Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008014.1 Hibiscus syriacus cultivar Beakdansim tig00110480_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: 624021
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:616089 original size:14 final size:14
Alignment explanation
Indices: 616070--616105 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
616060 ATTGTTTAAT
616070 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
616084 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
616098 TGATTTGT
1 TGATTTGT
616106 TTAATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:616244 original size:19 final size:19
Alignment explanation
Indices: 616222--616289 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
616212 ATCGCAACGA
616222 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
616241 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
616260 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
616274 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
616290 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:616333 original size:20 final size:20
Alignment explanation
Indices: 616308--616345 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
616298 TCGCATTGCG
*
616308 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
616328 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
616346 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:617421 original size:24 final size:24
Alignment explanation
Indices: 617394--617447 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
617384 GTATTCGAAA
* *
617394 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
617418 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
617442 TTTGAT
1 TTTGAT
617448 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:619963 original size:33 final size:33
Alignment explanation
Indices: 619921--620043 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
619911 ATTACTATCC
619921 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
* ** *
619954 CAATGCGAAATGAAAATCACAACGCTA-ATTTCG
1 CAATGCGAAATGAAAATCGCAACGAGAGA-ATCG
* *
619987 CAATGCGAAATAAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
620020 CAATGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
620044 CGAATTTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 75 0.97
34 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:620027 original size:66 final size:66
Alignment explanation
Indices: 619921--620050 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 66
619911 ATTACTATCC
* *
619921 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCTAATTTC
1 CAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAATTTC
619986 G
66 G
* *
619987 CAATGCGAAATAAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 CAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAATTT
620051 AATTCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (66 bp):
CAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAATTTC
G
Found at i:620064 original size:18 final size:20
Alignment explanation
Indices: 620043--620084 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
620033 AAATCGCAAC
620043 GCGAATTT-A-ATTCGCGTT
1 GCGAATTTCATATTCGCGTT
* *
620061 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCATATTCGCGTT
620081 GCGA
1 GCGA
620085 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 1 0.05
20 12 0.60
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (20 bp):
GCGAATTTCATATTCGCGTT
Found at i:620244 original size:14 final size:14
Alignment explanation
Indices: 620225--620261 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
620215 CATCAATTAA
620225 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
620239 ACAAATCATCTTTT
1 ACAAATCAACTTTT
620253 ACAAATCAA
1 ACAAATCAA
620262 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:621680 original size:42 final size:42
Alignment explanation
Indices: 621634--621713 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
621624 CGATAACAAT
* * *
621634 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
621676 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
621714 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:623771 original size:14 final size:14
Alignment explanation
Indices: 623752--623788 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
623742 GGAAATGACT
*
623752 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
623766 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
623780 ATCGCAACG
1 ATCGCAACG
623789 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:623816 original size:47 final size:50
Alignment explanation
Indices: 623713--623818 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 50
623703 TTGAAATGAA
* * *
623713 AATCGCAACGAGATAAGAGATCGCAACGCGGAAATGACTATCGCAACGATAG
1 AATCGCAACGAG--AAGAGATCGCAACGCGGAAATGACTATCGCAACCAGAC
*
623765 AATCGCAACGAG-AGA-ATCGCAACGC-GAAATGACTATCGCGACCAGAC
1 AATCGCAACGAGAAGAGATCGCAACGCGGAAATGACTATCGCAACCAGAC
623812 AATCGCA
1 AATCGCA
623819 CGCGAAATGA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 25 0.50
48 10 0.20
49 3 0.06
52 12 0.24
ACGTcount: A:0.40, C:0.25, G:0.24, T:0.12
Consensus pattern (50 bp):
AATCGCAACGAGAAGAGATCGCAACGCGGAAATGACTATCGCAACCAGAC
Found at i:623835 original size:32 final size:33
Alignment explanation
Indices: 623765--623876 Score: 100
Period size: 39 Copynumber: 3.2 Consensus size: 33
623755 GCAACGATAG
* * *
623765 AATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
623798 TATCGCGACCAGACAATCGC-ACGCGAAATGAA
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
623830 AATCGCAACCGCGAAATAAAAATCGCAACGCGAAATGAA
1 AATCGCAA-C-C---A-GACAATCGCAACGCGAAATGAA
623869 AATCGCAA
1 AATCGCAA
623877 TGCGAAATAA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
32 17 0.27
33 17 0.27
34 1 0.02
37 1 0.02
38 7 0.11
39 20 0.32
ACGTcount: A:0.44, C:0.25, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACCAGACAATCGCAACGCGAAATGAA
Found at i:623861 original size:19 final size:19
Alignment explanation
Indices: 623812--623900 Score: 126
Period size: 19 Copynumber: 4.7 Consensus size: 19
623802 GCGACCAGAC
*
623812 AATCGC-ACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
623830 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATAAA
*
623850 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
*
623869 AATCGCAATGCGAAATAAA
1 AATCGCAACGCGAAATAAA
*
623888 AATCGCAATGCGA
1 AATCGCAACGCGA
623901 TTTTTGTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
18 6 0.09
19 41 0.63
20 18 0.28
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:623895 original size:38 final size:39
Alignment explanation
Indices: 623812--623900 Score: 146
Period size: 38 Copynumber: 2.3 Consensus size: 39
623802 GCGACCAGAC
623812 AATCGC-ACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
*
623850 AATCGCAACGCGAAATGAAAATCGCAA-TGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
*
623888 AATCGCAATGCGA
1 AATCGCAACGCGA
623901 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 28 0.58
39 20 0.42
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (39 bp):
AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
Found at i:623918 original size:19 final size:20
Alignment explanation
Indices: 623896--623943 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
623886 AAAATCGCAA
*
623896 TGCGATTTTTGTTT-CGCGT
1 TGCGATTTTTATTTCCGCGT
**
623915 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTTCCGCGT
623935 TGCGATTTT
1 TGCGATTTT
623944 CATTCTCGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.48
Consensus pattern (20 bp):
TGCGATTTTTATTTCCGCGT
Done.