Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003063.1 Hibiscus syriacus cultivar Beakdansim tig00006385_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: 217600
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:175642 original size:2 final size:2
Alignment explanation
Indices: 175635--175661 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
175625 GAACCAGGCA
175635 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
175662 GGTTTACTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:187074 original size:67 final size:67
Alignment explanation
Indices: 186966--187095 Score: 251
Period size: 67 Copynumber: 1.9 Consensus size: 67
186956 CTATTTAAAA
186966 ATGAGATATAGTTATGTTACACAATGTAAAACTCTTTTAGTTTTACACAAATTTAGAACCGTTTG
1 ATGAGATATAGTTATGTTACACAATGTAAAACTCTTTTAGTTTTACACAAATTTAGAACCGTTTG
187031 AT
66 AT
*
187033 ATGAGATATAGTTATGTTACGCAATGTAAAACTCTTTTAGTTTTACACAAATTTAGAACCGTT
1 ATGAGATATAGTTATGTTACACAATGTAAAACTCTTTTAGTTTTACACAAATTTAGAACCGTT
187096 GGATGAATGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (67 bp):
ATGAGATATAGTTATGTTACACAATGTAAAACTCTTTTAGTTTTACACAAATTTAGAACCGTTTG
AT
Found at i:191218 original size:34 final size:34
Alignment explanation
Indices: 191175--191242 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
191165 CTCAAAGCAT
*
191175 GTGAGTTGACTCGTTTGTTCGTTAATGGTAGCCA
1 GTGAGTTGACTCGCTTGTTCGTTAATGGTAGCCA
191209 GTGAGTTGACTCGCTTGTTCGTTAATGGTAGCCA
1 GTGAGTTGACTCGCTTGTTCGTTAATGGTAGCCA
191243 ATAGTTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.37
Consensus pattern (34 bp):
GTGAGTTGACTCGCTTGTTCGTTAATGGTAGCCA
Found at i:193406 original size:10 final size:10
Alignment explanation
Indices: 193391--193415 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
193381 TATCTATTTA
193391 TTTATTTTTC
1 TTTATTTTTC
193401 TTTATTTTTC
1 TTTATTTTTC
193411 TTTAT
1 TTTAT
193416 CTTTGATTTA
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:203939 original size:15 final size:14
Alignment explanation
Indices: 203919--203956 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
203909 TCCTAAGTTG
203919 AAAAAAAACAAACAA
1 AAAAAAAACAAA-AA
203934 AAAAAAAACAAAAA
1 AAAAAAAACAAAAA
203948 AAAACAAAA
1 AAAA-AAAA
203957 AGAGAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAAA
Found at i:203946 original size:10 final size:10
Alignment explanation
Indices: 203921--203957 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
203911 CTAAGTTGAA
203921 AAAAAACAAAC
1 AAAAAA-AAAC
203932 AAAAAAAAAAC
1 -AAAAAAAAAC
203943 AAAAAAAAAC
1 AAAAAAAAAC
203953 AAAAA
1 AAAAA
203958 GAGAAAAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 15 0.60
11 4 0.16
12 6 0.24
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:204926 original size:105 final size:105
Alignment explanation
Indices: 204744--205680 Score: 1563
Period size: 105 Copynumber: 9.0 Consensus size: 105
204734 TTTTACCCAT
*
204744 AGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
204809 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTTAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
204849 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
204914 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGA-TTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCA-ATTTCAG
* *
204954 AGTCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
205019 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGA-TTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCA-ATTTCAG
* *
205059 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
205124 AAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
205164 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
205229 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGA-TTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCA-ATTTCAG
*
205269 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
205334 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
205374 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
205439 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* ***
205479 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* ** *
205544 AAGGAACCGCTGACTGT---C-AAC--TTCTCAATTTTAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* *
205578 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAAC-ACGCAAGTTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
205642 AAGGGACCGCT-GTTGTCAATAAACATTTCCCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
205681 CTTCACAACG
Statistics
Matches: 787, Mismatches: 35, Indels: 22
0.93 0.04 0.03
Matches are distributed among these distances:
97 3 0.00
98 28 0.04
99 51 0.06
101 6 0.01
102 1 0.00
103 11 0.01
104 2 0.00
105 683 0.87
106 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
Found at i:205763 original size:20 final size:20
Alignment explanation
Indices: 205738--205779 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
205728 CCAGAACTCT
205738 GAGTTCGATTTCAACTTCAC
1 GAGTTCGATTTCAACTTCAC
*
205758 GAGTTCGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
205778 GA
1 GA
205780 CGAAGGATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:207373 original size:10 final size:10
Alignment explanation
Indices: 207358--207382 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
207348 TATCTATTTA
207358 TTTATTTTTC
1 TTTATTTTTC
207368 TTTATTTTTC
1 TTTATTTTTC
207378 TTTAT
1 TTTAT
207383 CTTTGATTTA
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:213807 original size:23 final size:23
Alignment explanation
Indices: 213739--213797 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
213729 ACATTTTATA
*
213739 TGGCACTTCGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
*
213762 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
213785 TGGCACTTCGGTG
1 TGGCACTTCGGTG
213798 TATTTATACG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Done.