CPGAVAS2

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WARNINGS and NOTES

1. CPGAVAS2 is just an automatic tool. All results need to be inspected by experts before they are submitted to public databases or included in any publication. CPGAVAS2 cannot take any responsibility for generating any results with errors. Thanks for your understanding!
2. All analysis results will be stored on our server for at least three months. The users are encouraged to download the analyses results for long term storage. In any case, it will only take 10 minutes for the user to rerun the same analysis.
3. There is no storage limit set at this time.
4. The content for dataset 2 will be updated quarterly on the last Sunday of each quarter.

Annotate a New Plastome

The inputs are mostly self-evident, you just need to provide your assembled genome in FASTA format to run the annotator. Only "A", "T", "C" and "G" are allowed in the plastome sequence.

General information

Project Name	-
Species Name	-
Upload your input file in FASTA format with a postfix of ".fas" or ".fasta". Here is a sample file.	-
(Optional) Enter your email address to receive a notice for job completion.	-

Reference Dataset

Three Options:	- 1. 43-plastomes 2. 2544-plastomes 3. Custom reference in GenBank format
If you select option 3: please upload a file in GenBank format with a postfix of ".gb" or ".gbf". Here is a sample file.	-

Repeat identification

Repeat Type	Search Parameters
1. Microsatelite Sequence Repeats	- Short explanation of the parameters: the numbers before and after the "-" represent the unit size and minimal numbers of repeats respectively.
2. Tandem Repeats	- Short explanation of the parameters: 2,7,7: weights for match, mismatch and indels, respectively; 80 and 10: detection parameters, matching probability Pm=80 and indel probability Pi=10; 50: minimum alignment score; 500: maxmum period size.
3. Dispersed Repeats	- Short explanation of the parameters: -f: compute maximal forward repeats; -p compute maximal palindromes; -h search for repeats up to the given hamming distance; -l: specify that repeats must have the given length.