Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001101.1 Hibiscus syriacus cultivar Beakdansim tig00002182_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: 65531
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7073 original size:11 final size:11
Alignment explanation
Indices: 7049--7110 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
7039 ATTTATTCTC
*
7049 TTTTCTTTTTAT
1 TTTTC-TTTCAT
7061 TTTTCTTTCAT
1 TTTTCTTTCAT
*
7072 TTTTTTTTCAT
1 TTTTCTTTCAT
*
7083 TCATT-TTTCAT
1 T-TTTCTTTCAT
7094 TTTTC---CAT
1 TTTTCTTTCAT
7102 TTTTCTTTC
1 TTTTCTTTC
7111 TTCATGCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 8 0.20
10 2 0.05
11 24 0.59
12 7 0.17
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCTTTCAT
Found at i:7080 original size:15 final size:15
Alignment explanation
Indices: 7050--7112 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
7040 TTTATTCTCT
*
7050 TTTCTTTTTATTTTTC
1 TTTCATTTT-TTTTTC
7066 TTTCATTTTTTTTTC
1 TTTCATTTTTTTTTC
* *
7081 ATTCATTTTTCATTT-
1 TTTCATTTTT-TTTTC
* *
7096 TTCCATTTTTCTTTC
1 TTTCATTTTTTTTTC
7111 TT
1 TT
7113 CATGCGAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 3 0.08
15 25 0.64
16 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTCATTTTTTTTTC
Found at i:15531 original size:24 final size:23
Alignment explanation
Indices: 15505--15550 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
15495 ATGTACAGTG
15505 GGGGAATCGGTACCCCTGTAGCA
1 GGGGAATCGGTACCCCTGTAGCA
15528 GGGGAATCGGTACCCCTGTAGCA
1 GGGGAATCGGTACCCCTGTAGCA
15551 TTATGGAAAA
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:0.22, C:0.26, G:0.35, T:0.17
Consensus pattern (23 bp):
GGGGAATCGGTACCCCTGTAGCA
Found at i:16070 original size:46 final size:46
Alignment explanation
Indices: 15996--16122 Score: 159
Period size: 46 Copynumber: 2.8 Consensus size: 46
15986 GATAAAATCT
** *
15996 CTTACCATTT-ATCCCATAAGCTTGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATAACATAAGATTGTAAGCTTATTTTACCAATATA
*
16041 CTTACCATTTAATAACATAAGATTTTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATAACATAAGATTGTAAGCTTATTTTACCAATATA
* ** *
16087 CTAACCATTTAATCTCATAA-ACTCGTAAGCTTATTT
1 CTTACCATTTAATAACATAAGA-TTGTAAGCTTATTT
16123 GCCAGTTTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
45 11 0.15
46 60 0.85
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATAACATAAGATTGTAAGCTTATTTTACCAATATA
Found at i:19249 original size:28 final size:28
Alignment explanation
Indices: 19192--19254 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
19182 TCAATTCGAG
* *
19192 GGGAAACACCTCCTTATATCCATACCGA
1 GGGAAACACCTCCTAATATCCATAACGA
* * *
19220 GGGAAACACCTTCTAATGTCCATAAGGA
1 GGGAAACACCTCCTAATATCCATAACGA
19248 GGTGAAA
1 GG-GAAA
19255 ACCATCACGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (28 bp):
GGGAAACACCTCCTAATATCCATAACGA
Found at i:20417 original size:131 final size:132
Alignment explanation
Indices: 20174--20528 Score: 552
Period size: 131 Copynumber: 2.7 Consensus size: 132
20164 ATAATTTTAA
*
20174 GAGAGAAAACGATAAAATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* ** * *
20239 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTTGTCTT-AAAATTCAATATTGAT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAAATAAATATTGAT
20303 TC
131 TC
* * *
20305 GAGTGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
*
20370 ATCATTTATTACTCCAATCGTAATGAAGAGATATCACTATTCCGTCTTAAAAAATAAATATTGAT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAAATAAATATTGAT
20435 TC
131 TC
* *
20437 GAGAGAAAATGATAATATTTAATTATTTCAAATCGAGAATAAAAT-ACCTCTCATGCCTTAAAGC
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAAT-AAATGACCTCTCATGCCTTAAAGC
* * *
20501 AATCATTTATTAATCAAACCGAAATGAA
65 AATCATTTATTACTCCAATCGAAATGAA
20529 AATATATTAT
Statistics
Matches: 203, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
131 105 0.52
132 94 0.46
133 4 0.02
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (132 bp):
GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAAATAAATATTGAT
TC
Found at i:28019 original size:16 final size:16
Alignment explanation
Indices: 27974--28033 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
27964 TGTCTTTTCG
27974 GGTCAAAGTCAACTCT
1 GGTCAAAGTCAACTCT
*
27990 GATCAAAGTCAACTCT
1 GGTCAAAGTCAACTCT
* * *
28006 GGTCATAGTAAACTAT
1 GGTCAAAGTCAACTCT
*
28022 GGTCATAGTCAA
1 GGTCAAAGTCAA
28034 AGGGTCAGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (16 bp):
GGTCAAAGTCAACTCT
Found at i:28078 original size:23 final size:23
Alignment explanation
Indices: 28052--28107 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
28042 GAAAATTCAA
*
28052 CGGGTCTGGTCGGGTTAACAGTT
1 CGGGTCGGGTCGGGTTAACAGTT
**
28075 CGGGTCGGGTTTGGTTAACAGTT
1 CGGGTCGGGTCGGGTTAACAGTT
28098 CGGGTCGGGT
1 CGGGTCGGGT
28108 TGGATCGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.11, C:0.16, G:0.43, T:0.30
Consensus pattern (23 bp):
CGGGTCGGGTCGGGTTAACAGTT
Found at i:28108 original size:23 final size:23
Alignment explanation
Indices: 28064--28108 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
28054 GGTCTGGTCG
28064 GGTTAACAGTTCGGGTCGGGTTT
1 GGTTAACAGTTCGGGTCGGGTTT
28087 GGTTAACAGTTCGGGTCGGGTT
1 GGTTAACAGTTCGGGTCGGGTT
28109 GGATCGAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.13, G:0.40, T:0.33
Consensus pattern (23 bp):
GGTTAACAGTTCGGGTCGGGTTT
Found at i:30574 original size:18 final size:19
Alignment explanation
Indices: 30536--30574 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
30526 AAGGAAAAAG
*
30536 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
30555 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
30573 AA
1 AA
30575 AAAAGCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:42898 original size:21 final size:21
Alignment explanation
Indices: 42872--42912 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42862 ATCATTCTTT
*
42872 TTGTTCCTTTGTTATTGATTC
1 TTGTTCCTTTCTTATTGATTC
*
42893 TTGTTCCTTTCTTCTTGATT
1 TTGTTCCTTTCTTATTGATT
42913 TTCACTCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.17, G:0.12, T:0.63
Consensus pattern (21 bp):
TTGTTCCTTTCTTATTGATTC
Found at i:51387 original size:2 final size:2
Alignment explanation
Indices: 51380--51423 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
51370 TGTATGTATG
51380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
51423 T
1 T
51424 GTTTGTTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Done.