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If I go to ncbi site, apply customize view -> Customize -> All features -> Update view and then ctrl + f : Alu I can get all alu repeaing regions coordinates from this chromosome.

It looks like:

 repeat_region   complement(37490..37800)
                 /note="AluY"
                 /rpt_family="SINE/Alu"
                 /rpt_type=DISPERSED

How could I download all this coordinates and names of repeating regions from the internet to .txt file? Or some tool

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  • $\begingroup$ Hi @WhoAmI, an efetch command would be the best option. You can Blast them out ... but the genomic position might not follow (not sure). $\endgroup$
    – M__
    Jul 8 '20 at 12:40
  • $\begingroup$ @Michael could you write usage example? $\endgroup$
    – WhoAmI
    Jul 8 '20 at 12:58
  • $\begingroup$ Have a go yourself, thats the best way to get help on site. I don't work on human genomics so its not something I'd do ... but fishing out bits of Genbank annotation is certainly an efetch thing. $\endgroup$
    – M__
    Jul 8 '20 at 13:03
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Click on the 'GenBank' dropdown menu at the top left corner of this page to see a graphical view of the sequence. You should see a 'Repeat region' track in the Sequence Viewer. Click on the 'Download' button in the top right corner of the Sequence Viewer, choose 'Download Track Data' to launch a dialog box where you can enter a range, select the 'Repeat region' track and download data in BED format. Unfortunately, the names for the features are not great.

If you want the names to be the same ones in the flat file, you can download the feature table and parse it. To download the feature table, click on the 'Send To' link at the top right corner of this page, choose 'Complete Record', 'File' and 'Feature Table' as 'Format'. After you download the feature table, you can parse it using awk as shown below to create a 4-column table with the data.

cat seq.ft \
  | awk 'BEGIN{FS="\t";OFS="\t"}{
    if(NF==3) {print s,e,f,q ; s=$1; e=$2; f=$3; q=""} 
    else if(NF==2) {print s,e,f,q ; s=$1; e=$2; q=""} 
    else if(NF==5) {q=q"|"$4"="$5} }' \
  > feat_table.tsv
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