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Old 06-04-2013, 01:23 AM   #1
rahbz
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Location: Kharagpur, India

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Default help in Repeat Masker

Can any of you please let me know the interpretation of the repeat families

This is the part of .out file generated by the RepeatMasker

736 26.0 0.6 1.1 chr19 8015 8193 (299) C Eulor5B DNA? (0) 192 15 48785
390 26.9 4.3 10.0 chr19 76047 76220 (93229) C MamRep4096 DNA/hAT? (154) 272 107 48278
390 26.9 4.3 10.0 chr19 76851 76886 (92563) C MamRep4096 DNA/hAT? (320) 106 73 48278
523 25.6 15.0 0.0 chr19 3304 3463 (1384) C MER91A DNA/hAT-Tip100 (11) 185 2 40
268 25.2 4.8 16.2 chr19 6863 6996 (167262) + Charlie7a DNA/hAT-Charlie 1 122 (150) 99
268 25.2 4.8 16.2 chr19 7129 7217 (167041) + Charlie7a DNA/hAT-Charlie 123 203 (69) 99
268 25.2 4.8 16.2 chr19 7459 7527 (166731) + Charlie7a DNA/hAT-Charlie 204 265 (7) 99


What does DNA and DNA? mean
What does a question mark indicate at the end of the family.
Thank you in advance,

Last edited by rahbz; 06-04-2013 at 01:28 AM.
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Old 06-11-2013, 11:06 AM   #2
rhubley
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The "DNA" class stands for DNA Tranposon -- a cut and paste type of interspersed repeats.
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Old 06-11-2013, 11:22 PM   #3
rahbz
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Yah but what does 'DNA?' mean
what is the difference between 'DNA' and 'DNA?'
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Old 06-12-2013, 09:39 AM   #4
rhubley
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Sorry, I didn't see the "?" in your original question. The "?" following either a class for subclass is an indication that the curator is not confident in the call of the class or subclass. As we learn more about the element in question the classification is either changed or the "?" designation is removed.
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