# obsolete output files, at least for annotation purposes
tcsh> \rm -f 200401281130_rhythm/pos162b_on_chr8_hitseqf.fa.c[au]t   # *.cut possibly
tcsh> \rm -f 200401281130_rhythm/pos162b_on_chr8_hitseqf.fa.masked*
tcsh> \rm -f 200401281130_rhythm/pos162b_on_chr8_hitseqf.fa.stderr
tcsh> \rm -f 200401281130_rhythm/pos162b_on_chr8_hitseqf.fa.tbl
--------------------------------------------------------------------------------
# main syntax
tcsh> head 200401281130_rhythm/pos162b_on_chr8_hitseqf.fa.out
   SW  perc perc perc  query     position in query    matching repeat                position in  repeat
score  div. del. ins.  sequence  begin  end (left)    repeat   class/family          begin  end (left)  ID

  999  15.9  4.8  0.0  chr8          1  284 (6417) C  ALRa_    Satellite/centromeric   (0)  297      1     *
 1001  14.6  3.3  0.0  chr8         45  540 (6161) C  ALRa     Satellite/centromeric   (3)  512      1     *
 1110  13.4  0.3  0.3  chr8        461  799 (5902) C  ALRa_    Satellite/centromeric   (4)  339      1      
  951  17.5  0.3  0.3  chr8        715 1057 (5644) C  ALRa     Satellite/centromeric   (1)  343      1     *
 1005  14.2  0.0  0.0  chr8        977 1138 (5563) C  ALRa_    Satellite/centromeric   (4)  168      7      
  944  15.6  0.0  0.0  chr8       1152 1311 (5390) C  ALRa_    Satellite/centromeric   (8)  164      5     *
  963  16.2  0.0  0.6  chr8       1230 1487 (5214) C  ALRa     Satellite/centromeric   (0)  256      1      
...
--------------------------------------------------------------------------------
# syntax for reverse orientation
tcsh> head 200401281130_rhythm/pos162b_on_chr8_hitseqr.fa.out
   SW  perc perc perc  query     position in query         matching  repeat                position in  repeat
score  div. del. ins.  sequence   begin    end   (left)    repeat    class/family           begin  end (left)   ID

 1057  13.9  0.0  0.0  chr8           1    254 (302546) +  ALRa_     Satellite/centromeric      1  254    (0)       
 1133  12.0  0.6  2.6  chr8         426    776 (302024) +  ALRa_     Satellite/centromeric      1  344    (0)       
 1065  13.8  0.9  0.0  chr8         692   1032 (301768) +  ALRa      Satellite/centromeric      1  344    (0)      *
 1105  13.1  0.3  0.3  chr8         949   1291 (301509) +  ALRa_     Satellite/centromeric      1  343    (0)      *
 1171  13.0  1.6  0.1  chr8        1206   1884 (300916) +  ALRa      Satellite/centromeric      1  688    (0)       
 1068  14.3  0.6  0.0  chr8        1799   2140 (300660) +  ALRa_     Satellite/centromeric      1  343    (0)      *
 1037  15.8  0.6  0.0  chr8        2056   2397 (300403) +  ALRa      Satellite/centromeric      1  343    (0)      *
