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

+  555   32.8  8.2  1.1  clock       312   555 (4046) C MIR      SINE/MIR          (0)    262      2   1

ANNOTATION EVIDENCE:
  555  32.76 8.20 1.15  clock       312   555   3760 C MIR      SINE/MIR            2    262      0    
555 32.76 8.20 1.15 clock 312 555 (3760) C MIR#SINE/MIR (0) 262 2 m_b1s601i0

  clock                312 AAGAATAGCCAACATTTCTATGGGATTTCTTATGTACCAGATAAAATTAC 361
                             v      i       v vvi vii  vi     i    ii vvi  vi
C MIR#SINE/MIR         262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213

  clock                362 ACACACACAGACACACACACTGTCTCGGTTAAGC-------------TAT 398
                            vi i vi---i   iii i iv   iv    v -------------   
C MIR#SINE/MIR         212 AAGCGCTT---TACATGTATTAACTCATTTAATCCTCACAACAACCCTAT 166

  clock                399 GAGATAGG-ATTGTAATTATCCC-ATTTTAAAGATGACGAAATTAAAGAA 446
                              i    - i i v        -      v      v    i i i v 
C MIR#SINE/MIR         165 GAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCA 116

  clock                447 CAGAGA-----AATAACTTGCTTAAAGTCATGCAGAATATTAGTGGTGAA 491
                                 ----- i        ii  i    ii   vvvi v     iii 
C MIR#SINE/MIR         115 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 66

  clock                492 GCTATGATTTAAATCCAGGCAGTTAAGATCCTAATTTTGTACTCTTAACC 541
                             iiv    ii  i         ivi v   vi viii  i         
C MIR#SINE/MIR          65 GCCGGGATTCGAACCCAGGCAGTCTGGCTCCAGAGCCCGTGCTCTTAACC 16

  clock                542 ACTATGATACGTTG 555
                                 v  iii  
C MIR#SINE/MIR          15 ACTATGCTATACTG 2

Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 41.31
Transitions / transversions = 1.82 (51/28)
Gap_init rate = 0.03 (7 / 243), avg. gap size = 3.29 (23 / 7)

+ 1955   12.2  0.7  0.3  clock       770  1056 (3545) + AluSx    SINE/Alu            1    288   (24)   2

ANNOTATION EVIDENCE:
 1955  12.24 0.70 0.35  clock       770  1056   3545 + AluSx    SINE/Alu            1    288     24    
1955 12.24 0.70 0.35 clock 770 1056 (3545) AluSx#SINE/Alu 1 288 (24) c_b1s352i0

  clock                770 GGCTGGGTACAGTGGCTCGCGCCTGTTAATCCCAGCACTTTGGGTGGCTG 819
                              i   ii i       i       -                 v   i 
  AluSx#SINE/Al          1 GGCCGGGCGCGGTGGCTCACGCCTGT-AATCCCAGCACTTTGGGAGGCCG 49

  clock                820 AGGTGGGTGGATCACTTGAGGCCAGGAGTTCAAGACCAGCCTGGCCAACA 869
                              i   i       i     i         i                  
  AluSx#SINE/Al         50 AGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACA 99

  clock                870 TGGTGGAACCCCATCTCTACTAAAAATACAAAAATTAGCT-GGTGTGGTG 918
                                i      i                          i-  i      
  AluSx#SINE/Al        100 TGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTG 149

  clock                919 GTGGGAGTCTGTAATCACAGCTACTTGGAAGGCTGAGGCACAAGAATTGC 968
                            i v v i        v        i  i           vi     i  
  AluSx#SINE/Al        150 GCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGC 199

  clock                969 TTGAACCCGGGAGGCAGAGGTTTCAGTGAGCTGAGATCATGCCACTGTAC 1018
                                          i      v        i      ii       i  
  AluSx#SINE/Al        200 TTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAC 249

  clock               1019 TCCAG-CTGGGCAACAGAGCAAGACTCTGTCTCAAAAAA 1056
                                -      i       i      i           
  AluSx#SINE/Al        250 TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAA 288

Matrix = 14p51g.matrix
Kimura (with divCpGMod) = 6.18
Transitions / transversions = 4.83 (29/6)
Gap_init rate = 0.01 (3 / 286), avg. gap size = 1.00 (3 / 3)

+  434   23.1 17.9  4.4  clock      1476  1738 (2863) C MLT1K    LTR/ERVL-MaLR     (2)    593    297   3

ANNOTATION EVIDENCE:
  434  23.06 17.87 4.38  clock      1476  1738   2863 C MLT1K    LTR/ERVL-MaLR     297    593      2    
434 23.06 17.87 4.38 clock 1476 1738 (2863) C MLT1K#LTR/ERVL-MaLR (2) 593 297 m_b1s502i0

  clock               1476 TGTCAGTCGGGACTCTT--GATTACATGTGAAAGAAA---ACCTCTCACT 1520
                            i i    i        -- i  i  v    v     --- v   vv   
C MLT1K#LTR/ERV        593 TATTAGTCAGGACTCTTTCGGTTGCAAGTGACAGAAACCCAACTCAAACT 544

  clock               1521 GGTTTAAGCAATAAAACAGATGCAAGAATTTACTGACTGGTTTAAC-GAA 1569
                             i        v   i--------i       i  i  viiv    -   
C MLT1K#LTR/ERV        543 GGCTTAAGCAAAAAAG--------GGAATTTATTGGCTCACGTAACTGAA 502

  clock               1570 ATTTCCAGAGG--AATCTAATCT-----ACATTTGTTTCCAGGC-CTCAA 1611
                            vv     i  --i?   iiii -----  ivi  vv      ?-     
C MLT1K#LTR/ERV        501 AAGTCCAGGGGTAGNTCTGGCTTCAGGCACGGCTGGATCCAGGNGCTCAA 452

  clock               1612 AC-ATGTCTTTAGGCCAAACCTGTCT-----------TCAAATCTGCTTT 1649
                             -     v i   --- ?i      -----------  iiv        
C MLT1K#LTR/ERV        451 ACGATGTCATCAGG---ANTCTGTCTCTCTCCATCTCTCGGCTCTGCTTT 405

  clock               1650 TTTTCCGTGTTGCCTTCTTTCTCAGAA--------TTCACGTG-TGGAAA 1690
                           ii - i      v    v       iv--------ii      -   v  
C MLT1K#LTR/ERV        404 CCT-CTGTGTTGGCTTCATTCTCAGGCAGGCTCTCCCCACGTGGTGGCAA 356

  clock               1691 GATGGC----------TCCAGGTCTCCATTCTCCCAGATT--TAAACCCA 1728
                                 ----------      ii v   i  ?    v  --i  v    
C MLT1K#LTR/ERV        355 GATGGCCGCCAGCAGCTCCAGGCTTACATCCTNCCAGCTTAGCAACCCCA 306

  clock               1729 TTGGTAAAGA 1738
                           vi  -     
C MLT1K#LTR/ERV        305 GCGG-AAAGA 297

Matrix = 20p51g.matrix
Kimura (with divCpGMod) = 26.62
Transitions / transversions = 1.52 (35/23)
Gap_init rate = 0.10 (25 / 262), avg. gap size = 2.40 (60 / 25)

+  342   23.7 16.1  0.0  clock      1806  1898 (2703) C MLT1K    LTR/ERVL-MaLR   (469)    126     19   3

ANNOTATION EVIDENCE:
  342  23.66 16.13 0.00  clock      1806  1898   2703 C MLT1K    LTR/ERVL-MaLR      19    126    469    
342 23.66 16.13 0.00 clock 1806 1898 (2703) C MLT1K#LTR/ERVL-MaLR (469) 126 19 m_b1s502i1

  clock               1806 GTCCTGCTCAGACCATATGGACTGAGAGTGGATAAATGATAGTTCTTCAA 1855
                            i  ii i ii    i               ivi iv i i    ii   
C MLT1K#LTR/ERV        126 GCCCCACCCGAACCACATGGACTGAGAGTGGGGGAGGGGTGGTTCCCCAA 77

  clock               1856 AAGAAA------------TTATCAGAATA---GGGAATGAATGCTGAACA 1890
                            i    ------------   i     v ---       i      ii  
C MLT1K#LTR/ERV         76 AGGAAAATCGGGGTGCTGTTACCAGAAGAAGGGGGAATGGATGCTGGGCA 27

  clock               1891 GGCAAAAA 1898
                                   
C MLT1K#LTR/ERV         26 GGCAAAAA 19

Matrix = 20p51g.matrix
Kimura (with divCpGMod) = 29.03
Transitions / transversions = 6.33 (19/3)
Gap_init rate = 0.02 (2 / 92), avg. gap size = 7.50 (15 / 2)

+   12   12.8  5.6  2.7  clock      3025  3060 (1541) + G-rich   Low_complexity      1     37    (0)   4

ANNOTATION EVIDENCE:
   12  12.75 5.56 2.70  clock      3025  3060   1541 + (GGGAGA)n Simple_repeat       1     37      0    
12 12.75 5.56 2.70 clock 3025 3060 (1541) (GGGAGA)n#Simple_repeat 1 37 (0) m_b1s252i0

  clock               3025 GGGAAAGGGAGAGTGAG-GGGAG-GGGCGAGCGCAGAG 3060
                               i        v   -     -   v   - v    
  (GGGAGA)n#Sim          1 GGGAGAGGGAGAGGGAGAGGGAGAGGGAGAG-GGAGAG 37

Matrix = Unknown
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3)

+   14   11.6  3.5  0.0  clock      3306  3334 (1267) + GA-rich  Low_complexity      1     30    (0)   5

ANNOTATION EVIDENCE:
   14  11.59 3.45 0.00  clock      3306  3334   1267 + (GGAGG)n Simple_repeat       1     30      0    
14 11.59 3.45 0.00 clock 3306 3334 (1267) (GGAGG)n#Simple_repeat 1 30 (0) m_b1s252i2

  clock               3306 GGAGGGGAAGGGAAGGGAGGGG-GAGGAGG 3334
                                   i    i        - i     
  (GGAGG)n#Simp          1 GGAGGGGAGGGGAGGGGAGGGGAGGGGAGG 30

Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1)

+   14   16.3  4.7  2.3  clock      3705  3747  (854) + G-rich   Low_complexity      1     44    (0)   6

ANNOTATION EVIDENCE:
   14  16.28 4.65 2.27  clock      3705  3747    854 + (GCGGG)n Simple_repeat       1     44      0    
14 16.28 4.65 2.27 clock 3705 3747 (854) (GCGGG)n#Simple_repeat 1 44 (0) m_b1s252i3

  clock               3705 GCGGGGCAGGGGC-GGGAGTGG-GGTGCACGGCGGGGCCGGGCGG 3747
                                  -     -   v v  -  v  iv        v      
  (GCGGG)n#Simp          1 GCGGGGC-GGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGG 44

Matrix = Unknown
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3)