Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007049.1 Hibiscus syriacus cultivar Beakdansim tig00018275_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: 69502
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6335 original size:15 final size:16
Alignment explanation
Indices: 6315--6349 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
6305 CTAACGAAAA
6315 TAAAATATT-AACTCT
1 TAAAATATTAAACTCT
6330 TAAAATATTCAAACTCT
1 TAAAATATT-AAACTCT
6347 TAA
1 TAA
6350 TTCTAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAATATTAAACTCT
Found at i:7695 original size:15 final size:15
Alignment explanation
Indices: 7675--7716 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
7665 TTAATTTTTA
7675 GTTTTTAATAATTAT
1 GTTTTTAATAATTAT
7690 GTTTTT-ATAATATAT
1 GTTTTTAATAAT-TAT
*
7705 ATTTTTAA-AATT
1 GTTTTTAATAATT
7717 TTATGACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.25
15 17 0.71
16 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
GTTTTTAATAATTAT
Found at i:12985 original size:19 final size:19
Alignment explanation
Indices: 12961--13010 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
12951 TAAAACTTGG
12961 TATTTTATTAAAATAAAAA
1 TATTTTATTAAAATAAAAA
*
12980 TATTTTATTAAAATACAAA
1 TATTTTATTAAAATAAAAA
12999 TATTTTATTAAA
1 TATTTTATTAAA
13011 TTATCCGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTTATTAAAATAAAAA
Found at i:18370 original size:2 final size:2
Alignment explanation
Indices: 18363--18435 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
18353 ATTATCCATA
18363 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
18405 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 A
18436 ATTAGGTATA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18882 original size:7 final size:7
Alignment explanation
Indices: 18865--18941 Score: 86
Period size: 7 Copynumber: 10.7 Consensus size: 7
18855 ATATTCAATT
18865 TTTTAATA
1 TTTT-ATA
18873 TTTTATA
1 TTTTATA
18880 TTTTATA
1 TTTTATA
18887 TTTTATA
1 TTTTATA
18894 TTTTAT-
1 TTTTATA
18900 TTTTAATA
1 TTTT-ATA
*
18908 TTTAATA
1 TTTTATA
18915 TTTTAATAA
1 TTTT-AT-A
18924 TTTTA-A
1 TTTTATA
*
18930 TTTTAAA
1 TTTTATA
18937 TTTTA
1 TTTTA
18942 AATTAAAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 11
0.83 0.03 0.15
Matches are distributed among these distances:
6 10 0.16
7 37 0.60
8 10 0.16
9 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TTTTATA
Found at i:18887 original size:35 final size:35
Alignment explanation
Indices: 18836--18919 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
18826 TAATTTTTTA
18836 TAATATTTTTAATATATATATATTCAATTTTTTAATATT
1 TAATA-TTTT-ATAT-TATATATTCAA-TTTTTAATATT
* * **
18875 TTATATTTTATATTTTATATTTTATTTTTAATATT
1 TAATATTTTATATTATATATTCAATTTTTAATATT
18910 TAATATTTTA
1 TAATATTTTA
18920 ATAATTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 20 0.50
36 8 0.20
37 4 0.10
38 4 0.10
39 4 0.10
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (35 bp):
TAATATTTTATATTATATATTCAATTTTTAATATT
Found at i:18966 original size:30 final size:29
Alignment explanation
Indices: 18893--18962 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
18883 TATATTTTAT
**
18893 ATTTTATTTTT-AATATTTAATATTTTAATA
1 ATTTTATTTTTAAAT-TTTAA-ATTAAAATA
*
18923 ATTTTAATTTTAAATTTTAAATTAAAATA
1 ATTTTATTTTTAAATTTTAAATTAAAATA
18952 ATTTTATTTTT
1 ATTTTATTTTT
18963 TAAAATTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.49
30 15 0.43
31 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTTATTTTTAAATTTTAAATTAAAATA
Found at i:39901 original size:11 final size:11
Alignment explanation
Indices: 39840--39920 Score: 75
Period size: 11 Copynumber: 7.6 Consensus size: 11
39830 TTAAAAATAT
39840 AATATTATTAA
1 AATATTATTAA
39851 AAT-TATATT-A
1 AATAT-TATTAA
* *
39861 TATGTATATT-A
1 AATAT-TATTAA
39872 AATATT-TT--
1 AATATTATTAA
39880 AATACTTATTAA
1 AATA-TTATTAA
39892 AATATTATTAA
1 AATATTATTAA
39903 AATATTATTAA
1 AATATTATTAA
39914 AATATTA
1 AATATTA
39921 ATCTAATATT
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 7 0.11
11 42 0.69
12 4 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (11 bp):
AATATTATTAA
Found at i:39919 original size:19 final size:18
Alignment explanation
Indices: 39897--39949 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
39887 ATTAAAATAT
*
39897 TATTAAAATATTATTAAAA
1 TATTAAAATAATATT-AAA
**
39916 TATTAATCTAATATTAAA
1 TATTAAAATAATATTAAA
39934 TATATAAAATAATATT
1 TAT-TAAAATAATATT
39950 TTTTTAAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TATTAAAATAATATTAAA
Found at i:39928 original size:22 final size:22
Alignment explanation
Indices: 39835--39931 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
39825 TTTATTTAAA
39835 AATATAATATTATT-AAA-ATT
1 AATATAATATTATTAAAATATT
* *
39855 -ATATTATATGTATATTAAATATT
1 AATATAATAT-TAT-TAAAATATT
39878 --T-TAATACTTATTAAAATATT
1 AATATAATA-TTATTAAAATATT
* *
39898 ATTAAAATATTATTAAAATATT
1 AATATAATATTATTAAAATATT
*
39920 AATCTAATATTA
1 AATATAATATTA
39932 AATATATAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
19 8 0.13
20 11 0.18
21 8 0.13
22 28 0.45
23 7 0.11
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (22 bp):
AATATAATATTATTAAAATATT
Found at i:40116 original size:42 final size:41
Alignment explanation
Indices: 40064--40151 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 41
40054 AATTACATTG
* * *
40064 GAAAATCAATTACAGCAATCAAACACTGAAAAATATTTTTC
1 GAAAACCAATTACAGCAATCAAACACCGAAAAACATTTTTC
* * *
40105 GTAAAACCAATTACATCTATCAAACGCCGAAAAACATTTTTC
1 G-AAAACCAATTACAGCAATCAAACACCGAAAAACATTTTTC
40147 GAAAA
1 GAAAA
40152 GAAATTTTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
41 5 0.12
42 35 0.88
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (41 bp):
GAAAACCAATTACAGCAATCAAACACCGAAAAACATTTTTC
Found at i:40338 original size:20 final size:20
Alignment explanation
Indices: 40313--40351 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40303 GATCAAGTCA
*
40313 ATCTTTGAATTTTTATGTCG
1 ATCTTTGAATCTTTATGTCG
*
40333 ATCTTTGAGTCTTTATGTC
1 ATCTTTGAATCTTTATGTC
40352 AAAGTTCCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.54
Consensus pattern (20 bp):
ATCTTTGAATCTTTATGTCG
Found at i:52209 original size:18 final size:18
Alignment explanation
Indices: 52186--52258 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
52176 ACTGAATATT
*
52186 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGAACCACTA
* *
52204 TGTCCCGAAGAACCATTGA
1 TGTCCCAAAGAACCACT-A
* **
52223 TTGTTCTGAAGAACCACTA
1 -TGTCCCAAAGAACCACTA
*
52242 TGTCCCAAAGGACCACT
1 TGTCCCAAAGAACCACT
52259 GATAATCCCT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 27 0.63
19 2 0.05
20 14 0.33
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (18 bp):
TGTCCCAAAGAACCACTA
Found at i:52901 original size:64 final size:64
Alignment explanation
Indices: 52829--52990 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 64
52819 ATCCCTTGAC
* * **
52829 GGTGCATCGATGCACAA-TCTATGCATCGGTACA-TAAATCCCATTCGATGTTTGTATTTTAAGG
1 GGTGCATCGATGCACAACT-TATGCATCGATACACT-AATCACATTCGATGTTTGTATTTTAAAA
52892 G
64 G
* * * *
52893 GGTGCATCGATGCACTACTTGTGCATCGATACACTAATGACATTCGATGTTTTTATTTTAAAAG
1 GGTGCATCGATGCACAACTTATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAAG
* *
52957 AGTGCATCGAT--ACACCTTATGTGCATCGATACAC
1 GGTGCATCGATGCACAACTTA--TGCATCGATACAC
52991 CTTGAACAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
62 5 0.06
64 75 0.91
65 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
GGTGCATCGATGCACAACTTATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAAG
Found at i:62606 original size:26 final size:26
Alignment explanation
Indices: 62570--62667 Score: 178
Period size: 26 Copynumber: 3.7 Consensus size: 26
62560 ATTTCAAGAA
62570 AAAAAACCTTTTTTCATTAAATCAAG
1 AAAAAACCTTTTTTCATTAAATCAAG
62596 AAAAAACCTTTTTTCATTAAATCAAG
1 AAAAAACCTTTTTTCATTAAATCAAG
62622 AAAAAACCTTTTTTCATTAAATCAAG
1 AAAAAACCTTTTTTCATTAAATCAAG
*
62648 AAAAAACCTTATTTTTATTA
1 AAAAAACCTT-TTTTCATTA
62668 GAAGAGACTG
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
26 62 0.89
27 8 0.11
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (26 bp):
AAAAAACCTTTTTTCATTAAATCAAG
Found at i:64218 original size:2 final size:2
Alignment explanation
Indices: 64213--64254 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
64203 GTTATTTCCT
*
64213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64255 ATAATAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:67348 original size:30 final size:31
Alignment explanation
Indices: 67303--67380 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 31
67293 GGTGACCACA
67303 TTTGTATATTTTTCACAATGTCAAC-CTTTTT
1 TTTGTATA-TTTTCACAATGTCAACTCTTTTT
*
67334 TTTGTATATTTTCACAATGTCAACTTTTTTTT
1 TTTGTATATTTTCACAATGTCAAC-TCTTTTT
*
67366 TTTGTATATATTCAC
1 TTTGTATATTTTCAC
67381 TTTCAAACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 16 0.37
31 8 0.19
32 19 0.44
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.56
Consensus pattern (31 bp):
TTTGTATATTTTCACAATGTCAACTCTTTTT
Done.