22 chromosome comments, example 2



Example 2

Example 2 shows one LTR from the family LTR8 that has many duplications of its central part. The region 285-323 bp of the consensus sequence was duplicated 16 times. The two long repeats flanking the amplified region thus belong to one element.

Part of unprocessed RepeatMasker output:

   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)

 2683  10.9  0.2  0.2  NT_001128    218627 219037 (160412) C  LTR8     LTR/Retroviral     (0)  691    285  
  311   2.6  0.0  0.0  NT_001128    219038 219076 (160373) C  LTR8     LTR/Retroviral   (368)  323    285  
  299   2.6  0.0  0.0  NT_001128    219077 219115 (160334) C  LTR8     LTR/Retroviral   (368)  323    285  
  263   2.3  0.0  0.0  NT_001128    219116 219158 (160291) C  LTR8     LTR/Retroviral   (368)  323    285  
  289   5.1  0.0  0.0  NT_001128    219159 219197 (160252) C  LTR8     LTR/Retroviral   (368)  323    285  
  322   0.0  0.0  0.0  NT_001128    219198 219236 (160213) C  LTR8     LTR/Retroviral   (368)  323    285  
  322   0.0  0.0  0.0  NT_001128    219237 219275 (160174) C  LTR8     LTR/Retroviral   (368)  323    285  
  299   2.6  0.0  0.0  NT_001128    219276 219314 (160135) C  LTR8     LTR/Retroviral   (368)  323    285  
  322   0.0  0.0  0.0  NT_001128    219315 219353 (160096) C  LTR8     LTR/Retroviral   (368)  323    285  
  240   3.2  0.0  0.0  NT_001128    219366 219396 (160053) C  LTR8     LTR/Retroviral   (376)  315    285  
  240   3.2  0.0  0.0  NT_001128    219409 219439 (160010) C  LTR8     LTR/Retroviral   (376)  315    285  
  248   4.7  0.0  0.0  NT_001128    219440 219482 (159967) C  LTR8     LTR/Retroviral   (368)  323    285  
  248   4.7  0.0  0.0  NT_001128    219483 219525 (159924) C  LTR8     LTR/Retroviral   (368)  323    285  
  242   2.4  0.0  0.0  NT_001128    219526 219566 (159883) C  LTR8     LTR/Retroviral   (368)  323    287  
  263   2.3  0.0  0.0  NT_001128    219569 219611 (159838) C  LTR8     LTR/Retroviral   (368)  323    285  
  263   2.3  0.0  0.0  NT_001128    219612 219654 (159795) C  LTR8     LTR/Retroviral   (368)  323    285  
 1785  13.8  0.6  0.6  NT_001128    219667 219991 (159458) C  LTR8     LTR/Retroviral   (376)  315      1  

Graphical representation of RepeatMasker output.

Corresponding parts of the chromosome sequence and the family consensus sequence are connected. The heights of boxes on the chromosome show Swiss-Waterman score (SW). Blue and dark blue colors mark repeats. Unique LTR sequences found by RepetMasker are in orange.

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