view repeathumfish.txt @ 54:d6b0feb22584 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 53aab6394c715dc2d7fdd9188d6c9834e0516b5c
author fubar
date Thu, 14 Mar 2024 00:59:36 +0000
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     Calypte Anna

     ==================================================
     file name: rm_input.fasta
     sequences:           159
     total length: 1059687259 bp  (1043590636 bp excl N/X-runs)
     GC level:         41.49 %
     bases masked:   79638300 bp ( 7.63 %)
     ==================================================
                    number of      length   percentage
                    elements*    occupied  of sequence
     --------------------------------------------------
     SINEs:            32491      3044030 bp    0.29 %
           ALUs            0            0 bp    0.00 %
           MIRs        23309      1792450 bp    0.17 %

     LINEs:           168150     56100653 bp    5.38 %
           LINE1         446        51456 bp    0.00 %
           LINE2        3520       419909 bp    0.04 %
           L3/CR1     161974     55206716 bp    5.29 %

     LTR elements:      3415      1802798 bp    0.17 %
           ERVL          649       266145 bp    0.03 %
           ERVL-MaLRs     15          814 bp    0.00 %
           ERV_classI   1341       795364 bp    0.08 %
           ERV_classII  1159       705705 bp    0.07 %

     DNA elements:     12073      1651025 bp    0.16 %
          hAT-Charlie    338        55376 bp    0.01 %
          TcMar-Tigger   787        83392 bp    0.01 %

     Unclassified:      3325       445147 bp    0.04 %

     Total interspersed repeats: 63043653 bp    6.04 %


     Small RNA:         5543       745245 bp    0.07 %

     Satellites:         109         8273 bp    0.00 %
     Simple repeats:  284418     12956749 bp    1.24 %
     Low complexity:   61652      3494878 bp    0.33 %
     ==================================================

     * most repeats fragmented by insertions or deletions
       have been counted as one element
       Runs of >=20 X/Ns in query were excluded in % calcs


     The query species was assumed to be homo sapiens
     RepeatMasker version 4.1.5 , default mode

     run with rmblastn version 2.13.0+
     FamDB: CONS-Dfam_3.7

Amphioxus
==================================================
file name: rm_input.fasta
sequences:            96
total length:  458494623 bp  (458485423 bp excl N/X-runs)
GC level:         41.61 %
bases masked:    9756877 bp ( 2.13 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
SINEs:            10212       946135 bp    0.21 %
      ALUs            0            0 bp    0.00 %
      MIRs         5121       527992 bp    0.12 %

LINEs:             4019       622661 bp    0.14 %
      LINE1         179        11937 bp    0.00 %
      LINE2         662        63166 bp    0.01 %
      L3/CR1       2144       286741 bp    0.06 %

LTR elements:       689       138371 bp    0.03 %
      ERVL           20         1005 bp    0.00 %
      ERVL-MaLRs      4          322 bp    0.00 %
      ERV_classI    584       118702 bp    0.03 %
      ERV_classII    28         1778 bp    0.00 %

DNA elements:       850        57478 bp    0.01 %
     hAT-Charlie     46         2708 bp    0.00 %
     TcMar-Tigger    73         5236 bp    0.00 %

Unclassified:       517        41430 bp    0.01 %

Total interspersed repeats:  1806075 bp    0.39 %


Small RNA:         5487       857233 bp    0.19 %

Satellites:         629        50630 bp    0.01 %
Simple repeats:  115914      6556304 bp    1.43 %
Low complexity:    9124       485904 bp    0.11 %
==================================================

* most repeats fragmented by insertions or deletions
  have been counted as one element
  Runs of >=20 X/Ns in query were excluded in % calcs


The query species was assumed to be homo sapiens
RepeatMasker version 4.1.5 , default mode

run with rmblastn version 2.13.0+
FamDB: CONS-Dfam_3.7