
                                          position in query-                       -position in repeat-
          %    %    %    query                               C matching repeat     (left)  end   begin  linkage
+ score  div. del. ins.  sequence         begin  end  (left) + repeat   class/fami begin   end   (left) id/graphic

+  202   30.0  1.7 15.4  UnnamedSequence      2   119  (781) C L2c      LINE/L2      (12)   3375   3272   1

ANNOTATION EVIDENCE:
  202  30.04 1.69 15.38  UnnamedSequence      2   119    781 C L2c_3end LINE/L2       363    466     12    
202 30.04 1.69 15.38 UnnamedSequence 2 119 (781) C L2c_3end#LINE/L2 (12) 466 363 m_b1s601i0

  UnnamedSequen          2 AATCAACATTTATTTAGTGCCTCTTGTATGTTCCGCATGCAGGTAGGCAC 51
                             iv          v  i    vi --    v  ----------    i 
C L2c_3end#LINE        466 AACAAACATTTATTGAGCGCCTACT--ATGTGCC----------AGGCGC 429

  UnnamedSequen         52 CTGGAATACAATGGTGACTAAGGTACCATGGTTCCCACC--CAGTGGAAA 99
                           iv  i      v i   v    i---  i   i  ii  --  i-   iv
C L2c_3end#LINE        428 TGGGGATACAAAGATGAATAAGA---CACGGTCCCTGCCCTCAA-GGAGC 383

  UnnamedSequen        100 CCATAATATAATGGGAAAGA 119
                           i  i i v  i   iii   
C L2c_3end#LINE        382 TCACAGTCTAGTGGAGGAGA 363

Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 34.48
Transitions / transversions = 2.33 (21/9)
Gap_init rate = 0.15 (17 / 117), avg. gap size = 1.06 (18 / 17)

+  212   28.9  5.3  4.2  UnnamedSequence    608   701  (199) + MIR3     SINE/MIR      105    199    (9)   2

ANNOTATION EVIDENCE:
  212  28.88 5.32 4.21  UnnamedSequence    608   701    199 + MIR3     SINE/MIR      105    199      9    
212 28.88 5.32 4.21 UnnamedSequence 608 701 (199) MIR3#SINE/MIR 105 199 (9) m_b1s601i1

  UnnamedSequen        608 TTCATATCTTTGTACCCTTGTTAGTTTC-TCAT--GTAAAAGATGAAAGT 654
                               iv   i  vi  ---- i      -    --      viv iii  
  MIR3#SINE/MIR        105 TTCACCTCTCTGGGCC----TCAGTTTCCTCATCTGTAAAATGAGGGGGT 150

  UnnamedSequen        655 CAGCTCAGATGACTTTTAAGGTCCTTT--AATTCTATCATTATATGATT 701
                           ii vii      ii i        i  -- ii   iv    v       
  MIR3#SINE/MIR        151 TGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATT 199

Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 38.88
Transitions / transversions = 2.71 (19/7)
Gap_init rate = 0.08 (7 / 93), avg. gap size = 1.29 (9 / 7)