RepeatMasker started 05-Nov-2009 05:59:38 PST

RepeatMasker version open-3.2.8
Search engine: ABBlast/WUBlast

analyzing file /usr/local/rmserver/tmp/RM2sequpload_1257429576

Checking for E. coli insertion elements
identifying simple repeats in batch 1 of 1
identifying full-length ALUs in batch 1 of 1
identifying full-length interspersed repeats in batch 1 of 1
identifying remaining ALUs in batch 1 of 1
identifying most interspersed repeats in batch 1 of 1
identifying long interspersed repeats in batch 1 of 1
identifying ancient repeats in batch 1 of 1
identifying retrovirus-like sequences in batch 1 of 1
identifying tough LINE1s in batch 1 of 1
identifying more simple repeats in batch 1 of 1
identifying low complexity regions in batch 1 of 1
refining SINE/Alu elements in batch 1 of 1
processing output...
Generating output...
masking
done
8.76user 2.30system 0:10.66elapsed 103%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+309083minor)pagefaults 0swaps

Summary:

==================================================
file name: RM2sequpload_1257429576  
sequences:             1
total length:      17731 bp  (17731 bp excl N/X-runs) 
GC level:         39.54 %
bases masked:       6570 bp ( 37.05 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
SINEs:               11         1965 bp   11.08 %
      ALUs            4         1040 bp    5.87 %
      MIRs            7          925 bp    5.22 %

LINEs:                6         2378 bp   13.41 %
      LINE1           2         1672 bp    9.43 %
      LINE2           3          483 bp    2.72 %
      L3/CR1          1          223 bp    1.26 %

LTR elements:         2          614 bp    3.46 %
      ERVL            2          614 bp    3.46 %
      ERVL-MaLRs      0            0 bp    0.00 %
      ERV_classI      0            0 bp    0.00 %
      ERV_classII     0            0 bp    0.00 %

DNA elements:         7         1505 bp    8.49 %
     hAT-Charlie      3          382 bp    2.15 %
     TcMar-Tigger     2          813 bp    4.59 %

Unclassified:         0            0 bp    0.00 %

Total interspersed repeats:     6462 bp   36.44 %


Small RNA:            0            0 bp    0.00 %

Satellites:           0            0 bp    0.00 %
Simple repeats:       1           43 bp    0.24 %
Low complexity:       2           65 bp    0.37 %
==================================================

* most repeats fragmented by insertions or deletions
  have been counted as one element
                                                      

The query species was assumed to be homo          
RepeatMasker version open-3.2.8 , default mode
                                   
run with blastp version 3.0-SE [2009-05-28] [linux26-x64-I32LPF64 2009-05-28T03:37:50]
RepBase Update 20090604, RM database version 20090604

Results