RepeatMasker started 01-May-2025 03:08:09 PDT

RepeatMasker version open-4.0.9
Search Engine: HMMER [ 3.3.2 (Nov 2020) ]
Master RepeatMasker Database: /u3/local/rmserver/share/Libraries/Dfam.hmm ( Complete Database: HMM-Dfam_3.0 )



analyzing file /usr/local/rmserver/tmp/RM2sequpload_1746094089
identifying Simple Repeats in batch 1 of 1
identifying matches to vertebrata metazoa sequences in batch 1 of 1
identifying Simple Repeats in batch 1 of 1
processing output: 
cycle 1 
cycle 2 
cycle 3 
cycle 4 
cycle 5 
cycle 6 
cycle 7 
cycle 8 
cycle 9 
cycle 10 
Generating output... 
masking
done
609.38user 3.39system 5:10.22elapsed 197%CPU (0avgtext+0avgdata 1341952maxresident)k
2982200inputs+6728outputs (1major+2636507minor)pagefaults 0swaps

Summary:

==================================================
file name: RM2sequpload_1746094089  
sequences:             1
total length:      49490 bp  (49490 bp excl N/X-runs) 
GC level:         44.89 %
bases masked:      19049 bp ( 38.49 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
Retroelements           17        18367 bp   37.11 %
   SINEs:                0            0 bp    0.00 %
   Penelope              0            0 bp    0.00 %
   LINEs:                5         3171 bp    6.41 %
    CRE/SLACS            0            0 bp    0.00 %
     L2/CR1/Rex          5         3171 bp    6.41 %
     R1/LOA/Jockey       0            0 bp    0.00 %
     R2/R4/NeSL          0            0 bp    0.00 %
     RTE/Bov-B           0            0 bp    0.00 %
     L1/CIN4             0            0 bp    0.00 %
   LTR elements:        12        15196 bp   30.71 %
     BEL/Pao             0            0 bp    0.00 %
     Ty1/Copia           0            0 bp    0.00 %
     Gypsy/DIRS1         0            0 bp    0.00 %
       Retroviral       12        15196 bp   30.71 %

DNA transposons          0            0 bp    0.00 %
   hobo-Activator        0            0 bp    0.00 %
   Tc1-IS630-Pogo        0            0 bp    0.00 %
   En-Spm                0            0 bp    0.00 %
   MuDR-IS905            0            0 bp    0.00 %
   PiggyBac              0            0 bp    0.00 %
   Tourist/Harbinger     0            0 bp    0.00 %
   Other (Mirage,        0            0 bp    0.00 %
    P-element, Transib)

Rolling-circles          0            0 bp    0.00 %

Unclassified:            0            0 bp    0.00 %

Total interspersed repeats:       18367 bp   37.11 %


Small RNA:               0            0 bp    0.00 %

Satellites:              0            0 bp    0.00 %
Simple repeats:         13          557 bp    1.13 %
Low complexity:          3          125 bp    0.25 %
==================================================

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

The query species was assumed to be vertebrata metazoa
RepeatMasker version open-4.0.9 , default mode
                                   
run with nhmmscan version 3.3.2 (Nov 2020)

Results