Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002889.1 Hibiscus syriacus cultivar Beakdansim tig00005971_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: 64328
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:9578 original size:21 final size:20
Alignment explanation
Indices: 9537--9589 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
9527 GGCTTCGGAT
* *
9537 TATAAGAAATTATTTTTAAAA
1 TATAA-AAATGATTTTCAAAA
9558 TATAAAAATGATGTTTCAAAA
1 TATAAAAATGAT-TTTCAAAA
9579 T-TGAAAAATGA
1 TAT-AAAAATGA
9590 AAATAAACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (20 bp):
TATAAAAATGATTTTCAAAA
Found at i:13423 original size:21 final size:21
Alignment explanation
Indices: 13391--13491 Score: 130
Period size: 21 Copynumber: 4.7 Consensus size: 21
13381 TTAGTGCGAA
* *
13391 GGGAACCAATTCCCCTTGAAG
1 GGGAACCGATTCCCCCTGAAG
**
13412 GGGAATTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TGAAG
*
13435 GGGAACCGATTCCCCCTGTAG
1 GGGAACCGATTCCCCCTGAAG
*
13456 GGGAACCGATTCCCCCTGTAG
1 GGGAACCGATTCCCCCTGAAG
13477 GGGAACCGATTCCCC
1 GGGAACCGATTCCCC
13492 ATGGGGTTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
21 52 0.73
23 19 0.27
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.21
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTGAAG
Found at i:13458 original size:44 final size:42
Alignment explanation
Indices: 13391--13491 Score: 130
Period size: 44 Copynumber: 2.4 Consensus size: 42
13381 TTAGTGCGAA
* * **
13391 GGGAACCAATTCCCCTTGAAGGGGAATTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTGAAGGGGAACCGATTCCCCC--TGAAG
* *
13435 GGGAACCGATTCCCCCTGTAGGGGAACCGATTCCCCCTGTAG
1 GGGAACCGATTCCCCCTGAAGGGGAACCGATTCCCCCTGAAG
13477 GGGAACCGATTCCCC
1 GGGAACCGATTCCCC
13492 ATGGGGTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 19 0.37
44 32 0.63
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.21
Consensus pattern (42 bp):
GGGAACCGATTCCCCCTGAAGGGGAACCGATTCCCCCTGAAG
Found at i:28070 original size:39 final size:40
Alignment explanation
Indices: 28018--28127 Score: 102
Period size: 43 Copynumber: 2.6 Consensus size: 40
28008 TAGGGTTGAG
28018 TTTT-TTTTGTATTAAAATAAT-ATTA-TTAA-TTAATAATA
1 TTTTATTTT-TATTAAAATAATAATTAGTTAACTT-ATAATA
* *
28056 TTTTATTATTTATTAAAAATAATAGATTAGTTAACTTATTATT
1 TTTTATT-TTTATT-AAAATAATA-ATTAGTTAACTTATAATA
28099 TTTTATTTTTATTAATAAATTAATAATTA
1 TTTTATTTTTATT-A-AAA-TAATAATTA
28128 TTATCTAGAT
Statistics
Matches: 61, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
38 4 0.07
39 6 0.10
40 10 0.16
42 12 0.20
43 22 0.36
44 7 0.11
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (40 bp):
TTTTATTTTTATTAAAATAATAATTAGTTAACTTATAATA
Found at i:28084 original size:21 final size:19
Alignment explanation
Indices: 28027--28079 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
28017 GTTTTTTTTG
28027 TATT-AAAATAATATTATT
1 TATTAAAAATAATATTATT
* **
28045 AATTAATAATATTTTATTATT
1 TATTAA-AA-ATAATATTATT
28066 TATTAAAAATAATA
1 TATTAAAAATAATA
28080 GATTAGTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
18 3 0.12
19 5 0.19
20 4 0.15
21 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTAAAAATAATATTATT
Found at i:28145 original size:43 final size:43
Alignment explanation
Indices: 28056--28147 Score: 109
Period size: 43 Copynumber: 2.1 Consensus size: 43
28046 ATTAATAATA
*
28056 TTTTATTATTTATTAAAAATAATAGATTAGTTAACTTATTATT
1 TTTTATTATTTATTAAAAATAATAGATTAGTTAACTGATTATT
*
28099 TTTTATT-TTTATTAATAAATTAATA-ATTA-TTATCTAGATTTATT
1 TTTTATTATTTATTAA-AAA-TAATAGATTAGTTAACT-GA-TTATT
28143 TTTTA
1 TTTTA
28148 AATGAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
42 13 0.30
43 15 0.35
44 15 0.35
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (43 bp):
TTTTATTATTTATTAAAAATAATAGATTAGTTAACTGATTATT
Found at i:42060 original size:2 final size:2
Alignment explanation
Indices: 42053--42158 Score: 212
Period size: 2 Copynumber: 53.0 Consensus size: 2
42043 ACATATTTCA
42053 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
42095 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
42137 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
42159 GTTAGATTTG
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 104 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45317 original size:5 final size:5
Alignment explanation
Indices: 45307--45374 Score: 59
Period size: 5 Copynumber: 13.8 Consensus size: 5
45297 GGGTCTGATT
* * * * *
45307 TTTTA TTTTA TTTTA -TATA CTTTTA TTTTA TTTTA TATAA ATGTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
*
45357 TTCTA TTTT- TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT
45375 GTTGCAGGAA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
4 7 0.15
5 38 0.79
6 3 0.06
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:45332 original size:20 final size:20
Alignment explanation
Indices: 45307--45345 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
45297 GGGTCTGATT
45307 TTTTATTTTATTTTATATAC
1 TTTTATTTTATTTTATATAC
45327 TTTTATTTTATTTTATATA
1 TTTTATTTTATTTTATATA
45346 AATGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTTTATTTTATATAC
Found at i:45353 original size:20 final size:20
Alignment explanation
Indices: 45310--45358 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
45300 TCTGATTTTT
** *
45310 TATTTTATTTTATATACTTT
1 TATTTTATTTTATATAAATG
45330 TATTTTATTTTATATAAATG
1 TATTTTATTTTATATAAATG
45350 TATTTTATT
1 TATTTTATT
45359 CTATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTTTATTTTATATAAATG
Found at i:46193 original size:73 final size:73
Alignment explanation
Indices: 46074--46219 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
46064 TACGATGCAG
46074 GTAAAACATTACACATCTTTTTCTGTTTCCTTTATATTTTGACTTTTTTATTTTCAAATAATCAA
1 GTAAAACATTACACATCTTTTTCTGTTTCCTTTATATTTTGACTTTTTTATTTTCAAATAATCAA
46139 AGTGTAAT
66 AGTGTAAT
46147 GTAAAACATTACACATCTTTTTCTGTTTCCTTTATATTTTGACTTTTTTATTTTCAAATAATCAA
1 GTAAAACATTACACATCTTTTTCTGTTTCCTTTATATTTTGACTTTTTTATTTTCAAATAATCAA
46212 AGTGTAAT
66 AGTGTAAT
46220 TTAATTATGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (73 bp):
GTAAAACATTACACATCTTTTTCTGTTTCCTTTATATTTTGACTTTTTTATTTTCAAATAATCAA
AGTGTAAT
Found at i:53693 original size:69 final size:68
Alignment explanation
Indices: 53613--53740 Score: 186
Period size: 69 Copynumber: 1.9 Consensus size: 68
53603 CTCGAGGTTT
* *
53613 CCTTAACTGTATGGT-ATGATGAATTACATTTTCATACTTTTTGAGCATTATATATATGGATGTC
1 CCTTAACTGTATGATGA-GATGAATTACATTTTCATAC-TTTTGAGCATTAGATATATGGATGTC
53677 GAGCA
64 GAGCA
* * *
53682 CCTTAATTGTATGATGAGATGAATTTCATTTTCATGCTTTTGAGCATTAGATATATGGA
1 CCTTAACTGTATGATGAGATGAATTACATTTTCATACTTTTGAGCATTAGATATATGGA
53741 GGGATATGGA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
68 21 0.40
69 31 0.58
70 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (68 bp):
CCTTAACTGTATGATGAGATGAATTACATTTTCATACTTTTGAGCATTAGATATATGGATGTCGA
GCA
Found at i:59623 original size:15 final size:15
Alignment explanation
Indices: 59605--59644 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
59595 CATCCGCCTT
59605 GCATCCGCCCGCCCC
1 GCATCCGCCCGCCCC
*
59620 GCATCCGCTCGCCCC
1 GCATCCGCCCGCCCC
*
59635 ACATCCGCCC
1 GCATCCGCCC
59645 ACCTAGCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.10, C:0.62, G:0.17, T:0.10
Consensus pattern (15 bp):
GCATCCGCCCGCCCC
Done.