Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005487.1 Hibiscus syriacus cultivar Beakdansim tig00012611_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: 79521
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1961 original size:14 final size:14
Alignment explanation
Indices: 1883--1976 Score: 57
Period size: 14 Copynumber: 6.6 Consensus size: 14
1873 TGAAAATGCT
*
1883 AAATGCAAAAAATAA
1 AAATGCAAAAAAT-G
***
1898 AAATGCAAACTTTG
1 AAATGCAAAAAATG
*
1912 AAATGCAAAAAA-C
1 AAATGCAAAAAATG
** *
1925 AAACACAAAAGTATG
1 AAATGCAAAA-AATG
*
1940 -AATACAAAAAATG
1 AAATGCAAAAAATG
*
1953 AAATGCAAAAATGTG
1 AAATGCAAAAA-ATG
1968 AAATGCAAA
1 AAATGCAAA
1977 TGCATGCATG
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
13 11 0.19
14 27 0.46
15 21 0.36
ACGTcount: A:0.62, C:0.11, G:0.12, T:0.16
Consensus pattern (14 bp):
AAATGCAAAAAATG
Found at i:8507 original size:39 final size:41
Alignment explanation
Indices: 8412--8519 Score: 112
Period size: 47 Copynumber: 2.5 Consensus size: 41
8402 GAATTACTCT
* *
8412 TATTTTAATAACTTAAATTTATTTTATTAATTTTTTATGACA
1 TATTTTAATAACTCAAATTTATTTTATT-ATATTTTATGACA
*
8454 TGGCATCTATTAATAACTCAAATTTATTTTATT-TATTTTATTA-A
1 T---AT-T-TTAATAACTCAAATTTATTTTATTATATTTTATGACA
8498 TATTTTAATAACTCAAAGTTTA
1 TATTTTAATAACTCAAA-TTTA
8520 AACTACTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
39 13 0.23
40 5 0.09
41 2 0.04
42 1 0.02
44 2 0.04
45 10 0.18
46 1 0.02
47 23 0.40
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (41 bp):
TATTTTAATAACTCAAATTTATTTTATTATATTTTATGACA
Found at i:9515 original size:24 final size:24
Alignment explanation
Indices: 9470--9515 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
9460 ATCAAAAGTT
*
9470 TAAAATTATTTTATATTATAAATA
1 TAAAATTATTTAATATTATAAATA
9494 TAAAATTATTTAAATATT-TAAA
1 TAAAATTATTT-AATATTATAAA
9516 AAATTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAAATTATTTAATATTATAAATA
Found at i:9559 original size:21 final size:21
Alignment explanation
Indices: 9525--9584 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
9515 AAAATTAATT
*
9525 ATAAATGTACTAAAAATAAAAA
1 ATAAAT-TATTAAAAATAAAAA
* *
9547 ATAAATTATTAAAAAATTAAAT
1 ATAAATTATT-AAAAATAAAAA
*
9569 ATACA-TATTAAAAATA
1 ATAAATTATTAAAAATA
9585 TTAAAACTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 6 0.19
21 7 0.22
22 19 0.59
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (21 bp):
ATAAATTATTAAAAATAAAAA
Found at i:18806 original size:20 final size:21
Alignment explanation
Indices: 18777--18818 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
18767 AATTGCACCA
18777 CCATTCCATTTT-CACAACAT
1 CCATTCCATTTTCCACAACAT
*
18797 CCATTTCATTTTGCCACAACAT
1 CCATTCCATTTT-CCACAACAT
18819 TCTCATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.36
Consensus pattern (21 bp):
CCATTCCATTTTCCACAACAT
Found at i:20500 original size:23 final size:23
Alignment explanation
Indices: 20470--20515 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
20460 CAAGGAGTCC
20470 TACTTCAAAGCCATAGTTCGTCG
1 TACTTCAAAGCCATAGTTCGTCG
20493 TACTTCAAAGCCATAGTTCGTCG
1 TACTTCAAAGCCATAGTTCGTCG
20516 CTAAGGGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (23 bp):
TACTTCAAAGCCATAGTTCGTCG
Found at i:32202 original size:21 final size:21
Alignment explanation
Indices: 32176--32215 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32166 CCCCCTTTGA
*
32176 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
32197 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
32216 TGGGGTTCTG
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:35722 original size:18 final size:18
Alignment explanation
Indices: 35695--35729 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35685 AGTCCCTAGC
35695 CTGCGAAACCTGAAGAGT
1 CTGCGAAACCTGAAGAGT
*
35713 CTGCGGAACCTGAAGAG
1 CTGCGAAACCTGAAGAG
35730 CCCGATAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.14
Consensus pattern (18 bp):
CTGCGAAACCTGAAGAGT
Found at i:36543 original size:12 final size:11
Alignment explanation
Indices: 36527--36566 Score: 53
Period size: 11 Copynumber: 3.4 Consensus size: 11
36517 AAAACCCACT
36527 AAAAAATGAAA
1 AAAAAATGAAA
36538 ACAAAAATTTGAAA
1 A-AAAAA--TGAAA
36552 AAAAAATGAAA
1 AAAAAATGAAA
36563 AAAA
1 AAAA
36567 TGAAGTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.38
12 5 0.19
13 5 0.19
14 6 0.23
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:38695 original size:20 final size:22
Alignment explanation
Indices: 38667--38707 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38657 ATTGCACCAC
38667 CATTCCA-TTT-CCACAACATA
1 CATTCCATTTTGCCACAACATA
*
38687 CATTTCATTTTGCCACAACAT
1 CATTCCATTTTGCCACAACAT
38708 TCTCATTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (22 bp):
CATTCCATTTTGCCACAACATA
Found at i:41402 original size:21 final size:20
Alignment explanation
Indices: 41376--41414 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
41366 ATCTGATTAA
*
41376 AAATATTTCTAAATCATATTC
1 AAATATTTCGAAA-CATATTC
41397 AAATATTTCGAAACATAT
1 AAATATTTCGAAACATAT
41415 ATTTTGGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATATTTCGAAACATATTC
Found at i:42377 original size:20 final size:22
Alignment explanation
Indices: 42348--42389 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42338 AATTGCACCA
42348 CCATTCCA-TTT-CCACAACAT
1 CCATTCCATTTTGCCACAACAT
*
42368 CCATTTCATTTTGCCACAACAT
1 CCATTCCATTTTGCCACAACAT
42390 TCTCATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 9 0.47
ACGTcount: A:0.29, C:0.36, G:0.02, T:0.33
Consensus pattern (22 bp):
CCATTCCATTTTGCCACAACAT
Found at i:46821 original size:24 final size:24
Alignment explanation
Indices: 46791--46836 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
46781 ACGGTTCAGT
*
46791 GGTTCTGGCCGGTTCACTAGTAGC
1 GGTTCTGGCAGGTTCACTAGTAGC
*
46815 GGTTCTGGCATGTTCACTAGTA
1 GGTTCTGGCAGGTTCACTAGTA
46837 TCGATTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.22, G:0.30, T:0.33
Consensus pattern (24 bp):
GGTTCTGGCAGGTTCACTAGTAGC
Found at i:48993 original size:31 final size:30
Alignment explanation
Indices: 48954--49045 Score: 114
Period size: 31 Copynumber: 3.1 Consensus size: 30
48944 GTCAGATTTA
48954 TAAG-TTAAATTAATATTTTATTTAAAGTT
1 TAAGATTAAATTAATATTTTATTTAAAGTT
* *
48983 TAATATTTAAATTAATATTTTATTTAAAGTC
1 TAAGA-TTAAATTAATATTTTATTTAAAGTT
* * * *
49014 TAAGATCAAATTAATACTTTATATAAATTT
1 TAAGATTAAATTAATATTTTATTTAAAGTT
49044 TA
1 TA
49046 GGGGTTAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 3 0.06
30 22 0.42
31 28 0.53
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (30 bp):
TAAGATTAAATTAATATTTTATTTAAAGTT
Found at i:55025 original size:15 final size:15
Alignment explanation
Indices: 55005--55041 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
54995 GGAGTTGGGT
55005 GTTCAGCAAGGTGGA
1 GTTCAGCAAGGTGGA
55020 GTTCAGCAAGGTGGA
1 GTTCAGCAAGGTGGA
55035 GTTCAGC
1 GTTCAGC
55042 TGCTTTGCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (15 bp):
GTTCAGCAAGGTGGA
Found at i:56200 original size:25 final size:29
Alignment explanation
Indices: 56160--56211 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
56150 GATATATATC
56160 AAAATATTTATCAATAT-ATC-CCATGAG
1 AAAATATTTATCAATATAATCACCATGAG
56187 AAAAT-TTTAT-AATATAATCACCATG
1 AAAATATTTATCAATATAATCACCATG
56212 GTACAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.22
26 8 0.35
27 10 0.43
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (29 bp):
AAAATATTTATCAATATAATCACCATGAG
Found at i:58350 original size:14 final size:15
Alignment explanation
Indices: 58333--58369 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
58323 TAAAAAAATA
58333 TTTTATTTTTTAT-T
1 TTTTATTTTTTATGT
*
58347 TTTTATGTTTTATGT
1 TTTTATTTTTTATGT
58362 TTTT-TTTT
1 TTTTATTTT
58370 GGCAGAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (15 bp):
TTTTATTTTTTATGT
Found at i:61109 original size:23 final size:23
Alignment explanation
Indices: 61081--61134 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
61071 AACTTTTTTA
61081 ATATAAAGTACAATATTTTATTT
1 ATATAAAGTACAATATTTTATTT
* *
61104 CTATAAAGTACACTATTTTATTT
1 ATATAAAGTACAATATTTTATTT
61127 ATATAAAG
1 ATATAAAG
61135 ATTGCGAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (23 bp):
ATATAAAGTACAATATTTTATTT
Found at i:66143 original size:31 final size:31
Alignment explanation
Indices: 66099--66182 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
66089 TAACATGATT
* *
66099 TGTCACCATTTTAAATATGTAACATGTGTCA
1 TGTCACCACTTTAAATATGTAACACGTGTCA
* * ** *
66130 TGTCATCACTTTAAACACATAATACGTGTCA
1 TGTCACCACTTTAAATATGTAACACGTGTCA
* *
66161 TGTTACCACTTTGAATATGTAA
1 TGTCACCACTTTAAATATGTAA
66183 TGTATTGCAT
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (31 bp):
TGTCACCACTTTAAATATGTAACACGTGTCA
Found at i:70686 original size:28 final size:28
Alignment explanation
Indices: 70646--70701 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
70636 TTGATTGTTT
70646 GATTGTTTTCGGTTCGAATCGATATCGG
1 GATTGTTTTCGGTTCGAATCGATATCGG
70674 GATTGTTTTCGGTTCGAATCGATATCGG
1 GATTGTTTTCGGTTCGAATCGATATCGG
70702 ATTAATTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.39
Consensus pattern (28 bp):
GATTGTTTTCGGTTCGAATCGATATCGG
Found at i:74617 original size:112 final size:112
Alignment explanation
Indices: 74389--74595 Score: 280
Period size: 111 Copynumber: 1.9 Consensus size: 112
74379 ACATGAAAAT
74389 TAAAAATTCAATTAAAAGACTCAACAAAAAATAAATACGAATAAATATAATTGTTAGAGAATAAA
1 TAAAAATTCAATTAAAAGACTCAACAAAAAATAAATACGAATAAATATAATTGTTAGAGAATAAA
* * * * *
74454 TTATAAAAAATGATTAAATTATATATATATATATATATATATAAAGT
66 TCATAAAAAATAATTAAATTATATAAATATATATAGATATATAAAGC
* * *
74501 TAAAAATTCAA-TCAAAGACTCGAAC-AAAAATAAATACGAATAAATCTGATTGTATCAGAGAAT
1 TAAAAATTCAATTAAAAGACTC-AACAAAAAATAAATACGAATAAATATAATTGT-T-AGAGAAT
74564 AAATCAT-AAAAATAATTAAATTAT-TAAA-ATAT
63 AAATCATAAAAAATAATTAAATTATATAAATATAT
74596 CATTGAGATT
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
110 4 0.05
111 38 0.44
112 31 0.36
113 13 0.15
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (112 bp):
TAAAAATTCAATTAAAAGACTCAACAAAAAATAAATACGAATAAATATAATTGTTAGAGAATAAA
TCATAAAAAATAATTAAATTATATAAATATATATAGATATATAAAGC
Done.