22 chromosome comments, example 3



Example 3

Example 3 shows an element from the family HERVL with other repetitive elements (MLT1) inserted.

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)

 1438  28.4 10.7 10.7  NT_001454  14534990 14535446  (8667645) C  LTR33    LTR/Retroviral    (15)   506      4  
  487  33.9  5.8  5.8  NT_001454  14535696 14535952  (8667139) C  HERVL    LTR/Retroviral   (384)  5380   5110  
 1220  25.2 14.9 14.9  NT_001454  14536095 14536589  (8666502) +  MLT1F1   LTR/MaLR            15   558    (3)  
  683  31.2  0.9  0.9  NT_001454  14536641 14537489  (8665602) C  HERVL    LTR/Retroviral   (694)  5070   4150  
 1316  29.2  8.8  8.8  NT_001454  14537594 14538273  (8664818) C  HERVL    LTR/Retroviral  (2781)  2873   2133  
 2458  17.3  5.1  5.1  NT_001454  14538274 14538747  (8664344) C  MLT1E2   LTR/MaLR           (0)   593    103  
  359  25.2 12.2 12.2  NT_001454  14538755 14538885  (8664206) C  MLT1E2   LTR/MaLR         (497)   144      1  
 1042  31.4  6.9  6.9  NT_001454  14538889 14539652  (8663439) C  HERVL    LTR/Retroviral  (3589)  2175   1407  
  380  28.4  7.9  7.9  NT_001454  14539952 14539979  (8663112) +  MLT1G1   LTR/MaLR            13    38  (341)  
 2140  18.9  2.9  2.9  NT_001454  14539980 14540360  (8662731) C  MLT1B    LTR/MaLR           (0)   390      1  
  380  28.4  7.9  7.9  NT_001454  14540361 14540542  (8662549) +  MLT1G1   LTR/MaLR            38   249  (130)  
 1352  30.8  2.4  2.4  NT_001454  14541580 14542031  (8661060) C  LTR33    LTR/Retroviral    (58)   463     58

Graphical representation of RepeatMasker output.

Corresponding parts of the chromosome sequence and the family consensus sequence are connected. The height of boxes on the chromosome shows Swiss-Waterman score (SW). Blue and orange colors are used for internal and LTR sequences, respectivelly. Unrelated repetitive elements found by RepetMasker are in red.

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Last modified: $Date: 2001/10/05 11:21:07 $ site: herv.img.cas.cz