAAAACAGACAAAAATTGAT
15865 AAACTTTAAGTATTAAAACAGACAAAAATTGAT
1 AAACTTTAAGTATTAAAACAGACAAAAATTGAT
15898 AA
1 AA
15900 TATAAGTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (33 bp):
AAACTTTAAGTATTAAAACAGACAAAAATTGAT
Found at i:18160 original size:19 final size:19
Alignment explanation
Indices: 18133--18184 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
18123 GCTAATTTGG
*
18133 GTACTGATACCCCCATACT
1 GTACCGATACCCCCATACT
* *
18152 GTACCGATACCCCTATAGT
1 GTACCGATACCCCCATACT
18171 GTACCGATACCCCC
1 GTACCGATACCCCC
18185 TCAAGGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.38, G:0.13, T:0.23
Consensus pattern (19 bp):
GTACCGATACCCCCATACT
Found at i:19370 original size:20 final size:20
Alignment explanation
Indices: 19342--19390 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
19332 TACTGTTCAT
* * *
19342 TACTGTTCACATAGTATCGA
1 TACTATTCACACAATATCGA
*
19362 TACTATTCATACAATATCGA
1 TACTATTCACACAATATCGA
*
19382 TATTATTCA
1 TACTATTCA
19391 TAAAAACATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (20 bp):
TACTATTCACACAATATCGA
Found at i:36853 original size:11 final size:11
Alignment explanation
Indices: 36837--36878 Score: 66
Period size: 11 Copynumber: 3.6 Consensus size: 11
36827 GTCCTAAGTT
36837 GAAAAAAAAAA
1 GAAAAAAAAAA
36848 GAAAAAAAAAA
1 GAAAAAAAAAA
36859 GAGAGAAAAAAAA
1 GA-A-AAAAAAAA
36872 GAAAAAA
1 GAAAAAA
36879 GGAAAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 17 0.59
12 2 0.07
13 10 0.34
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:36876 original size:18 final size:17
Alignment explanation
Indices: 36849--36903 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
36839 AAAAAAAAAG
36849 AAAAAAAAAAGAGAGAA
1 AAAAAAAAAAGAGAGAA
*
36866 AAAAAAGAAAAAAG-GAA
1 AAAAAA-AAAAGAGAGAA
*
36883 AAAGAACAAAAGAAGAGAA
1 AAA-AAAAAAAG-AGAGAA
36902 AA
1 AA
36904 TAAGACGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAGAGAA
Found at i:37831 original size:105 final size:105
Alignment explanation
Indices: 37649--38734 Score: 1729
Period size: 105 Copynumber: 10.4 Consensus size: 105
37639 AGGTTTTACC
37649 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
37714 ACGAAAGGACCGCTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
37754 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
37819 ACGAAGGGACCGCTGGTT-TCCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGT-CAACAAACATTTCTCAATTT
37859 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
37924 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
37964 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
38029 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
38069 CAGAGCCAATTTCAACTTCACAATGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
38134 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
38174 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
38239 ACGAAGGGACCACTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
38279 CATAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
38344 ACGAATGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* ***
38384 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** *
38449 ACGAAGGGACCGCTGACTGT---C-AAC--TGCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
38483 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
38548 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * * * ** * * *
38589 CGGATCCAATTTCAACTTCACAGCGAAGGACATTAGACTTGAGACAGCACAAGCTCAACTTCAC-
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * ** * * *
38653 AGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTC
66 A-CGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * *
38695 CAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
38735 GGAACAATAC
Statistics
Matches: 915, Mismatches: 56, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
99 88 0.10
101 3 0.00
102 1 0.00
103 3 0.00
104 1 0.00
105 689 0.75
106 130 0.14
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:40098 original size:19 final size:20
Alignment explanation
Indices: 40059--40101 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
40049 GTTTTTGAGC
*
40059 ATCGGTACTGTTCACACAGT
1 ATCGGTACTGATCACACAGT
*
40079 ATCGGTACT-ATCATACAGT
1 ATCGGTACTGATCACACAGT
40098 ATCG
1 ATCG
40102 ATATTATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (20 bp):
ATCGGTACTGATCACACAGT
Found at i:41960 original size:53 final size:53
Alignment explanation
Indices: 41799--41948 Score: 257
Period size: 53 Copynumber: 2.8 Consensus size: 53
41789 TAATGTAACA
*
41799 AAATGGTAATTCACAACCTCATTATGAATACCATAGG-TGCACACATAGTGTCG
1 AAATGGTAATTCACAAACTCATTATGAATACCAT-GGATGCACACATAGTGTCG
* *
41852 AAATGGTAATTCAAAAACTCATTATGAATACCATGGATACACACATAGTGTCG
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTCG
41905 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACAC
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACAC
41949 CTAGAGCCGA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
52 2 0.02
53 89 0.98
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (53 bp):
AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTCG
Found at i:49856 original size:53 final size:53
Alignment explanation
Indices: 49773--49924 Score: 241
Period size: 53 Copynumber: 2.9 Consensus size: 53
49763 TAACGGAATA
* * * * * *
49773 GTAATTCACAACCTCATTATTAATATCATGGGTGCACACATAGTGTCGAAATG
1 GTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAATG
*
49826 GTAATTCACAAACTCATTATGAATACCATGGATGCACATATAGTGCCAAAATG
1 GTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAATG
49879 GTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGC
1 GTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGC
49925 TGAAAGTACA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 91 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (53 bp):
GTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAATG
Found at i:51210 original size:18 final size:18
Alignment explanation
Indices: 51187--51227 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
51177 CAATTTCATA
51187 AAACCATAATGTGAACAC
1 AAACCATAATGTGAACAC
51205 AAACCATAATGTGAACAC
1 AAACCATAATGTGAACAC
51223 AAACC
1 AAACC
51228 CTAAAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.24, G:0.10, T:0.15
Consensus pattern (18 bp):
AAACCATAATGTGAACAC
Found at i:57522 original size:16 final size:17
Alignment explanation
Indices: 57501--57534 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
57491 GTACACAACC
57501 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
57517 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
57534 T
1 T
57535 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:57843 original size:2 final size:2
Alignment explanation
Indices: 57836--57891 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
57826 CAATAAGTAC
57836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- 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
57876 AT AT AT AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT
57892 GTTTGGATGC
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 4 0.08
2 46 0.92
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58040 original size:12 final size:12
Alignment explanation
Indices: 58023--58048 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58013 CGTAGGTTAA
58023 AGAAGCGAGAAG
1 AGAAGCGAGAAG
58035 AGAAGCGAGAAG
1 AGAAGCGAGAAG
58047 AG
1 AG
58049 TAAGACAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (12 bp):
AGAAGCGAGAAG
Done.