Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007597.1 Hibiscus syriacus cultivar Beakdansim tig00021946_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: 240653
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:228022 original size:19 final size:19
Alignment explanation
Indices: 227998--228039 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
227988 TCGGCAACGC
* *
227998 TTGAACCGGTTTAATCGGT
1 TTGAACCGGGTTAACCGGT
*
228017 TTGAACCGGGTTGACCGGT
1 TTGAACCGGGTTAACCGGT
228036 TTGA
1 TTGA
228040 CCCGACCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (19 bp):
TTGAACCGGGTTAACCGGT
Found at i:228084 original size:22 final size:22
Alignment explanation
Indices: 228057--228110 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
228047 GTTGACCGGT
228057 CCAACCCGA-TCCGACCGTAGAC
1 CCAACCCGACT-CGACCGTAGAC
*
228079 CCAACCCGACTCGACCGTTGAC
1 CCAACCCGACTCGACCGTAGAC
*
228101 CCGACCCGAC
1 CCAACCCGAC
228111 CGTTGACCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.24, C:0.48, G:0.19, T:0.09
Consensus pattern (22 bp):
CCAACCCGACTCGACCGTAGAC
Found at i:228102 original size:17 final size:17
Alignment explanation
Indices: 228082--228118 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
228072 CGTAGACCCA
*
228082 ACCCGACTCGACCGTTG
1 ACCCGACCCGACCGTTG
228099 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
228116 ACC
1 ACC
228119 GTTAACTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14
Consensus pattern (17 bp):
ACCCGACCCGACCGTTG
Found at i:228287 original size:86 final size:85
Alignment explanation
Indices: 228162--228329 Score: 239
Period size: 86 Copynumber: 2.0 Consensus size: 85
228152 AAATGGTGGA
** *
228162 ATTTTAGTAATTATTTTTAAAATGGTTTTATATTCGTAATTATTTTTAAAA-GTGCTATTTTTTG
1 ATTTTAGTAATTATTTTTAAAATGGTGCTATATTCGTAATTATTTTTAAAACGTGCTA-TTTTCG
228226 TAAATTTTTTTAAAAAAGTGTT
65 T-AATTTTTTTAAAAAAGTGTT
* * * *
228248 ATTTTTGTAATTATTTTTAAAATGGTGCTATTTTTGTAATTATTTTTAAAACGGTGTTATTTTCG
1 ATTTTAGTAATTATTTTTAAAATGGTGCTATATTCGTAATTATTTTTAAAAC-GTGCTATTTTCG
228313 TAATTTTTTTAAAAAAG
65 TAATTTTTTTAAAAAAG
228330 GGTGATAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
86 62 0.85
87 6 0.08
88 5 0.07
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (85 bp):
ATTTTAGTAATTATTTTTAAAATGGTGCTATATTCGTAATTATTTTTAAAACGTGCTATTTTCGT
AATTTTTTTAAAAAAGTGTT
Found at i:228297 original size:58 final size:58
Alignment explanation
Indices: 228134--228326 Score: 241
Period size: 58 Copynumber: 3.4 Consensus size: 58
228124 CTGGGTGGTT
* * ** * * *
228134 TTTTGGTAATTATTTTGAAAATGGTGGAATTTTAGTAATTATTTTTAAAATGGTTTTA
1 TTTTCGTAATTATTTTTAAAATGGTGCTATTTTTGTAATTATTTTTAAAAAGGTGTTA
* *
228192 TATTCGTAATTATTTTTAAAA--GTGCTATTTTTTGTAAATT-TTTTTAAAAAAGTGTTA
1 TTTTCGTAATTATTTTTAAAATGGTGCTA-TTTTTGT-AATTATTTTTAAAAAGGTGTTA
* *
228249 TTTTTGTAATTATTTTTAAAATGGTGCTATTTTTGTAATTATTTTTAAAACGGTGTTA
1 TTTTCGTAATTATTTTTAAAATGGTGCTATTTTTGTAATTATTTTTAAAAAGGTGTTA
228307 TTTTCGTAATT-TTTTTAAAA
1 TTTTCGTAATTATTTTTAAAA
228327 AAGGGTGATA
Statistics
Matches: 116, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
56 4 0.03
57 52 0.45
58 54 0.47
59 6 0.05
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (58 bp):
TTTTCGTAATTATTTTTAAAATGGTGCTATTTTTGTAATTATTTTTAAAAAGGTGTTA
Found at i:228327 original size:29 final size:29
Alignment explanation
Indices: 228133--228326 Score: 216
Period size: 29 Copynumber: 6.7 Consensus size: 29
228123 ACTGGGTGGT
* **
228133 TTTTTGGTAATTATTTTGAAAATGGTGGAA
1 TTTTT-GTAATTATTTTTAAAATGGTGTTA
* *
228163 TTTTAGTAATTATTTTTAAAATGGTTTTA
1 TTTTTGTAATTATTTTTAAAATGGTGTTA
* * *
228192 TATTCGTAATTATTTTTAAAA--GTGCTA
1 TTTTTGTAATTATTTTTAAAATGGTGTTA
**
228219 TTTTTTGTAAATT-TTTTTAAAAAAGTGTTA
1 -TTTTTGT-AATTATTTTTAAAATGGTGTTA
*
228249 TTTTTGTAATTATTTTTAAAATGGTGCTA
1 TTTTTGTAATTATTTTTAAAATGGTGTTA
*
228278 TTTTTGTAATTATTTTTAAAACGGTGTTA
1 TTTTTGTAATTATTTTTAAAATGGTGTTA
*
228307 TTTTCGTAATT-TTTTTAAAA
1 TTTTTGTAATTATTTTTAAAA
228327 AAGGGTGATA
Statistics
Matches: 141, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.03
28 27 0.19
29 101 0.72
30 9 0.06
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.54
Consensus pattern (29 bp):
TTTTTGTAATTATTTTTAAAATGGTGTTA
Found at i:234217 original size:20 final size:20
Alignment explanation
Indices: 234192--234233 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
234182 GCAGATGAGC
234192 GACGTAAGGATATCGAGTTT
1 GACGTAAGGATATCGAGTTT
234212 GACGTAAGGATATCGAGTTT
1 GACGTAAGGATATCGAGTTT
234232 GA
1 GA
234234 GGTTGGAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GACGTAAGGATATCGAGTTT
Found at i:237136 original size:15 final size:16
Alignment explanation
Indices: 237116--237148 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
237106 AAATCTTACA
*
237116 TTTAATTTGTT-TTAT
1 TTTAATTCGTTATTAT
237131 TTTAATTCGTTATTAT
1 TTTAATTCGTTATTAT
237147 TT
1 TT
237149 ATGAATTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTAATTCGTTATTAT
Found at i:238703 original size:19 final size:20
Alignment explanation
Indices: 238663--238703 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
238653 AGATGACGAT
238663 TATATTTCCTTTATACTACA
1 TATATTTCCTTTATACTACA
*
238683 TATATTTCTTTTATACT-CA
1 TATATTTCCTTTATACTACA
238702 TA
1 TA
238704 ACTAAGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTTCCTTTATACTACA
Done.