I'd like to ask about the meaning of the 5th column (an integer number) in BED format results from repeatmasker. 

    9	100663131	100663387	LTR22_SS	475	+
    9	70254161	70254685	ALTR2B_SSc	3460	+
    9	96468811	96469391	LTR8_SSc	3756	-
    9	116391614	116392469	LTR78	1152	+
    9	4980341	4980930	LTR39_SSc	3300	-
    9	16908116	16908359	MamGypLTR3	512	+
    9	17432426	17432886	ALTR2B2_SSc	1914	-
    9	18742941	18743430	LTR5_SS	2771	+
    9	27131556	27132076	ERV3-1_SSc-LTR	969	-
    9	30539515	30539909	LTR39B3_SSc	787	-

Searched around but did not find a definite answer, so seeking help here from repeatmasker experts. It is clearly not length of the repeat. Is it something indicating how repetitive this feature is in the genome? Or some identity scores indicating its match to some sort of repeat consensus?
It is the [Smith-Waterman alignment score][1] of matches with coding sequence. 

I think (but am not 100% certain) a higher score means greater similarity with coding sequence, indicating a less repetitive region. It is used for cutoff filters, which are specific to different classes of repeats.

I don't know how useful it is to use these scores directly. Also see "[How to read the results][2]" from the [Repeatmasker documentation][3]:

> Smith-Waterman score of the match, usually complexity adjusted
        The SW scores are not always directly comparable. Sometimes
        the complexity adjustment has been turned off, and a variety of
        scoring-matrices are used.

It may be worthwhile to [contact the developers directly][4].


  [1]: https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/rmsk2bed.html#column-mapping
  [2]: http://www.repeatmasker.org/webrepeatmaskerhelp.html#reading
  [3]: http://www.repeatmasker.org/
  [4]: http://www.repeatmasker.org/cgi-bin/form2mail?template=feedback.tmpl&title=Feedback%20Form