Body: <p>I'm running Repeatscout. I built the l-mer table called myfile.freq of myfile.fa
  Can anyone tell me what do they mean the second and third columns produced as output?
  here I report an example:</p>
  
  <pre><code>AAAAAAAAGCGGGA  3       107776875 
  AAAAAAACTGTATG  10  83440519
  AAAAAAAAGGCGTA  3   41037187
  AAAAAAACTTGAAT  7   94493612
  CATACATGCATGCA  1065    125671338
  CATACATGCTTGAA  7   121799834
  AAAAAAATCATGCA  10  95493021
  AAAAAAAGTCCAGT  3   125127980
  AATTCACATGTATG  7   102505668
  </code></pre>
  
  <p>I read the tutorial that explains how to run the program: <a href="https://bix.ucsd.edu/repeatscout/readme.1.0.3.txt" rel="nofollow noreferrer">https://bix.ucsd.edu/repeatscout/readme.1.0.3.txt</a>. 
  It says: "First, build_lmer_table creates a file that tabulates the frequency of all l-mers in the sequence to be analyzed"</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-29T14:48:15.220Z
Comments.Text: Welcome to the site Jonny. Did you read the documentation of the software you are using, or any tutorial where it is used? Did you try searching on the internet for this format/output?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-29T15:13:58.737Z
Comments.Text: Yes, I searched and I read some manuals but I really don't understand what they mean. I know that it's built this table of l-mer from the original genome fasta file
Comments.UserDisplayName: jonny
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-29T20:11:04.843Z
Comments.Text: If you could link and cite what parts you don't understand we could help you better
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-29T21:15:29.877Z
Comments.Text: " First, build_lmer_table
  creates a file that tabulates the frequency of all l-mers in the
  sequence to be analyzed."  I SUPPOSED that the second column could indicate the number of l-mer, but I don't understand what the third column is showing
Comments.UserDisplayName: jonny
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-29T21:32:41.697Z
Comments.Text: Where are you taking this from? Could you provide also the link?  Do not forget to [edit] the question to include this relevant information
Comments.UserDisplayName: llrs
Tags: <transposable-elements><repeatmasker>
Title: repeatscout freq table
ThreadText: # repeatscout freq table
  
  (Asked by: username_0 on 2019-04-29)
  
  I'm running Repeatscout. I built the l-mer table called myfile.freq of myfile.fa
  Can anyone tell me what do they mean the second and third columns produced as output?
  here I report an example:
  
  ```
  AAAAAAAAGCGGGA  3       107776875 
  AAAAAAACTGTATG  10  83440519
  AAAAAAAAGGCGTA  3   41037187
  AAAAAAACTTGAAT  7   94493612
  CATACATGCATGCA  1065    125671338
  CATACATGCTTGAA  7   121799834
  AAAAAAATCATGCA  10  95493021
  AAAAAAAGTCCAGT  3   125127980
  AATTCACATGTATG  7   102505668
  
  ```
  
  I read the tutorial that explains how to run the program: <https://bix.ucsd.edu/repeatscout/readme.1.0.3.txt>.
  It says: "First, build\_lmer\_table creates a file that tabulates the frequency of all l-mers in the sequence to be analyzed"
  
  **Tags:** transposable-elements, repeatmasker
  
  > **Comments:**
  > **username_1**: Welcome to the site username_0. Did you read the documentation of the software you are using, or any tutorial where it is used? Did you try searching on the internet for this format/output?  
  > **username_0**: Yes, I searched and I read some manuals but I really don't understand what they mean. I know that it's built this table of l-mer from the original genome fasta file  
  > **username_1**: If you could link and cite what parts you don't understand we could help you better  
  > **username_0**: " First, build_lmer_table creates a file that tabulates the frequency of all l-mers in the sequence to be analyzed."  I SUPPOSED that the second column could indicate the number of l-mer, but I don't understand what the third column is showing  
  > **username_1**: Where are you taking this from? Could you provide also the link?  Do not forget to [edit] the question to include this relevant information  
  
  ---
  
  ## 0 answers
  
  