
                                     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

+  551   21.0  0.0 25.2  UnnamedSeq    374   532 (7368) C PB1        SINE/Alu         (0)    127      1   1

ANNOTATION EVIDENCE:
  551  21.02 0.00 25.20  UnnamedSeq    374   532   7303 C PB1        SINE/Alu           1    127      0    
551 21.02 0.00 25.20 UnnamedSeq 374 532 (7303) C PB1#SINE/Alu (0) 127 1 c_b1s355i0

  UnnamedSeq           374 TGTTTTGTTTTTGAGACAGGGTCTTACTGTGTTGCCCAGGCTGGAGTACG 423
                                      -            ii  i               ------
C PB1#SINE/Alu         127 TGTTTTGTTTT-GAGACAGGGTCTCGCTATGTTGCCCAGGCTGG------ 85

  UnnamedSeq           424 GTGGTGCGATTATGGCTTACTGCAGCCTCAACCTCCTAGGCTCAATCTAT 473
                           -------------------------    i v     i i     viv  
C PB1#SINE/Alu          84 -------------------------CCTCGAACTCCTGGACTCAAGTGAT 60

  UnnamedSeq           474 CCTCCTGCCTCAACTGCCCAAGTAGCTGGGACTATAGGTGCATGTCACCA 523
                                       i iv   i              i   i iii i    i
C PB1#SINE/Alu          59 CCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGTGCGCCACCG 10

  UnnamedSeq           524 CACTCAACT 532
                            i i ii  
C PB1#SINE/Alu           9 CGCCCGGCT 1

Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 15.83
Transitions / transversions = 5.25 (21/4)
Gap_init rate = 0.20 (32 / 158), avg. gap size = 1.00 (32 / 32)

+  249    7.9  0.0  0.0  UnnamedSeq    547   584 (7316) C PB1D11     SINE/Alu         (5)    113     76   2

ANNOTATION EVIDENCE:
  249   7.89 0.00 0.00  UnnamedSeq    547   584   7251 C PB1D11     SINE/Alu          76    113      5    
249 7.89 0.00 0.00 UnnamedSeq 547 584 (7251) C PB1D11#SINE/Alu (5) 113 76 m_b1s501i0

  UnnamedSeq           547 TTTTTTAGAGACAGGGTCTTGCTATGTTGCCCGGGTTG 584
                                 ?            i            i  i  
C PB1D11#SINE/A        113 TTTTTTNGAGACAGGGTCTCGCTATGTTGCCCAGGCTG 76

Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 6.02
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)

+   36    2.9  0.0  0.0  UnnamedSeq   2990  3024 (4876) + (TG)n      Simple_repeat      1     35    (0)   3

ANNOTATION EVIDENCE:
   36   2.94 0.00 0.00  UnnamedSeq   2990  3024   4876 + (TG)n      Simple_repeat      1     35      0    
36 2.94 0.00 0.00 UnnamedSeq 2990 3024 (4876) (TG)n#Simple_repeat 1 35 (0) c_b1s251i0

  UnnamedSeq          2990 TGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGT 3024
                                          i                   
  (TG)n#Simple_          1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35

Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0)

+  950   17.0  0.4  6.4  UnnamedSeq   3287  3519 (4381) C L1ME2z     LINE/L1          (3)   6441   6222   4

ANNOTATION EVIDENCE:
  950  16.96 0.43 6.36  UnnamedSeq   3287  3519   4350 C L1ME2z_3end LINE/L1          969   1188      3    
950 16.96 0.43 6.36 UnnamedSeq 3287 3519 (4350) C L1ME2z_3end#LINE/L1 (3) 1188 969 m_b1s551i0

  UnnamedSeq          3287 TTTATCCAACATTGTGTTATGAAAAATTTCAAACACACAAAAAAGCTGAA 3336
                              vi        v i         v         i   i     i    
C L1ME2z_3end#L       1188 TTTTCCCAACATTTTATTATGAAAATTTTCAAACATACAGAAAAGTTGAA 1139

  UnnamedSeq          3337 GGAACTTTACAGTGAACACCTGTATACTTAGCACTTATATTCTACTATTA 3386
                           i   i               ii     ii v   i  v       ?    
C L1ME2z_3end#L       1138 AGAATTTTACAGTGAACACCCATATACCCACCACCTAGATTCTACNATTA 1089

  UnnamedSeq          3387 ATATTGCATTATCAACATGTTTTATCACATATCTATCCATCCTTCTGTCC 3436
                            i   vi i   --  v  i                     iv  ii   
C L1ME2z_3end#L       1088 ACATTTTACTAT--ACTTGCTTTATCACATATCTATCCATCTATCCATCC 1041

  UnnamedSeq          3437 ATTTTATCAATCCACCAATGTTGCTGCATTTTA-TTTTTGATGCACGCAC 3485
                           -i i    v     i   ------ v   i   -           -----
C L1ME2z_3end#L       1040 -CTCTATCCATCCATCAA------TCCATCTTATTTTTTGATGCA----- 1003

  UnnamedSeq          3486 TTCCAAATTAGTTTGCAGACATCAGTACACTTCC 3519
                             i    v  iv                      
C L1ME2z_3end#L       1002 TTTCAAAGTAAGTTGCAGACATCAGTACACTTCC 969

Matrix = 20p51g.matrix
Kimura (with divCpGMod) = 19.65
Transitions / transversions = 2.08 (25/12)
Gap_init rate = 0.06 (15 / 232), avg. gap size = 1.00 (15 / 15)

+   14   21.4  1.9  3.9  UnnamedSeq   4302  4357 (3543) + (CCGGCCG)n Simple_repeat      1     54    (0)   5

ANNOTATION EVIDENCE:
   14  21.42 1.92 3.92  UnnamedSeq   4302  4353   3516 + (CCGGCCG)n Simple_repeat      1     51      0    
14 21.42 1.92 3.92 UnnamedSeq 4302 4353 (3516) (CCGGCCG)n#Simple_repeat 1 51 (0) m_b1s252i0

  UnnamedSeq          4302 CCTGCCGCGTGCCCGCGCGCCGCCGGCCGCCCGCCTGCCGGGC-CCAGTC 4350
                             v     -i v    vv             v   -     v -  i i 
  (CCGGCCG)n#Si          1 CCGGCCGC-CGGCCGCCGGCCGCCGGCCGCCGGCC-GCCGGCCGCCGGCC 48

  UnnamedSeq          4351 GCC 4353
                              
  (CCGGCCG)n#Si         49 GCC 51

Matrix = Unknown
Transitions / transversions = 0.50 (3/6)
Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3)

   14  20.55 5.77 1.85  UnnamedSeq   4306  4357   3512 + (CCGC)n    Simple_repeat      1     54      0    
14 20.55 5.77 1.85 UnnamedSeq 4306 4357 (3512) (CCGC)n#Simple_repeat 1 54 (0) m_b1s252i1

  UnnamedSeq          4306 CCGCGTGCCCGCGCG-CCG-CCGGCCGCCCGCCTGCCGGGCCCAGTCGCC 4353
                               vi      v  -   -   v         i   -v    ivi    
  (CCGC)n#Simpl          1 CCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCC-CGCCCGCCCGCC 49

  UnnamedSeq          4354 C-CCC 4357
                            -   
  (CCGC)n#Simpl         50 CGCCC 54

Matrix = Unknown
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4)

+   19   25.6  4.5  1.4  UnnamedSeq   4386  4452 (3448) + (GC)n      Simple_repeat      1     69    (0)   6

ANNOTATION EVIDENCE:
   19  25.55 4.48 1.45  UnnamedSeq   4386  4452   3417 + (GC)n      Simple_repeat      1     69      0    
19 25.55 4.48 1.45 UnnamedSeq 4386 4452 (3417) (GC)n#Simple_repeat 1 69 (0) m_b1s252i2

  UnnamedSeq          4386 GCCCGAGCGGGCACGAGGGCGCGGGGGCGCGC-CAGGAGACGCGGGGGCG 4434
                             v  v   v  i  v v     v v      - iv v -    v v   
  (GC)n#Simple_          1 GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCG-CGCGCGCGCG 49

  UnnamedSeq          4435 CGCG-GCGCGC-CGCGAGCG 4452
                               -      -    v   
  (GC)n#Simple_         50 CGCGCGCGCGCGCGCGCGCG 69

Matrix = Unknown
Transitions / transversions = 0.17 (2/12)
Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.00 (4 / 4)

+   16   30.3  0.0  3.0  UnnamedSeq   4627  4703 (3197) + (GGCGG)n   Simple_repeat      1     74    (0)   7

ANNOTATION EVIDENCE:
   16  30.30 0.00 3.03  UnnamedSeq   4627  4694   3175 + (GGCGG)n   Simple_repeat      1     66      0    
16 30.30 0.00 3.03 UnnamedSeq 4627 4694 (3175) (GGCGG)n#Simple_repeat 1 66 (0) m_b1s252i3

  UnnamedSeq          4627 GGCGGGGGTGGGGCAGAGGCGCGGCGAGCCCGAGAGGGGCGGGGAGAGGA 4676
                              -    i     - i    v    i v v i v         v i  v
  (GGCGG)n#Simp          1 GGC-GGGGCGGGGC-GGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGC 48

  UnnamedSeq          4677 GCAGCCTGGCGGGGTGGG 4694
                            vi  vv       i   
  (GGCGG)n#Simp         49 GGGGCGGGGCGGGGCGGG 66

Matrix = Unknown
Transitions / transversions = 0.78 (7/9)
Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.00 (2 / 2)

   12  26.67 4.55 2.99  UnnamedSeq   4638  4703   3166 + (GGCGA)n   Simple_repeat      1     67      0    
12 26.67 4.55 2.99 UnnamedSeq 4638 4703 (3166) (GGCGA)n#Simple_repeat 1 67 (0) m_b1s252i4

  UnnamedSeq          4638 GGCAGAGGCGCGGCGAGCCCGA-GAGGGGCGGGGAGAGGAGCAGCCTGGC 4686
                              -      v      -v   - v i    i  v    v vi  vv   
  (GGCGA)n#Simp          1 GGC-GAGGCGAGGCGAG-GCGAGGCGAGGCGAGGCGAGGCGAGGCGAGGC 48

  UnnamedSeq          4687 GGGGTG-GGC-AGCCGAGG 4703
                            i  i -   -  v     
  (GGCGA)n#Simp         49 GAGGCGAGGCGAGGCGAGG 67

Matrix = Unknown
Transitions / transversions = 0.56 (5/9)
Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.00 (5 / 5)

+   14   13.1  0.0  0.0  UnnamedSeq   5395  5420 (2480) + (GGC)n     Simple_repeat      1     26    (0)   8

ANNOTATION EVIDENCE:
   14  13.12 0.00 0.00  UnnamedSeq   5395  5420   2449 + (GGC)n     Simple_repeat      1     26      0    
14 13.12 0.00 0.00 UnnamedSeq 5395 5420 (2449) (GGC)n#Simple_repeat 1 26 (0) m_b1s252i5

  UnnamedSeq          5395 GGTGGCGGCGGCAGCAGCGGCGGCGG 5420
                             i         i  i          
  (GGC)n#Simple          1 GGCGGCGGCGGCGGCGGCGGCGGCGG 26

Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)

+   34    0.0  0.0  0.0  UnnamedSeq   6747  6778 (1122) + (T)n       Simple_repeat      1     32    (0)   9

ANNOTATION EVIDENCE:
   34   0.00 0.00 0.00  UnnamedSeq   6747  6778   1122 + (T)n       Simple_repeat      1     32      0    
34 0.00 0.00 0.00 UnnamedSeq 6747 6778 (1122) (T)n#Simple_repeat 1 32 (0) c_b1s251i1

  UnnamedSeq          6747 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6778
                                                           
  (T)n#Simple_r          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)

+   12   14.9  3.3  0.0  UnnamedSeq   7029  7058  (842) + (GCTGCA)n  Simple_repeat      1     31    (0)  10

ANNOTATION EVIDENCE:
   12  14.91 3.33 0.00  UnnamedSeq   7029  7058    842 + (GCTGCA)n  Simple_repeat      1     31      0    
12 14.91 3.33 0.00 UnnamedSeq 7029 7058 (842) (GCTGCA)n#Simple_repeat 1 31 (0) m_b1s252i6

  UnnamedSeq          7029 GCTGCAGCT-CACCTGGAGCTGCAGGTGGAG 7058
                                    -  v   v        v  v  
  (GCTGCA)n#Sim          1 GCTGCAGCTGCAGCTGCAGCTGCAGCTGCAG 31

Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1)

+   19   30.7  0.0  5.4  UnnamedSeq   7504  7600  (300) + (CCCCCT)n  Simple_repeat      1     92    (0)  11

ANNOTATION EVIDENCE:
   19  30.71 0.00 5.43  UnnamedSeq   7504  7600    300 + (CCCCCT)n  Simple_repeat      1     92      0    
19 30.71 0.00 5.43 UnnamedSeq 7504 7600 (300) (CCCCCT)n#Simple_repeat 1 92 (0) m_b1s252i7

  UnnamedSeq          7504 CCCACTCCCCCTCCGGGCTTTCGCCCGCCCTCTCTCCCTCCCTTTTTTGC 7553
                              v          --- ii  v   v   i   i       ii iiiv 
  (CCCCCT)n#Sim          1 CCCCCTCCCCCTCC---CCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCC 47

  UnnamedSeq          7554 CCGCCCTGGCCCTGCCCCTGCCCCTGCCCCCTCCTCTCAGCCCCTCC 7600
                           i v    vv    v     v     -        - i vv       
  (CCCCCT)n#Sim         48 TCCCCCTCCCCCTCCCCCTCCCCCT-CCCCCTCC-CCCTCCCCCTCC 92

Matrix = Unknown
Transitions / transversions = 1.00 (11/11)
Gap_init rate = 0.05 (5 / 96), avg. gap size = 1.00 (5 / 5)