Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002598.1 Hibiscus syriacus cultivar Beakdansim tig00005255_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: 86349
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13544 original size:133 final size:133
Alignment explanation
Indices: 13356--13623 Score: 470
Period size: 133 Copynumber: 2.0 Consensus size: 133
13346 TAAATTATCC
*
13356 GAAACCATATTTTGAGAAACAAAAAAATCTAGAAATTCAGATAAGCCCAATAAGATCAATCAATC
1 GAAACCATATTTTGAGAAACAAAAAAATCTAGAAACTCAGATAAGCCCAATAAGATCAATCAATC
13421 AGAATTTGGAAATAAAAAGTCGAACGAAGAATAATGTCTAAGATAGT-A-A-GACAGATAGGCAC
66 AGAATTTGGAAATAAAAAGTCGAACGAAGAATAATGTCTAAGATAGTAAGATGACAGATAGGCAC
13483 ATA
131 ATA
*
13486 GAAATCATATTTTGAGAAACAAAAAAAATCTAGAAACTCAGGGATAAGCCCAATAAGATCAATCA
1 GAAACCATATTTTGAGAAAC-AAAAAAATCTAGAAACTCA--GATAAGCCCAATAAGATCAATCA
13551 ATCAGAATTTGGAAATAAAAAGTCGAACGAAGAATAATGTCTAAGATAGTAAGATGACAGATAGG
63 ATCAGAATTTGGAAATAAAAAGTCGAACGAAGAATAATGTCTAAGATAGTAAGATGACAGATAGG
13616 CACATA
128 CACATA
13622 GA
1 GA
13624 GAGCATTATA
Statistics
Matches: 130, Mismatches: 2, Indels: 6
0.94 0.01 0.04
Matches are distributed among these distances:
130 19 0.15
131 18 0.14
133 73 0.56
134 1 0.01
135 1 0.01
136 18 0.14
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.21
Consensus pattern (133 bp):
GAAACCATATTTTGAGAAACAAAAAAATCTAGAAACTCAGATAAGCCCAATAAGATCAATCAATC
AGAATTTGGAAATAAAAAGTCGAACGAAGAATAATGTCTAAGATAGTAAGATGACAGATAGGCAC
ATA
Found at i:15439 original size:139 final size:139
Alignment explanation
Indices: 15189--15464 Score: 516
Period size: 139 Copynumber: 2.0 Consensus size: 139
15179 AGCATAAGGC
15189 AGCTCTTGTAGAAATAAATAATGATAGCTGACAACTACTAAAAGATATATTGTGTTAGTAAAACA
1 AGCTCTTGTAGAAATAAATAATGATAGCTGACAACTACTAAAAGATATATTGTGTTAGTAAAACA
15254 AGTCAAACCATCCAAGAGTTTTTGGAACCAACATCGGCATAAGGCAGCTCTTTGAATATAAAGTT
66 AGTCAAACCATCCAAGAGTTTTTGGAACCAACATCGGCATAAGGCAGCTCTTTGAATATAAAGTT
15319 CTTATTTAA
131 CTTATTTAA
*
15328 AGCTCTTGTAGAAATAAATAATGATAGCTGACAACTACTAAAAGCTATATTGTGTTAGTAAAACA
1 AGCTCTTGTAGAAATAAATAATGATAGCTGACAACTACTAAAAGATATATTGTGTTAGTAAAACA
* *
15393 AGTCAAACCATCCAAGAGTTTTTGGAACCAACATTGGCATAAGGCAGCTCTTTGAATTTAAAGTT
66 AGTCAAACCATCCAAGAGTTTTTGGAACCAACATCGGCATAAGGCAGCTCTTTGAATATAAAGTT
*
15458 TTTATTT
131 CTTATTT
15465 GCCACAGTTT
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 133 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (139 bp):
AGCTCTTGTAGAAATAAATAATGATAGCTGACAACTACTAAAAGATATATTGTGTTAGTAAAACA
AGTCAAACCATCCAAGAGTTTTTGGAACCAACATCGGCATAAGGCAGCTCTTTGAATATAAAGTT
CTTATTTAA
Found at i:20341 original size:12 final size:10
Alignment explanation
Indices: 20314--20338 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20304 TTTTTTTCCC
20314 TTTTTCAACT
1 TTTTTCAACT
20324 TTTTTCAACT
1 TTTTTCAACT
20334 TTTTT
1 TTTTT
20339 TTCCTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTCAACT
Found at i:23084 original size:30 final size:30
Alignment explanation
Indices: 23050--23113 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
23040 TTTTATTATT
**
23050 TAAAGTTAGGGGTCAAAATAATATT-TCATC
1 TAAAGTTAAAGGTCAAAATAATATTCT-ATC
*
23080 TAAAGTTAAAGGTCAAAATAGTATTCTATC
1 TAAAGTTAAAGGTCAAAATAATATTCTATC
23110 TAAA
1 TAAA
23114 ATTCAGAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (30 bp):
TAAAGTTAAAGGTCAAAATAATATTCTATC
Found at i:35528 original size:64 final size:64
Alignment explanation
Indices: 35424--35553 Score: 226
Period size: 64 Copynumber: 2.0 Consensus size: 64
35414 TTCAAAATCA
35424 TCCCAAATCATTCTAGCTTTCTCCCAATACTAAAACATTTAGAGAGTTTTCTCGAGAGTTGTTT
1 TCCCAAATCATTCTAGCTTTCTCCCAATACTAAAACATTTAGAGAGTTTTCTCGAGAGTTGTTT
* *
35488 TCCCAAATCATTCTAGCTTTCTCTCAATACTAGAAA-ATTTAGAGAGTTTTCTCGATAGTTGTTT
1 TCCCAAATCATTCTAGCTTTCTCCCAATACTA-AAACATTTAGAGAGTTTTCTCGAGAGTTGTTT
35552 TC
1 TC
35554 TCCTTTTTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 60 0.95
65 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (64 bp):
TCCCAAATCATTCTAGCTTTCTCCCAATACTAAAACATTTAGAGAGTTTTCTCGAGAGTTGTTT
Found at i:35605 original size:34 final size:35
Alignment explanation
Indices: 35546--35612 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
35536 TTCTCGATAG
* *
35546 TTGTTTTCTCCTTTTTATAAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTGTTAGAAAGAGAGAAGTTGTTA
**
35580 TTGTTTTCTCCTTGTTAGATCGAGAGAAGTTGT
1 TTGTTTTCTCCTTGTTAGAAAGAGAGAAGTTGT
35613 AATTCCTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.48
Consensus pattern (35 bp):
TTGTTTTCTCCTTGTTAGAAAGAGAGAAGTTGTTA
Found at i:39806 original size:20 final size:20
Alignment explanation
Indices: 39720--39808 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
39710 AAAAGGTGGA
* *
39720 AGAAGGAACTGTAGATATGC
1 AGAAGGGACGGTAGATATGC
* *
39740 AGAATGAACGGTAGATATGC
1 AGAAGGGACGGTAGATATGC
39760 AGAAGGGACGGTAGATATGC
1 AGAAGGGACGGTAGATATGC
39780 AGAAGGGACGGTAGATATGC
1 AGAAGGGACGGTAGATATGC
39800 AGAAGGGAC
1 AGAAGGGAC
39809 ATACCAAAGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.38, C:0.10, G:0.36, T:0.16
Consensus pattern (20 bp):
AGAAGGGACGGTAGATATGC
Found at i:42128 original size:16 final size:15
Alignment explanation
Indices: 42089--42148 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
42079 ATCGGAATCC
* *
42089 AAAATAATCTGAATTT
1 AAAATAAT-TAAAATT
42105 AAAA-AATTAATAATT
1 AAAATAATTAA-AATT
* *
42120 AAACTAATTTAAACTT
1 AAAATAA-TTAAAATT
42136 AAAATAATTAAAA
1 AAAATAATTAAAA
42149 CCCAAATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
14 2 0.06
15 14 0.40
16 15 0.43
17 4 0.11
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAATAATTAAAATT
Found at i:42149 original size:16 final size:16
Alignment explanation
Indices: 42103--42149 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
42093 TAATCTGAAT
42103 TTAAAA-AATTAATAA-
1 TTAAAATAATTAA-AAC
* *
42118 TTAAACTAATTTAAAC
1 TTAAAATAATTAAAAC
42134 TTAAAATAATTAAAAC
1 TTAAAATAATTAAAAC
42150 CCAAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAATAATTAAAAC
Found at i:70669 original size:33 final size:33
Alignment explanation
Indices: 70629--70723 Score: 190
Period size: 33 Copynumber: 2.9 Consensus size: 33
70619 TGTTCAAAGT
70629 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
70662 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
70695 TTGGCCACCAACCAAGATGAAATTTCCAA
1 TTGGCCACCAACCAAGATGAAATTTCCAA
70724 CTTGTCAACT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.39, C:0.25, G:0.15, T:0.21
Consensus pattern (33 bp):
TTGGCCACCAACCAAGATGAAATTTCCAATAAG
Found at i:81570 original size:16 final size:16
Alignment explanation
Indices: 81549--81581 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
81539 CACACATCCA
81549 ATTTTACCATCGGAAG
1 ATTTTACCATCGGAAG
81565 ATTTTACCATCGGAAG
1 ATTTTACCATCGGAAG
81581 A
1 A
81582 ATCTTTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (16 bp):
ATTTTACCATCGGAAG
Done.