Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003211.1 Hibiscus syriacus cultivar Beakdansim tig00006762_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: 81424
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:4311 original size:42 final size:41
Alignment explanation
Indices: 4239--4327 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 41
4229 CGGATGGCCC
* * * *
4239 GAAGGATTTATCTTCTTGCTCGAAATACTTACA-GAT-GACCT
1 GAAGGATTTATCATCATACTCGAAAGACTTA-ATGATAGA-CT
4280 GAAGGATTTAATCATCATACTCGAAAGACTTAATGATAGACT
1 GAAGGATTT-ATCATCATACTCGAAAGACTTAATGATAGACT
4322 GAAGGA
1 GAAGGA
4328 CTTACCAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 10 0.24
42 29 0.71
43 2 0.05
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (41 bp):
GAAGGATTTATCATCATACTCGAAAGACTTAATGATAGACT
Found at i:6517 original size:14 final size:14
Alignment explanation
Indices: 6500--6531 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
6490 TTTTCTCTCA
6500 CTTTTTTTTTTCCT
1 CTTTTTTTTTTCCT
*
6514 CTTTTTTTTTTCTT
1 CTTTTTTTTTTCCT
6528 CTTT
1 CTTT
6532 CTATTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
CTTTTTTTTTTCCT
Found at i:13564 original size:42 final size:41
Alignment explanation
Indices: 13492--13587 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 41
13482 AAACATCATG
* * *
13492 CCCGAAGGACTTATCATCTTGCTTGAAAGACTTGTAGATGA
1 CCCGAAGGACTTATCATCATGCTCGAAAGACTTATAGATGA
* * *
13533 CTCGAAGGATTTATACATCATGCTCGAAAGACTTATTGATGA
1 CCCGAAGGACTTAT-CATCATGCTCGAAAGACTTATAGATGA
13575 CCCGAAGGACTTA
1 CCCGAAGGACTTA
13588 CTAAGTAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 12 0.26
42 34 0.74
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (41 bp):
CCCGAAGGACTTATCATCATGCTCGAAAGACTTATAGATGA
Found at i:13568 original size:22 final size:22
Alignment explanation
Indices: 13484--13568 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 22
13474 TCAATTGGAA
* *
13484 ACATCATGCCCGAAGGACTTAT
1 ACATCATGCTCGAAAGACTTAT
* * *
13506 -CATCTTGCTTGAAAGACTTGT
1 ACATCATGCTCGAAAGACTTAT
* * * *
13527 AGATGA--CTCGAAGGATTTAT
1 ACATCATGCTCGAAAGACTTAT
13547 ACATCATGCTCGAAAGACTTAT
1 ACATCATGCTCGAAAGACTTAT
13569 TGATGACCCG
Statistics
Matches: 44, Mismatches: 16, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
20 14 0.32
21 16 0.36
22 14 0.32
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (22 bp):
ACATCATGCTCGAAAGACTTAT
Found at i:14011 original size:242 final size:242
Alignment explanation
Indices: 13491--14054 Score: 769
Period size: 242 Copynumber: 2.3 Consensus size: 242
13481 GAAACATCAT
* * *
13491 GCCCGAAGGACTTATCATCTTGCTTGAAAGACTTGTAGATGACTCGAAGGATTTATACATCATGC
1 GCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGAC-CGAAGGATTTAAACATCATGC
* * * *
13556 TCGAAAGACTTATTGATGACCCGAAGGACTTACTAAGTAAGAAACTTTAGAAATCGCTTTCTTAC
65 TCGAAAGACTTACTGATGACCCAAAGGACTTACTAAGAAAGAAACTTTAGAAATCACTTTCTTAC
* * * ** * *
13621 TTTTCAAGAAAAAATAGTCTTTCAGAAAAAGATTTAAATGAGTAATTTTGGAAATTAATTTCTCA
130 TTTTCAAGAAAAAATAATCTTTCAGAAAAAGATTTAAATGAGAAACTTCAGAAATCAACTTCTCA
* *
13686 TTTTTCAAAAAACATGTGAAAACATCCTACCTGAAGGTCTTATGGATG
195 TTTTTCAAAAAACATGTGAAAACATCCTACCTGAAAGTCATATGGATG
13734 GCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCAGAAGGATTTAAACATCATGC
1 GCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACC-GAAGGATTTAAACATCATGC
* * * *
13799 TCAAAAAACTTACTGATGGCCCAAAGGACTTACTCAA-AAAGAAACTTTGGAAATCACTTTCTTA
65 TCGAAAGACTTACTGATGACCCAAAGGACTTACT-AAGAAAGAAACTTTAGAAATCACTTTCTTA
* * **
13863 CTTTTCAAG-AAAAATCAATCTTTCA-TAAAAGATTTGAATGAGAAACTTCAGAAATCGCCTTCT
129 CTTTTCAAGAAAAAAT-AATCTTTCAGAAAAAGATTTAAATGAGAAACTTCAGAAATCAACTTCT
*
13926 CATTTTT-AAAAAATCATGTGAAAACATCCT-GCTCGAAAGTCATATGGATG
193 CATTTTTCAAAAAA-CATGTGAAAACATCCTACCT-GAAAGTCATATGGATG
* ** *
13976 GCCCAAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGAACCGAATAATTTAAGCATCATGC
1 GCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATG-ACCGAAGGATTTAAACATCATGC
14041 TCGAAAGACTTACT
65 TCGAAAGACTTACT
14055 TATTTCCTGA
Statistics
Matches: 284, Mismatches: 31, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
241 8 0.03
242 141 0.50
243 133 0.47
244 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (242 bp):
GCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCGAAGGATTTAAACATCATGCT
CGAAAGACTTACTGATGACCCAAAGGACTTACTAAGAAAGAAACTTTAGAAATCACTTTCTTACT
TTTCAAGAAAAAATAATCTTTCAGAAAAAGATTTAAATGAGAAACTTCAGAAATCAACTTCTCAT
TTTTCAAAAAACATGTGAAAACATCCTACCTGAAAGTCATATGGATG
Found at i:14256 original size:57 final size:57
Alignment explanation
Indices: 14131--14300 Score: 218
Period size: 57 Copynumber: 3.0 Consensus size: 57
14121 GTTTACAGTT
* * *
14131 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAATTCTTTGGGAATA
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTC-TTTAAAAATTCATTGGAAATA
* * *
14189 ATCA-CTAAGAAAACTCTGAAAATTAGGCTTAGCTTCTTTAAAAATAT-ATTGGAAATA
1 ATCATC-AAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAAT-TCATTGGAAATA
* * *
14246 ATTATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAA
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTGGAAA
14301 CATCAAGAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
56 1 0.01
57 63 0.66
58 32 0.33
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (57 bp):
ATCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTGGAAATA
Found at i:28412 original size:96 final size:97
Alignment explanation
Indices: 28271--28467 Score: 249
Period size: 96 Copynumber: 2.0 Consensus size: 97
28261 AGTAGTAACT
* *
28271 AGTAGATTTCATGATCCAGAAAATCAGGAACGACCATATTTTCCAGTGAAAACA-ATAAACCAGA
1 AGTAGATTTCATGATCCAGAAAATCAAGAACGAACATATTTTCCAGTGAAAACAGAT-AACCAG-
* * *
28335 T-AACCCATTTCAGGTAACCATAGTTTATAAACC
64 TGAACACATTTCAAGTAACCATAGTTCATAAACC
* * *
28368 AGTAGA-TTCTATGATCCA-TAAATCAAGAACGAACATATTTTCCAGTGAAAATAGGTAACCAGT
1 AGTAGATTTC-ATGATCCAGAAAATCAAGAACGAACATATTTTCCAGTGAAAACAGATAACCAGT
* *
28431 GAACATATTTCAAGTAACTATAGTTCATAAACC
65 GAACACATTTCAAGTAACCATAGTTCATAAACC
28464 AGTA
1 AGTA
28468 AATTAGTCAT
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
95 1 0.01
96 71 0.82
97 15 0.17
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (97 bp):
AGTAGATTTCATGATCCAGAAAATCAAGAACGAACATATTTTCCAGTGAAAACAGATAACCAGTG
AACACATTTCAAGTAACCATAGTTCATAAACC
Found at i:48134 original size:41 final size:41
Alignment explanation
Indices: 48089--48176 Score: 176
Period size: 41 Copynumber: 2.1 Consensus size: 41
48079 TTAAGCGTAT
48089 TATTATTGTCCATGCCCATAATAATAATTGACTATGGACTC
1 TATTATTGTCCATGCCCATAATAATAATTGACTATGGACTC
48130 TATTATTGTCCATGCCCATAATAATAATTGACTATGGACTC
1 TATTATTGTCCATGCCCATAATAATAATTGACTATGGACTC
48171 TATTAT
1 TATTAT
48177 AAAAATATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (41 bp):
TATTATTGTCCATGCCCATAATAATAATTGACTATGGACTC
Found at i:49684 original size:21 final size:21
Alignment explanation
Indices: 49660--49740 Score: 92
Period size: 21 Copynumber: 3.7 Consensus size: 21
49650 AAAGTGCCAT
*
49660 AGTACACAAAGTACTACTACA
1 AGTACACAAAGTACTACTCCA
*
49681 AGTACACAGAGTACT-CTTGCCA
1 AGTACACAAAGTACTAC-T-CCA
*
49703 TAGTACACAAAGAACTACTCCA
1 -AGTACACAAAGTACTACTCCA
49725 AGTACACAAAAGTACT
1 AGTACAC-AAAGTACT
49741 CTTACAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.02
21 22 0.44
22 12 0.24
23 14 0.28
24 1 0.02
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.20
Consensus pattern (21 bp):
AGTACACAAAGTACTACTCCA
Found at i:49703 original size:44 final size:45
Alignment explanation
Indices: 49654--49743 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 45
49644 GCACACAAAG
* *
49654 TGCCATAGTACACAAAGTACTACTACAAGTACAC-AGAGTACTCT
1 TGCCATAGTACACAAAGAACTACTACAAGTACACAAAAGTACTCT
*
49698 TGCCATAGTACACAAAGAACTACTCCAAGTACACAAAAGTACTCT
1 TGCCATAGTACACAAAGAACTACTACAAGTACACAAAAGTACTCT
49743 T
1 T
49744 ACAAAAATGA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 32 0.76
45 10 0.24
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.22
Consensus pattern (45 bp):
TGCCATAGTACACAAAGAACTACTACAAGTACACAAAAGTACTCT
Found at i:67780 original size:17 final size:18
Alignment explanation
Indices: 67758--67800 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
67748 AAATTTAAAG
67758 TTGAAAAAAAAAT-TATT
1 TTGAAAAAAAAATGTATT
**
67775 TTGAAAGAAAACTTGTATT
1 TTGAAA-AAAAAATGTATT
67794 TTGAAAA
1 TTGAAAA
67801 CCAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 6 0.27
19 10 0.45
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (18 bp):
TTGAAAAAAAAATGTATT
Found at i:68345 original size:17 final size:17
Alignment explanation
Indices: 68323--68355 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
68313 TCTTTAGTTA
*
68323 TATTTCTATGTATTAAT
1 TATTTCTAGGTATTAAT
68340 TATTTCTAGGTATTAA
1 TATTTCTAGGTATTAA
68356 ATAAATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (17 bp):
TATTTCTAGGTATTAAT
Found at i:75857 original size:31 final size:32
Alignment explanation
Indices: 75759--75843 Score: 140
Period size: 32 Copynumber: 2.8 Consensus size: 32
75749 CATATTACAT
*
75759 AACTTTTA--AAATTTTACACTTTGATCCCTA
1 AACTTTTACCAAAGTTTACACTTTGATCCCTA
75789 AACTTTTACCAAAGTTTACACTTTGATCCCTA
1 AACTTTTACCAAAGTTTACACTTTGATCCCTA
75821 AACTTTTACC-AAGTTTACACTTT
1 AACTTTTACCAAAGTTTACACTTT
75844 AACCATAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
30 8 0.15
31 13 0.25
32 31 0.60
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (32 bp):
AACTTTTACCAAAGTTTACACTTTGATCCCTA
Found at i:77184 original size:22 final size:22
Alignment explanation
Indices: 77159--77220 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
77149 ATGTTATTAA
77159 ATTTTAACAAATC-TTTTCAAAC
1 ATTTTAAC-AATCATTTTCAAAC
*
77181 ATTTTATCAATCATTTTCAAAC
1 ATTTTAACAATCATTTTCAAAC
*
77203 ATTTTATCAATCATTTTC
1 ATTTTAACAATCATTTTC
77221 CACTTTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 4 0.11
22 34 0.89
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTTAACAATCATTTTCAAAC
Found at i:77190 original size:12 final size:12
Alignment explanation
Indices: 77175--77219 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
77165 ACAAATCTTT
77175 TCAAACATTTTA
1 TCAAACATTTTA
*
77187 TCAATCA-TTT-
1 TCAAACATTTTA
77197 TCAAACATTTTA
1 TCAAACATTTTA
*
77209 TCAATCATTTT
1 TCAAACATTTT
77220 CCACTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 6 0.21
11 6 0.21
12 16 0.57
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.47
Consensus pattern (12 bp):
TCAAACATTTTA
Found at i:77310 original size:20 final size:21
Alignment explanation
Indices: 77260--77319 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
77250 TATTTTCTGG
*
77260 TAAATAGTATCAATATTGTTC
1 TAAATAGTATCAATATTGTTA
77281 TCAAAT--TATCAATATTG-TA
1 T-AAATAGTATCAATATTGTTA
* *
77300 TAAATAGTATCGATAGTGTT
1 TAAATAGTATCAATATTGTT
77320 CTTGTGGTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 20 0.62
21 2 0.06
22 4 0.12
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (21 bp):
TAAATAGTATCAATATTGTTA
Done.