parsing sorted dsim2-dmel-dna.gff to gff: dsim2-dmel-algn.gff
filters: skipsubseg=42840, joinoverlap=5630, minsizecut=5216 
Chr               cover       gaps     n_segs  n_targets       prob
chr2L          21569186     467740       1157        698   6.00e-07
chr2L_random     845297      53638         28         18   2.50e-14
chr2R          19324982     272736        889        482   7.21e-07
chr2R_random    2782184     209540        212        137   1.29e-08
chr2h_random    2132550    1044633        829        628   1.56e-06
chr3L          22171883     381105       1062        620   3.05e-08
chr3L_random    1006270      43361         22         17   9.09e-08
chr3R          27197897     320142       1122        628   5.21e-08
chr3R_random    1255391      49587         27         22   2.59e-29
chr3h_random     975552     469059        406        307   2.18e-06
chr4             862082      52713        217        159   2.89e-06
chr4_random      130773       1600          6          4   0.00e+00
chrU            8611575    7177676       2857       2205   1.26e-06
chrX           16652269     390069        781        573   7.36e-07
chrX_random     5494123     200190        144        108   2.09e-07
chrXh_random       9277      68627         23         18   2.15e-06
chrYh_random      53152      31635          9          6   3.33e-09
Total         131074443   11234051       9791       6630   8.67e-07
===========================================================================
chr x targets over 1% of 131074443 cover, from n=  6 targets 
dmelchr:3R     28688248   21.9%   chr3R   93.6%  chr3R_random    4.2%
dmelchr:3L     26895606   20.5%   chr3L   81.3%    chrU    7.9%
dmelchr:2R     26136051   19.9%   chr2R   71.6%  chr2R_random   10.0%
dmelchr:X      24871384   19.0%    chrX   65.6%  chrX_random   21.5%
dmelchr:2L     23245277   17.7%   chr2L   90.4%    chrU    3.7%
---------------------------------------------------------------------------