Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002518.1 Hibiscus syriacus cultivar Beakdansim tig00005121_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: 50741
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:3806 original size:32 final size:32
Alignment explanation
Indices: 3744--3805 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
3734 CTGGGTAAAT
3744 TTTGTGTTTAATACCTAAACTATTAGTTTTTA
1 TTTGTGTTTAATACCTAAACTATTAGTTTTTA
* * * *
3776 TTTGT-TTTAGTACTTAAACTTTTAATTTTT
1 TTTGTGTTTAATACCTAAACTATTAGTTTTT
3806 TCAAAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (32 bp):
TTTGTGTTTAATACCTAAACTATTAGTTTTTA
Found at i:7767 original size:28 final size:28
Alignment explanation
Indices: 7727--7804 Score: 129
Period size: 28 Copynumber: 2.8 Consensus size: 28
7717 AACCGAGAAT
*
7727 CGTTGTCTAGTCCGATTCAATCGGGAAC
1 CGTTGTCTAGTCCGATTCAATCAGGAAC
7755 CGTTGTCTAGTCCGATTCAATCAGGAAC
1 CGTTGTCTAGTCCGATTCAATCAGGAAC
* *
7783 TGTTGTCTAGTCCGGTTCAATC
1 CGTTGTCTAGTCCGATTCAATC
7805 TAAACCGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CGTTGTCTAGTCCGATTCAATCAGGAAC
Found at i:15404 original size:19 final size:19
Alignment explanation
Indices: 15380--15434 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
15370 ATGTACTACA
15380 GTACTAATACGATTGCTGT
1 GTACTAATACGATTGCTGT
*
15399 GTACTAATAAGATTGCTGT
1 GTACTAATACGATTGCTGT
15418 GTACTAATACGATTGCT
1 GTACTAATACGATTGCT
15435 TTGAACTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (19 bp):
GTACTAATACGATTGCTGT
Found at i:36640 original size:2 final size:2
Alignment explanation
Indices: 36633--36659 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36623 TGTATGATTG
36633 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 T
36660 TCCGTGATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40081 original size:14 final size:14
Alignment explanation
Indices: 40045--40083 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
40035 TGAAGCACAT
40045 CTTCTATTA-TTCC
1 CTTCTATTATTTCC
*
40058 CTTTCAATTATTTCC
1 C-TTCTATTATTTCC
40073 CTTCTATTATT
1 CTTCTATTATT
40084 ACCCAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 1 0.05
14 16 0.73
15 5 0.23
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (14 bp):
CTTCTATTATTTCC
Found at i:44037 original size:18 final size:18
Alignment explanation
Indices: 44014--44096 Score: 66
Period size: 18 Copynumber: 4.7 Consensus size: 18
44004 ATATATATAT
44014 ATATATAAATTAAATTAA
1 ATATATAAATTAAATTAA
* *
44032 ATATATAAAATTATA-TAT
1 ATATAT-AAATTAAATTAA
*
44050 ATAT-TAATTTAAATTAA
1 ATATATAAATTAAATTAA
* * *
44067 AT-TATTAATATATATTAT
1 ATATATAAAT-TAAATTAA
44085 ATATAT-AATTAA
1 ATATATAAATTAA
44097 TTATTTTATA
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
16 7 0.14
17 10 0.20
18 23 0.46
19 10 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATATAAATTAAATTAA
Found at i:44063 original size:40 final size:38
Alignment explanation
Indices: 44004--44098 Score: 119
Period size: 35 Copynumber: 2.6 Consensus size: 38
43994 GTATCGAGCC
*
44004 ATATA-TATATATATA-TAAATTAAATTAAA-TAT-AT
1 ATATATTATATATATATTAATTTAAATTAAATTATAAT
*
44038 A-AAATTATATATATATTAATTTAAATTAAATTATTAAT
1 ATATATTATATATATATTAATTTAAATTAAATTA-TAAT
44076 ATATATTATATATATAATTAATT
1 ATATATTATATATAT-ATTAATT
44099 ATTTTATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
33 2 0.04
34 11 0.22
35 13 0.25
36 2 0.04
37 1 0.02
38 3 0.06
39 12 0.24
40 7 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (38 bp):
ATATATTATATATATATTAATTTAAATTAAATTATAAT
Found at i:44069 original size:26 final size:28
Alignment explanation
Indices: 44039--44108 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 28
44029 TAAATATATA
*
44039 AAATTATATATATATTA-ATTTA-AATT
1 AAATTATATATATATTATATATATAATT
44065 AAATTATTAATATATATTATATATATAATT
1 AAATTA-T-ATATATATTATATATATAATT
*
44095 -AATTAT-TTTATATT
1 AAATTATATATATATT
44109 TATCGGGCCG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 13 0.34
27 1 0.03
28 11 0.29
29 9 0.24
30 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAATTATATATATATTATATATATAATT
Found at i:45180 original size:56 final size:58
Alignment explanation
Indices: 45075--45189 Score: 128
Period size: 56 Copynumber: 2.0 Consensus size: 58
45065 AGTTTAAGGG
* * * * * **
45075 TGAAATTGGAATATTCAAGAGTTTAATGACTAATTTATAATGAGTATCAT-TTGAAGA
1 TGAAATTAGAATACTCAAGAGTTTAAAGACTAATTTAAAATAAAAATCATGTTGAAGA
45132 TGAAATTAGAATACTCAA-AGTTTAAAGAAC-AATTTAAAATAAAAATCATGGTTGAAGA
1 TGAAATTAGAATACTCAAGAGTTTAAAG-ACTAATTTAAAATAAAAATCAT-GTTGAAGA
45190 CATAGGGTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
56 23 0.48
57 18 0.38
58 7 0.15
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (58 bp):
TGAAATTAGAATACTCAAGAGTTTAAAGACTAATTTAAAATAAAAATCATGTTGAAGA
Found at i:46386 original size:16 final size:16
Alignment explanation
Indices: 46365--46420 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
46355 ACATACTTGT
46365 GAAAATAAAAATAAAA
1 GAAAATAAAAATAAAA
* *
46381 GAAAATAGAAATACAA
1 GAAAATAAAAATAAAA
* *
46397 TATAA-AAAAAT-AAA
1 GAAAATAAAAATAAAA
46411 -AAAATAAAAA
1 GAAAATAAAAA
46421 ATTTATACGC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 3 0.09
14 7 0.22
15 5 0.16
16 17 0.53
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (16 bp):
GAAAATAAAAATAAAA
Found at i:46835 original size:30 final size:30
Alignment explanation
Indices: 46801--46868 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
46791 TTTAATTCAT
*
46801 AATGATTAAT-CGCTGAATGATT-AAATATTG
1 AATGATTAATAC-C-GAATGATTCAAATACTG
46831 AATGATTAATACCGAATGATTCAAATACTG
1 AATGATTAATACCGAATGATTCAAATACTG
46861 AATGATTA
1 AATGATTA
46869 GATGCTCTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
29 8 0.23
30 26 0.74
31 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (30 bp):
AATGATTAATACCGAATGATTCAAATACTG
Found at i:46863 original size:16 final size:15
Alignment explanation
Indices: 46813--46868 Score: 78
Period size: 16 Copynumber: 3.7 Consensus size: 15
46803 TGATTAATCG
46813 CTGAATGATTAAATA
1 CTGAATGATTAAATA
*
46828 TTGAATGATT-AATA
1 CTGAATGATTAAATA
*
46842 CCGAATGATTCAAATA
1 CTGAATGATT-AAATA
46858 CTGAATGATTA
1 CTGAATGATTA
46869 GATGCTCTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
14 12 0.34
15 10 0.29
16 13 0.37
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (15 bp):
CTGAATGATTAAATA
Done.