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During NCBI BLAST+ segmasker output exploration, I found out that for some sequences, the program returns the same interval twice:

>tr|A0A0D2B4V6|A0A0D2B4V6_9EURO Uncharacterized protein OS=Cladophialophora immunda OX=569365 GN=PV07_04097 PE=3 SV=1
131 - 139
131 - 139

This seems not to be a planned behaviour, but maybe someone has an explanation.

The command I ran was:

segmasker -in <input_file> -out <output_file> -locut 1.5 -hicut 1.8 -window 15

Exemplary sequences triggering such an event:

>sequence1
MDSHNSSTLIILSLPPKTFVGLDLVSFDSSPNFQGIAKIPVGIHFLYTGTDASLSIRHGRWLNLTSTHPIQVLRWNSDGETLQPVDQNDQTARNAIAAISNGRGLVDYGALQSATSELSTRESQSHDASSLAAAAAAAAADEDRAESTDWPALTAHISSPLLTRILSPDWIVSSISSAPTDTETIPGLSHLEASNALHQLPLDLLPVNLKQTWAGGDIGRARTERARDRSWYLGQLIEQAARPQGGDKTAGAREVLGELQFCFLMVLTLANYSCLEQWKRLLSVFFTCRTALDEVEGYFVQVIRVLRLQIKHVDDVEGGLFELRDESGSAWLRTLWARFRSVVDDADKGERVSLKKEVDALEKLFEGKYGWQSERDILRRGMLELEDGERVEVTMHGVDEDEETGEYAPVIVET
>sequence2
VDKLFKKNAMGNNIFHEIAIQGSLMLLQTIRDNVDGQMDTYLSEINDQNESCITIVADRHRGLLAKDLIEIFVDLGADINETDNWGNTALHYSVFHRDHVLAEWLCQQPGINLNAINNDEHTPLGLAILWNIQSIKTLLESKGARFNNIEFSDSETSDDDDDDDDDGHDENDE
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    $\begingroup$ What command are you running? What options? $\endgroup$
    – terdon
    Commented Nov 28, 2022 at 16:52
  • $\begingroup$ Right, I should have include it. segmasker -in <input_file> -out <output_file> -locut 1.5 -hicut 1.8 -window 15. $\endgroup$
    – maciejwww
    Commented Nov 28, 2022 at 20:27
  • $\begingroup$ Could there be something silly like having duplicate sequences in your input? Which are then combined in the output? $\endgroup$
    – terdon
    Commented Nov 29, 2022 at 19:13
  • $\begingroup$ Nah, I've just run segmasker on the given example and got. $\endgroup$
    – maciejwww
    Commented Nov 29, 2022 at 21:30
  • $\begingroup$ I'm using segmasker locally. Installed last week. $\endgroup$
    – maciejwww
    Commented Nov 29, 2022 at 21:31

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