RepeatMasker started 02-May-2025 09:31:40 PDT

RepeatMasker version open-4.0.9
Search Engine: NCBI/RMBLAST [ 2.14.1+ ]
Master RepeatMasker Database: /u3/local/rmserver/share/Libraries/RepeatMaskerLib.embl ( Complete Database: CONS-Dfam_3.0 )



analyzing file /usr/local/rmserver/tmp/RM2_insertions_008.fa_1746203498

Checking for E. coli insertion elements
identifying Simple Repeats in batch 1 of 3
identifying full-length ALUs in batch 1 of 3
identifying full-length interspersed repeats in batch 1 of 3
identifying remaining ALUs in batch 1 of 3
identifying most interspersed repeats in batch 1 of 3
identifying long interspersed repeats in batch 1 of 3
identifying ancient repeats in batch 1 of 3
identifying retrovirus-like sequences in batch 1 of 3
identifying Simple Repeats in batch 1 of 3

Checking for E. coli insertion elements
identifying Simple Repeats in batch 2 of 3
identifying full-length ALUs in batch 2 of 3
identifying full-length interspersed repeats in batch 2 of 3
identifying remaining ALUs in batch 2 of 3
identifying most interspersed repeats in batch 2 of 3
identifying long interspersed repeats in batch 2 of 3
identifying ancient repeats in batch 2 of 3
identifying retrovirus-like sequences in batch 2 of 3
identifying Simple Repeats in batch 2 of 3

Checking for E. coli insertion elements
identifying Simple Repeats in batch 3 of 3
identifying full-length ALUs in batch 3 of 3
identifying full-length interspersed repeats in batch 3 of 3
identifying remaining ALUs in batch 3 of 3
identifying most interspersed repeats in batch 3 of 3
identifying long interspersed repeats in batch 3 of 3
identifying ancient repeats in batch 3 of 3
identifying retrovirus-like sequences in batch 3 of 3
identifying Simple Repeats in batch 3 of 3
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
34.05user 3.46system 0:31.38elapsed 119%CPU (0avgtext+0avgdata 798704maxresident)k
384inputs+108168outputs (0major+1273506minor)pagefaults 0swaps

Summary:

==================================================
file name: RM2_insertions_008.fa_1746203498
sequences:          1152
total length:     173455 bp  (173455 bp excl N/X-runs)
GC level:         43.05 %
bases masked:     143372 bp ( 82.66 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
SINEs:              311        88466 bp   51.00 %
      ALUs          311        88466 bp   51.00 %
      MIRs            0            0 bp    0.00 %

LINEs:               72        10827 bp    6.24 %
      LINE1          70        10667 bp    6.15 %
      LINE2           2          160 bp    0.09 %
      L3/CR1          0            0 bp    0.00 %

LTR elements:        29         2407 bp    1.39 %
      ERVL            6          574 bp    0.33 %
      ERVL-MaLRs      7          734 bp    0.42 %
      ERV_classI     14          988 bp    0.57 %
      ERV_classII     2          111 bp    0.06 %

DNA elements:         3          231 bp    0.13 %
     hAT-Charlie      1           74 bp    0.04 %
     TcMar-Tigger     1           89 bp    0.05 %

Unclassified:        13         1444 bp    0.83 %

Total interspersed repeats:   103375 bp   59.60 %


Small RNA:            4          240 bp    0.14 %

Satellites:           8         1131 bp    0.65 %
Simple repeats:     555        38041 bp   21.93 %
Low complexity:      10          585 bp    0.34 %
==================================================

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

The query species was assumed to be homo sapiens  
RepeatMasker Combined Database: Dfam_3.0
                                         
run with rmblastn version 2.14.1+

Results