Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009382.1 Hibiscus syriacus cultivar Beakdansim tig00113268_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: 20662
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:5601 original size:12 final size:12
Alignment explanation
Indices: 5580--5621 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5570 CTTTTCTTCG
*
5580 ATATTGAAAATA
1 ATATTTAAAATA
5592 ATATTTAAAATA
1 ATATTTAAAATA
*
5604 AT-TTAAAAATA
1 ATATTTAAAATA
*
5615 TTATTTA
1 ATATTTA
5622 TTATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
ATATTTAAAATA
Found at i:7104 original size:14 final size:15
Alignment explanation
Indices: 7085--7118 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7075 GTCTGTAATT
7085 ATTTATTT-ATATAG
1 ATTTATTTAATATAG
*
7099 ATTTATTTAATATAT
1 ATTTATTTAATATAG
7114 ATTTA
1 ATTTA
7119 ATAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTATTTAATATAG
Found at i:7125 original size:3 final size:3
Alignment explanation
Indices: 7117--7190 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
7107 AATATATATT
*
7117 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7165 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
7191 TGGGTAAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:10369 original size:35 final size:35
Alignment explanation
Indices: 10330--10438 Score: 166
Period size: 35 Copynumber: 3.1 Consensus size: 35
10320 ACATTCCTCG
10330 ATTTCATTCTAAACCCCAAATTCCAAAATAATTCA
1 ATTTCATTCTAAACCCCAAATTCCAAAATAATTCA
*
10365 ATTTCATTCTAAACCCTAAATTCCAAAATAATTCA
1 ATTTCATTCTAAACCCCAAATTCCAAAATAATTCA
* * *
10400 ATTAT-ATTCTAAAACCCAAATTCTAAAATATTTCA
1 ATT-TCATTCTAAACCCCAAATTCCAAAATAATTCA
10435 ATTT
1 ATTT
10439 AAGGAGGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
34 1 0.01
35 66 0.97
36 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (35 bp):
ATTTCATTCTAAACCCCAAATTCCAAAATAATTCA
Found at i:11541 original size:35 final size:35
Alignment explanation
Indices: 11492--11599 Score: 146
Period size: 35 Copynumber: 3.1 Consensus size: 35
11482 AAAAAAGACA
* * *
11492 GAAATTGAAGTATTTTAGAATTTGAGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGAGGTTTAGAAT
*
11527 GTAATTGAATTATTTTGGAATTT-AGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGA-GGTTTAGAAT
* *
11562 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGAGGTTTAGAAT
11597 GAA
1 GAA
11600 GGATTGTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
34 1 0.02
35 63 0.98
ACGTcount: A:0.34, C:0.01, G:0.22, T:0.43
Consensus pattern (35 bp):
GAAATTGAATTATTTTGGAATTTGAGGTTTAGAAT
Found at i:14400 original size:18 final size:18
Alignment explanation
Indices: 14377--14429 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
14367 TTTCGTTCTG
14377 GAATGATCAAAGAATTAA
1 GAATGATCAAAGAATTAA
14395 GAATGATCAAAGAATTAA
1 GAATGATCAAAGAATTAA
*
14413 GAACGATCAAAGAATTA
1 GAATGATCAAAGAATTA
14430 GGATCAACTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.55, C:0.08, G:0.17, T:0.21
Consensus pattern (18 bp):
GAATGATCAAAGAATTAA
Found at i:15086 original size:19 final size:19
Alignment explanation
Indices: 15062--15168 Score: 124
Period size: 19 Copynumber: 5.6 Consensus size: 19
15052 ACTGTTCACG
15062 GTACTATTCATACCATATA
1 GTACTATTCATACCATATA
* *
15081 GTACTATTTAAACCATATA
1 GTACTATTCATACCATATA
* *
15100 GTACTATTTATACAATATA
1 GTACTATTCATACCATATA
* * * *
15119 ATACTATTTAAACCGTATA
1 GTACTATTCATACCATATA
*
15138 GTACTATTCATACAATATA
1 GTACTATTCATACCATATA
*
15157 GTATTATTCATA
1 GTACTATTCATA
15169 AAAACGTTTC
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 74 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (19 bp):
GTACTATTCATACCATATA
Found at i:15118 original size:38 final size:38
Alignment explanation
Indices: 15062--15164 Score: 161
Period size: 38 Copynumber: 2.7 Consensus size: 38
15052 ACTGTTCACG
*
15062 GTACTATTCATACCATATAGTACTATTTAAACCATATA
1 GTACTATTCATACAATATAGTACTATTTAAACCATATA
* * *
15100 GTACTATTTATACAATATAATACTATTTAAACCGTATA
1 GTACTATTCATACAATATAGTACTATTTAAACCATATA
*
15138 GTACTATTCATACAATATAGTATTATT
1 GTACTATTCATACAATATAGTACTATT
15165 CATAAAAACG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (38 bp):
GTACTATTCATACAATATAGTACTATTTAAACCATATA
Done.