Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004509.1 Hibiscus syriacus cultivar Beakdansim tig00009945_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: 57713
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:5946 original size:59 final size:59
Alignment explanation
Indices: 5854--6221 Score: 529
Period size: 59 Copynumber: 6.2 Consensus size: 59
5844 ACCAGATGGT
* * *
5854 ACTTTGTATGCTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTCCGTATAAGGC
1 ACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTTCGTATAGGGC
*
5913 ACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTCCGTATAGGGC
1 ACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTTCGTATAGGGC
* * *
5972 ACTTTGTGTGCTAACATGAGAAGAAATTTATACGAAGTGTATGAATTTTCGTATAGGGC
1 ACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTTCGTATAGGGC
* *
6031 ACTTTGTGTACTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTTCTTATAGGGC
1 ACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTTCGTATAGGGC
* * * **
6090 ACTTTGTATGCTAATATGAGAAGAAATTCATACTAAGTGTATAGATTTTCGTACGGGGC
1 ACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTTCGTATAGGGC
* * * * * * * *
6149 ACTTCGTGTGCTAACATGATAAGAAATTAATACTAAGTGTGTGAATTTTTGTGTTGGGC
1 ACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTTCGTATAGGGC
*
6208 ACCTTGTGTGCTAA
1 ACTTTGTGTGCTAA
6222 AATTATGAAA
Statistics
Matches: 277, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 277 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (59 bp):
ACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTTCGTATAGGGC
Found at i:12791 original size:59 final size:59
Alignment explanation
Indices: 12718--13040 Score: 461
Period size: 59 Copynumber: 5.5 Consensus size: 59
12708 TATGCGTGGT
* *
12718 GATTTCCGTATAGGGCACTTTCTGTGCTAATATGAGAAGAAATTCATACTAAGTGTATG
1 GATTTCCGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATG
*
12777 TATTTCCGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATG
1 GATTTCCGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATG
* *
12836 GATTTCCGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACCAAGTGTATA
1 GATTTCCGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATG
* * * * *
12895 GATTTCCATATAGGGCACTTTGT-T-TTAAAATTAGAAGAAATTCATACTAAGTCTATG
1 GATTTCCGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATG
* ** * *
12952 GATTTTCGTATAGACCACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATG
1 GATTTCCGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATG
* * * *
13011 AATTTCTGTATTGGGCACCTTGTGTGCTAA
1 GATTTCCGTATAGGGCACTTTGTGTGCTAA
13041 AATTATGAAA
Statistics
Matches: 231, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
57 45 0.19
58 2 0.01
59 184 0.80
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (59 bp):
GATTTCCGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATG
Found at i:12983 original size:116 final size:118
Alignment explanation
Indices: 12718--13043 Score: 453
Period size: 116 Copynumber: 2.8 Consensus size: 118
12708 TATGCGTGGT
*
12718 GATTTCCGTATAGGGCACTTTC-TGTGCTAATATGAGAAGAAATTCATACTAAGTGTATGTATTT
1 GATTTCCGTATAGGGCAC-TTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGTATTT
* * *
12782 CCGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATG
65 CCATATAGGGCACTTTGTGTGCTAAAATGAGAAGAAATTCATACTAAGTCTATG
* *
12836 GATTTCCGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACCAAGTGTATAG-ATTT
1 GATTTCCGTATAGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTAT-GTATTT
* *
12900 CCATATAGGGCACTTTGT-T-TTAAAATTAGAAGAAATTCATACTAAGTCTATG
65 CCATATAGGGCACTTTGTGTGCTAAAATGAGAAGAAATTCATACTAAGTCTATG
* ** * *
12952 GATTTTCGTATAGACCACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTC
1 GATTTCCGTATAGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGTATTTC
** * *
13017 TGTATTGGGCACCTTGTGTGCTAAAAT
66 CATATAGGGCACTTTGTGTGCTAAAAT
13044 TATGAAAGAT
Statistics
Matches: 184, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
115 1 0.01
116 99 0.54
117 4 0.02
118 79 0.43
119 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (118 bp):
GATTTCCGTATAGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGTATTTC
CATATAGGGCACTTTGTGTGCTAAAATGAGAAGAAATTCATACTAAGTCTATG
Found at i:13036 original size:175 final size:177
Alignment explanation
Indices: 12718--13040 Score: 488
Period size: 175 Copynumber: 1.8 Consensus size: 177
12708 TATGCGTGGT
* * * *
12718 GATTTCCGTATAGGGCACTTTCTGTGCTAATATGAGAAGAAATTCATACTAAGTGTATGTATTTC
1 GATTTCCATATAGGGCACTTTCTGTGCTAAAATGAGAAGAAATTCATACTAAGTCTATGGATTTC
** * *
12783 CGTATAGGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGGATTTCCGTATA
66 CGTATAGACCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCGTATA
*
12848 GGGCACTTTGTGTGCTAACATGAGAAGAAATTCATACCAAGTGTATA
131 GGGCACCTTGTGTGCTAACATGAGAAGAAATTCATACCAAGTGTATA
** * *
12895 GATTTCCATATAGGGCAC-TT-TGTTTTAAAATTAGAAGAAATTCATACTAAGTCTATGGATTTT
1 GATTTCCATATAGGGCACTTTCTGTGCTAAAATGAGAAGAAATTCATACTAAGTCTATGGATTTC
* * *
12958 CGTATAGACCACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATT
66 CGTATAGACCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCGTATA
13023 GGGCACCTTGTGTGCTAA
131 GGGCACCTTGTGTGCTAA
13041 AATTATGAAA
Statistics
Matches: 130, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
175 111 0.85
176 2 0.02
177 17 0.13
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (177 bp):
GATTTCCATATAGGGCACTTTCTGTGCTAAAATGAGAAGAAATTCATACTAAGTCTATGGATTTC
CGTATAGACCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCGTATA
GGGCACCTTGTGTGCTAACATGAGAAGAAATTCATACCAAGTGTATA
Found at i:14081 original size:12 final size:12
Alignment explanation
Indices: 14064--14088 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14054 AGAATCCTAC
14064 ACAACAAGCTCA
1 ACAACAAGCTCA
14076 ACAACAAGCTCA
1 ACAACAAGCTCA
14088 A
1 A
14089 GTTCCAGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.08, T:0.08
Consensus pattern (12 bp):
ACAACAAGCTCA
Found at i:17572 original size:15 final size:15
Alignment explanation
Indices: 17552--17590 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
17542 ATAAAATGAA
17552 AATTGAATTT-AATT
1 AATTGAATTTAAATT
*
17566 GAATTGATTTTAAATT
1 -AATTGAATTTAAATT
17582 AATTGAATT
1 AATTGAATT
17591 GCATATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (15 bp):
AATTGAATTTAAATT
Found at i:17606 original size:23 final size:20
Alignment explanation
Indices: 17560--17609 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
17550 AAAATTGAAT
*
17560 TTAATTGAATTGATTTTAAA
1 TTAATTGAATTGATTATAAA
17580 TTAATTGAATTGCATATGATAAA
1 TTAATTGAATTG-AT-T-ATAAA
17603 TTAATTG
1 TTAATTG
17610 CTTAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 12 0.46
21 2 0.08
22 1 0.04
23 11 0.42
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (20 bp):
TTAATTGAATTGATTATAAA
Found at i:23181 original size:45 final size:45
Alignment explanation
Indices: 23120--23208 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
23110 ATTTCTCTCA
*
23120 CTATATTGAAGCTATTACCGA-CATTATCCAACTTATTCCCTAAGG
1 CTATATTGAAGCTATTACC-ATCATTACCCAACTTATTCCCTAAGG
* * *
23165 CTATATTGGAGTTATTACCATCATTACCCAACTTATTTCCTAAG
1 CTATATTGAAGCTATTACCATCATTACCCAACTTATTCCCTAAG
23209 ATCTCTCATC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (45 bp):
CTATATTGAAGCTATTACCATCATTACCCAACTTATTCCCTAAGG
Found at i:28287 original size:9 final size:9
Alignment explanation
Indices: 28244--28289 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
28234 AATTGTGATT
28244 ATGATAATG
1 ATGATAATG
* *
28253 ATGTTAATA
1 ATGATAATG
*
28262 ATGATAAGG
1 ATGATAATG
28271 ATGATAATG
1 ATGATAATG
28280 ATGATAATG
1 ATGATAATG
28289 A
1 A
28290 GGTTATATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.33
Consensus pattern (9 bp):
ATGATAATG
Found at i:40160 original size:20 final size:20
Alignment explanation
Indices: 40132--40190 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
40122 GATTTTTTTA
*
40132 TGAATAGTGAACAGT-ACAT
1 TGAACAGTGAACAGTAACAT
*
40151 GTGAACAGTGCACAGTAACAT
1 -TGAACAGTGAACAGTAACAT
*
40172 TGCACAGT-AACAGTGAACA
1 TGAACAGTGAACAGT-AACA
40191 GTGCTCGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.15
20 24 0.73
21 4 0.12
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (20 bp):
TGAACAGTGAACAGTAACAT
Found at i:40170 original size:13 final size:13
Alignment explanation
Indices: 40154--40192 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
40144 AGTACATGTG
40154 AACAGTGCACAGT
1 AACAGTGCACAGT
*
40167 AACATTGCACAGT
1 AACAGTGCACAGT
*
40180 AACAGTGAACAGT
1 AACAGTGCACAGT
40193 GCTCGTGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (13 bp):
AACAGTGCACAGT
Found at i:40760 original size:20 final size:20
Alignment explanation
Indices: 40735--40776 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40725 CATTATTCCT
* *
40735 TAACCATATACCATAGACAA
1 TAACCATAAACAATAGACAA
*
40755 TAACCATAAACAATAGATAA
1 TAACCATAAACAATAGACAA
40775 TA
1 TA
40777 GTCCAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.19, G:0.05, T:0.21
Consensus pattern (20 bp):
TAACCATAAACAATAGACAA
Found at i:57383 original size:20 final size:20
Alignment explanation
Indices: 57358--57412 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
57348 CAAACCCCTT
57358 TGAAAATACATGGTTTTTAA
1 TGAAAATACATGGTTTTTAA
*
57378 TGAAAATACAT-G-ATTTAA
1 TGAAAATACATGGTTTTTAA
* *
57396 TGAAGATACATGCTTTT
1 TGAAAATACATGGTTTT
57413 GGCCGAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 15 0.52
19 1 0.03
20 13 0.45
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGGTTTTTAA
Done.