Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006998.1 Hibiscus syriacus cultivar Beakdansim tig00018051_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: 50326
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:10056 original size:43 final size:43
Alignment explanation
Indices: 9977--10059 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
9967 ATTAGCGGCG
* * * *
9977 TTTGTTCAAAAAACGCTGTTATAGATTCGATCTTTTGCGGGCA
1 TTTGTTCAAAAAACGCCGCTATAGATCCAATCTTTTGCGGGCA
*
10020 TTTGTTCCAAAAACGCCGCTATAGATCCAA-CTTTTTGCGG
1 TTTGTTCAAAAAACGCCGCTATAGATCCAATC-TTTTGCGG
10060 CGTTTTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 33 0.97
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (43 bp):
TTTGTTCAAAAAACGCCGCTATAGATCCAATCTTTTGCGGGCA
Found at i:32593 original size:15 final size:15
Alignment explanation
Indices: 32573--32602 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32563 CTTTCTCATA
32573 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
32588 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
32603 CCAGCCTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:36802 original size:19 final size:17
Alignment explanation
Indices: 36778--36816 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
36768 GTCAAAGGAA
36778 GTCAACGGTCAACGGTCGG
1 GTCAACGGTC-A-GGTCGG
36797 GTCAACGGTCAGGTCGG
1 GTCAACGGTCAGGTCGG
36814 GTC
1 GTC
36817 GGTCGGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
19 10 0.50
ACGTcount: A:0.18, C:0.26, G:0.38, T:0.18
Consensus pattern (17 bp):
GTCAACGGTCAGGTCGG
Found at i:45632 original size:12 final size:12
Alignment explanation
Indices: 45617--45658 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
45607 AATTGTTGAT
45617 GGAATTACTGAG
1 GGAATTACTGAG
*
45629 GGAATTTA-TGAC
1 GGAA-TTACTGAG
*
45641 AGAATTACTGAG
1 GGAATTACTGAG
45653 GGAATT
1 GGAATT
45659 TATGACGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (12 bp):
GGAATTACTGAG
Found at i:45645 original size:24 final size:24
Alignment explanation
Indices: 45618--45670 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
45608 ATTGTTGATG
45618 GAATTACTGAGGGAATTTATGACA
1 GAATTACTGAGGGAATTTATGACA
*
45642 GAATTACTGAGGGAATTTATGACG
1 GAATTACTGAGGGAATTTATGACA
45666 GAATT
1 GAATT
45671 TAAGTTTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (24 bp):
GAATTACTGAGGGAATTTATGACA
Found at i:45668 original size:12 final size:12
Alignment explanation
Indices: 45629--45672 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
45619 AATTACTGAG
45629 GGAATTTATGAC
1 GGAATTTATGAC
* *
45641 AGAA-TTACTGAG
1 GGAATTTA-TGAC
45653 GGAATTTATGAC
1 GGAATTTATGAC
45665 GGAATTTA
1 GGAATTTA
45673 AGTTTAGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (12 bp):
GGAATTTATGAC
Found at i:45833 original size:2 final size:2
Alignment explanation
Indices: 45822--45860 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
45812 ATCAGTCGGA
45822 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45861 TTTATGTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46060 original size:14 final size:14
Alignment explanation
Indices: 46041--46070 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
46031 CATTCCCTTC
46041 AAAATATTATTATG
1 AAAATATTATTATG
46055 AAAATATTATTATG
1 AAAATATTATTATG
46069 AA
1 AA
46071 TCTAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (14 bp):
AAAATATTATTATG
Found at i:46779 original size:31 final size:31
Alignment explanation
Indices: 46741--46813 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
46731 AACTCTAAAC
*
46741 TTTGTGACGGAACATATGAACCCGTCAGAAA
1 TTTGTGACGGAACAGATGAACCCGTCAGAAA
* * * *
46772 TTTGTGACGGAATAGGTGAATCTGTCAGAAA
1 TTTGTGACGGAACAGATGAACCCGTCAGAAA
46803 TTTGTGACGGA
1 TTTGTGACGGA
46814 TCCACATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (31 bp):
TTTGTGACGGAACAGATGAACCCGTCAGAAA
Found at i:46835 original size:31 final size:31
Alignment explanation
Indices: 46795--46868 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
46785 AGGTGAATCT
* *
46795 GTCAGAAATTTGTGACGGATCCACATATTCC
1 GTCACAAATTTATGACGGATCCACATATTCC
* * *
46826 GTCACAAATTTATGATGGGTCGACATATTCC
1 GTCACAAATTTATGACGGATCCACATATTCC
**
46857 AACACAAATTTA
1 GTCACAAATTTA
46869 AAATACTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (31 bp):
GTCACAAATTTATGACGGATCCACATATTCC
Done.