Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008789.1 Hibiscus syriacus cultivar Beakdansim tig00111932_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: 56651
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:13331 original size:24 final size:24
Alignment explanation
Indices: 13303--13374 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
13293 TGGTAATCTT
*
13303 GGTCCATGTACTATTTGGCGATCA
1 GGTCCCTGTACTATTTGGCGATCA
13327 GGTCCCTGTACTATTTGGCGATCA
1 GGTCCCTGTACTATTTGGCGATCA
*
13351 GGTCCCTGTACTATTTGGCTATCA
1 GGTCCCTGTACTATTTGGCGATCA
13375 CTCTGCCTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (24 bp):
GGTCCCTGTACTATTTGGCGATCA
Found at i:22837 original size:34 final size:34
Alignment explanation
Indices: 22797--22873 Score: 127
Period size: 34 Copynumber: 2.3 Consensus size: 34
22787 AAGGTTTATT
22797 TTTAAAGGTTTATATTAATAAAAAATAATATTTA
1 TTTAAAGGTTTATATTAATAAAAAATAATATTTA
* * *
22831 TTTAAAGGTTTATATTAATACATAATAATATTTC
1 TTTAAAGGTTTATATTAATAAAAAATAATATTTA
22865 TTTAAAGGT
1 TTTAAAGGT
22874 AGTGAAAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (34 bp):
TTTAAAGGTTTATATTAATAAAAAATAATATTTA
Found at i:23423 original size:59 final size:59
Alignment explanation
Indices: 23354--23476 Score: 174
Period size: 59 Copynumber: 2.1 Consensus size: 59
23344 CAGCAGGATG
* * *
23354 CATATTTGGGACTGCACTAAAGTATAACTAGGGCATATGGTGGGCACAAACTTATGTGT
1 CATATCTGGGACTGCACTAAAGTATAACTAGGGCAGATGGTGGGCACAAACTTACGTGT
* * ** *
23413 CATATCTGGGACTGCACTAAAGTATAACTAGTGTAGATGGTGGGCATGACCTTACGTGT
1 CATATCTGGGACTGCACTAAAGTATAACTAGGGCAGATGGTGGGCACAAACTTACGTGT
23472 CATAT
1 CATAT
23477 TCGAGTTAGC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (59 bp):
CATATCTGGGACTGCACTAAAGTATAACTAGGGCAGATGGTGGGCACAAACTTACGTGT
Found at i:32941 original size:29 final size:29
Alignment explanation
Indices: 32890--32945 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
32880 TTTAACCGGT
* *
32890 TTTCAACCGGTTCTGATCGGTTTGACCTA
1 TTTCAACCGGTTCTGACCAGTTTGACCTA
32919 TTTCAACCGGTTC-GAACCAGTTTGACC
1 TTTCAACCGGTTCTG-ACCAGTTTGACC
32946 AGTCGGAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.34
Consensus pattern (29 bp):
TTTCAACCGGTTCTGACCAGTTTGACCTA
Found at i:32995 original size:17 final size:17
Alignment explanation
Indices: 32969--33041 Score: 128
Period size: 17 Copynumber: 4.3 Consensus size: 17
32959 TTGACCGGTC
* *
32969 TGACCTGACCTGACCGT
1 TGACCCGACCCGACCGT
32986 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
33003 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
33020 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
33037 TGACC
1 TGACC
33042 GTTGACCGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.15
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:40241 original size:9 final size:9
Alignment explanation
Indices: 40217--40303 Score: 93
Period size: 9 Copynumber: 9.3 Consensus size: 9
40207 GCTGCTGGAA
*
40217 ACCGGTTTA
1 ACCGGTTTG
*
40226 ACTGGTTTG
1 ACCGGTTTG
40235 ACCGGTTTG
1 ACCGGTTTG
*
40244 ACCGGTTTCA
1 ACCGGTTT-G
*
40254 ACCGGTTCG
1 ACCGGTTTG
40263 AACCGGTTTG
1 -ACCGGTTTG
*
40273 ACCGGTCTG
1 ACCGGTTTG
40282 AACCGGTTTG
1 -ACCGGTTTG
*
40292 ACCGGTCTG
1 ACCGGTTTG
40301 ACC
1 ACC
40304 CGACCCGATC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
9 42 0.65
10 23 0.35
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:40259 original size:19 final size:18
Alignment explanation
Indices: 40217--40297 Score: 90
Period size: 19 Copynumber: 4.3 Consensus size: 18
40207 GCTGCTGGAA
*
40217 ACCGGTTTAACTGGTTTG
1 ACCGGTTTAACCGGTTTG
* *
40235 ACCGGTTTGACCGGTTTCA
1 ACCGGTTTAACCGGTTT-G
*
40254 ACCGGTTCGAACCGGTTTG
1 ACCGGTT-TAACCGGTTTG
*
40273 ACCGGTCTGAACCGGTTTG
1 ACCGGT-TTAACCGGTTTG
40292 ACCGGT
1 ACCGGT
40298 CTGACCCGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
18 15 0.28
19 30 0.56
20 9 0.17
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.30
Consensus pattern (18 bp):
ACCGGTTTAACCGGTTTG
Found at i:40298 original size:19 final size:19
Alignment explanation
Indices: 40229--40301 Score: 96
Period size: 19 Copynumber: 3.8 Consensus size: 19
40219 CGGTTTAACT
*
40229 GGTTTGACCGGTTTG-ACC
1 GGTTTGACCGGTCTGAACC
*
40247 GGTTTCAACCGGT-TCGAACC
1 GGTTT-GACCGGTCT-GAACC
40267 GGTTTGACCGGTCTGAACC
1 GGTTTGACCGGTCTGAACC
40286 GGTTTGACCGGTCTGA
1 GGTTTGACCGGTCTGA
40302 CCCGACCCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
18 6 0.12
19 34 0.69
20 9 0.18
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.29
Consensus pattern (19 bp):
GGTTTGACCGGTCTGAACC
Found at i:40328 original size:22 final size:22
Alignment explanation
Indices: 40300--40342 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
40290 TGACCGGTCT
*
40300 GACCCGACCCGATCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
40322 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
40343 GTTGACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:47217 original size:54 final size:54
Alignment explanation
Indices: 47135--47239 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
47125 CACTGGTTCA
* *
47135 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTTTGCCCAGATTTTCG
1 TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTTTCG
47189 TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTT
1 TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTT
47240 CTTGTTAGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (54 bp):
TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTTTCG
Found at i:49304 original size:1 final size:1
Alignment explanation
Indices: 49285--49467 Score: 231
Period size: 1 Copynumber: 183.0 Consensus size: 1
49275 ATTCAATTTC
* * * * * *
49285 TTTTTTCTTCTTTTCTTTTTTTTTCTTTTTTCTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
49350 TTTTTTTTTTTTTTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTTTTTTTCTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
49415 CTTTTTTCTTTTTTTCTTTTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
49468 CTTTGGATGA
Statistics
Matches: 152, Mismatches: 30, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 152 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:55572 original size:2 final size:2
Alignment explanation
Indices: 55565--55593 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55555 TAAAAAGTAA
55565 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 A
55594 GGTTTTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55906 original size:2 final size:2
Alignment explanation
Indices: 55899--55938 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
55889 TTACAAATCT
55899 TA TA TA TA TA TA TA -A 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 TA TA TA TA TA TA TA T
55939 TAAATAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.