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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"

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  • $\begingroup$ 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? $\endgroup$
    – llrs
    Apr 29, 2019 at 14:48
  • $\begingroup$ 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 $\endgroup$
    – jonny
    Apr 29, 2019 at 15:13
  • $\begingroup$ If you could link and cite what parts you don't understand we could help you better $\endgroup$
    – llrs
    Apr 29, 2019 at 20:11
  • $\begingroup$ " 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 $\endgroup$
    – jonny
    Apr 29, 2019 at 21:15
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    $\begingroup$ Where are you taking this from? Could you provide also the link? Do not forget to edit the question to include this relevant information $\endgroup$
    – llrs
    Apr 29, 2019 at 21:32

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