
                                          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

+ 2360    8.2  0.0  0.7  UnnamedSequence     29   334 (2726) + AluSx    SINE/Alu            1    304    (8)   1

ANNOTATION EVIDENCE:
 2360   8.22 0.00 0.66  UnnamedSequence     29   334   2726 + AluSx    SINE/Alu            1    304      8    
2360 8.22 0.00 0.66 UnnamedSequence 29 334 (2726) AluSx#SINE/Alu 1 304 (8) c_b1s352i0

  UnnamedSequen         29 GGCCGGGCGCGGTGGCTCACACCTGTAATCTCAGCACTTTGGGAAGCAGA 78
                                               i         i             i  v  
  AluSx#SINE/Al          1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50

  UnnamedSequen         79 AGCGGGTGGATTACCTGAGGTCAGGAGTTCGAGACCAGCCTGATCAACAT 128
                           i     i    i                              ii      
  AluSx#SINE/Al         51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100

  UnnamedSequen        129 GGTGAAACCCTGCCTCTACTAAAAATACAAAAAAAGTAGTTGGGCGTGGT 178
                                     i i                    --v   ii         
  AluSx#SINE/Al        101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAA--TTAGCCGGGCGTGGT 148

  UnnamedSequen        179 GGCGGGCACCTATAATCCCAGCTACTTGGGAGGCTGAGGCGGGAGAGTCG 228
                               v  i   i              i             i     i   
  AluSx#SINE/Al        149 GGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCG 198

  UnnamedSequen        229 CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCA 278
                                                                             
  AluSx#SINE/Al        199 CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCA 248

  UnnamedSequen        279 CTCCAGCCTGAACGACTGAGCAAAACTCCGTCTCAAAAAAAAAAAAAAAA 328
                                     ii    v    i i                          
  AluSx#SINE/Al        249 CTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 298

  UnnamedSequen        329 AAAAAA 334
                                 
  AluSx#SINE/Al        299 AAAAAA 304

Matrix = 14p53g.matrix
Kimura (with divCpGMod) = 6.49
Transitions / transversions = 5.25 (21/4)
Gap_init rate = 0.01 (2 / 305), avg. gap size = 1.00 (2 / 2)

+ 2567    4.2  0.0  0.0  UnnamedSequence    336   675 (2385) + AluY     SINE/Alu            2    311    (0)   2

ANNOTATION EVIDENCE:
   12  16.16 0.00 3.45  UnnamedSequence    646   675   2130 + (AAAGA)n Simple_repeat       1     29      0    
12 16.16 0.00 3.45 UnnamedSequence 646 675 (2130) (AAAGA)n#Simple_repeat 1 29 (0) m_b1s252i0

  UnnamedSequen        646 AAAGAAAAGAAAAAAGAATAAACAGAAGAG 675
                                        i i  v   -    i  
  (AAAGA)n#Simp          1 AAAGAAAAGAAAAGAAAAGAAA-AGAAAAG 29

Matrix = Unknown
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1)

 2567   4.21 0.00 0.00  UnnamedSequence    336   644   2416 + AluY     SINE/Alu            2    310      1    
2567 4.21 0.00 0.00 UnnamedSequence 336 644 (2416) AluY#SINE/Alu 2 310 (1) c_b1s352i1

  UnnamedSequen        336 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTGTGGGAGGCCGAG 385
                                                                v            
  AluY#SINE/Alu          2 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 51

  UnnamedSequen        386 GCGGGTGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGT 435
                                i                                            
  AluY#SINE/Alu         52 GCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGT 101

  UnnamedSequen        436 GAAACCCCGTCTCTACTAAAAATACAAAAACTTAGCCGGGCGCGGTGGCG 485
                                                         v           i       
  AluY#SINE/Alu        102 GAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCG 151

  UnnamedSequen        486 GGTGCCTGTAGACTCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGCG 535
                             i        v i                                  i 
  AluY#SINE/Alu        152 GGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTG 201

  UnnamedSequen        536 AACCCGGGAGGCGGAGCTTGCAGTGAGCCCGGATCGCGCCACTGCACTCC 585
                                                        vi                   
  AluY#SINE/Alu        202 AACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC 251

  UnnamedSequen        586 AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAGAAAATAAAA 635
                                                                   i    v    
  AluY#SINE/Alu        252 AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAA 301

  UnnamedSequen        636 AAAAAGAAA 644
                                i   
  AluY#SINE/Alu        302 AAAAAAAAA 310

Matrix = 14p53g.matrix
Kimura (with divCpGMod) = 3.72
Transitions / transversions = 1.60 (8/5)
Gap_init rate = 0.00 (0 / 308), avg. gap size = 0.0 (0 / 0)

+   12   15.6  3.3 10.5  UnnamedSequence   1340  1400 (1660) + G-rich   Low_complexity      1     57    (0)   3

ANNOTATION EVIDENCE:
   12  15.60 3.28 10.53  UnnamedSequence   1340  1400   1405 + (GCCGGG)n Simple_repeat       1     57      0    
12 15.60 3.28 10.53 UnnamedSequence 1340 1400 (1405) (GCCGGG)n#Simple_repeat 1 57 (0) m_b1s252i1

  UnnamedSequen       1340 GCTGGGG-CGGTGCCGCTGGGGCGGGGCCTGCGGGGTGGGGCTGACGGCA 1388
                             i    -   v    --   v       - -   vi     i -v   -
  (GCCGGG)n#Sim          1 GCCGGGGCCGGGGCCG--GGGCCGGGGCC-G-GGGCCGGGGCCG-GGGC- 44

  UnnamedSequen       1389 CGGGG-CGGGGCC 1400
                                -       
  (GCCGGG)n#Sim         45 CGGGGCCGGGGCC 57

Matrix = Unknown
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.13 (8 / 60), avg. gap size = 1.00 (8 / 8)

+  268   33.2  1.6  8.8  UnnamedSequence   1986  2107  (953) + MIRb     SINE/MIR           48    161  (107)   4

ANNOTATION EVIDENCE:
  268  33.25 1.64 8.77  UnnamedSequence   1986  2107    698 + MIRb     SINE/MIR           48    161    107    
268 33.25 1.64 8.77 UnnamedSequence 1986 2107 (698) MIRb#SINE/MIR 48 161 (107) m_b1s601i0

  UnnamedSequen       1986 GATAGACCAGGGTCCAGACCTGTCCGGTCCCAGGCTAGCTACGAG--GTG 2033
                             i     v    i ii i ---    ii i--  i vi   v  --   
  MIRb#SINE/MIR         48 GACAGACCTGGGTTCGAATC---CCGGCTCT--GCCACTTACTAGCTGTG 92

  UnnamedSequen       2034 CCGTCCTGGGCAAGTCACTTCAGTTTTCTCGGGCTTAGTTCCCTCCTCAA 2083
                           ivii i         i    v vi i   vi v  i    i    v  --
  MIRb#SINE/MIR         93 TGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATC-- 140

  UnnamedSequen       2084 GATTTCAAAAGTAAAATAGTAATA 2107
                           --- vi    vviii   i     
  MIRb#SINE/MIR        141 ---TGTAAAATGGGGATAATAATA 161

Matrix = 25p53g.matrix
Kimura (with divCpGMod) = 44.58
Transitions / transversions = 2.08 (25/12)
Gap_init rate = 0.09 (11 / 121), avg. gap size = 1.09 (12 / 11)

+  312   30.9  4.8 10.0  UnnamedSequence   2309  2505  (555) C L2c      LINE/L2          (38)   3349   3156   5

ANNOTATION EVIDENCE:
  312  30.93 4.76 10.00  UnnamedSequence   2309  2505    555 C L2c_3end LINE/L2           247    440     38    
312 30.93 4.76 10.00 UnnamedSequence 2309 2505 (555) C L2c_3end#LINE/L2 (38) 440 247 m_b1s601i1

  UnnamedSequen       2309 TGTGCCACGT-TTGTGAAATTAAAGATGAGTAAGAT-CAGGCCCTGTCTC 2356
                                  v i-i  v i vvi        i     i- i v     i ii
C L2c_3end#LINE        440 TGTGCCAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCT 391

  UnnamedSequen       2357 CAAAGAGCGT----TTTAATCAGAGAGTCAGGTGTGCAAGCTAATGATTA 2402
                              i    vi---- i  i viii   v   iii? i  i vi ii    
C L2c_3end#LINE        390 CAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTA 341

  UnnamedSequen       2403 TAAGGTGCAA--TAATGATAAAAG--ATGCTGAACTTACTAGCCATACAG 2448
                           i  -- i   --         iv --  iv  iivv  -   ----    
C L2c_3end#LINE        340 CAA--TACAAGTTAATGATAAGTGCTATAATGGGAGTA-TAG----ACAG 298

  UnnamedSequen       2449 AGTA--ATGTAGGTAAGGAGAAGGG-GCCTGGGGAAGACAGTATGAGCAC 2495
                           i  i--   vii i vi   i    -i   -----    ---- ii? vi
C L2c_3end#LINE        297 GGTGCTATGGGAGCACAGAGGAGGGCACCT-----AGAC----TAGNCTT 257

  UnnamedSequen       2496 GGGAGGTGAC 2505
                              i   v v
C L2c_3end#LINE        256 GGGGGGTCAG 247

Matrix = 25p53g.matrix
Kimura (with divCpGMod) = 40.46
Transitions / transversions = 2.39 (43/18)
Gap_init rate = 0.12 (23 / 196), avg. gap size = 1.26 (29 / 23)

+ 1589   11.1  5.5  1.1  UnnamedSequence   2506  2761  (299) C AluSx    SINE/Alu         (11)    301     35   6

ANNOTATION EVIDENCE:
 1589  11.06 5.47 1.12  UnnamedSequence   2506  2761    299 C AluSx    SINE/Alu           35    301     11    
1589 11.06 5.47 1.12 UnnamedSequence 2506 2761 (299) C AluSx#SINE/Alu (11) 301 35 c_b1s352i2

  UnnamedSequen       2506 TTTTTTTTTTTTTTTTTTGGAGACAGGGGGTCTTGCTCTGGTCGCCCAGC 2555
                                             v     --  i    i      -        v
C AluSx#SINE/Al        301 TTTTTTTTTTTTTTTTTTTGAGAC--GGAGTCTCGCTCTG-TCGCCCAGG 255

  UnnamedSequen       2556 CTGGAGTTCAGTGGTGCAATCTCAGCTCACTGCAAACTCCACCTCCCAGG 2605
                                  v      i  i     i           v    i      i  
C AluSx#SINE/Al        254 CTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGG 205

  UnnamedSequen       2606 TTCAAGCGATTCTCCTGC---AGTCTCCCGAGTA----------CAGGCG 2642
                                             ---  i          ----------      
C AluSx#SINE/Al        204 TTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCG 155

  UnnamedSequen       2643 TCGGCCACCACACT-GGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTT 2691
                           ivv        i i-                            i      
C AluSx#SINE/Al        154 CGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTT 105

  UnnamedSequen       2692 CACTGTGTTGGTCAGGCTGGTCTCAAACTCCTGATCTCAAATGATCCCCA 2741
                              ii      i            i         i    ii      v v
C AluSx#SINE/Al        104 CACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCC 55

  UnnamedSequen       2742 CGCCTCGACCTCCCAAAGTG 2761
                                  i            
C AluSx#SINE/Al         54 CGCCTCGGCCTCCCAAAGTG 35

Matrix = 14p53g.matrix
Kimura (with divCpGMod) = 7.94
Transitions / transversions = 2.50 (20/8)
Gap_init rate = 0.02 (6 / 255), avg. gap size = 2.83 (17 / 6)

+  312   30.9  4.8 10.0  UnnamedSequence   2762  2836  (224) C L2c      LINE/L2         (232)   3155   3091   5

ANNOTATION EVIDENCE:
  312  30.93 4.76 10.00  UnnamedSequence   2762  2836    224 C L2c_3end LINE/L2           182    246    232    
312 30.93 4.76 10.00 UnnamedSequence 2762 2836 (224) C L2c_3end#LINE/L2 (232) 246 182 m_b1s601i1

  UnnamedSequen       2762 TGAGCCACTGCACCTGGCCTGAAGGTGACATTTGAACAGAGCCTTGAAGA 2811
                           vi  --i  v--  i  v-- i         i   i v   ?       i
C L2c_3end#LINE        246 GAAG--GCTT--CCCGGA--GGAGGTGACATCTGAGCTGAGNCTTGAAGG 203

  UnnamedSequen       2812 ATGCTGTGTAGAAAGTTTGACAGGT 2836
                              v---    -i    v v     
C L2c_3end#LINE        202 ATGA---GTAG-GAGTTAGCCAGGT 182

Matrix = 25p53g.matrix
Kimura (with divCpGMod) = 40.46
Transitions / transversions = 1.14 (8/7)
Gap_init rate = 0.14 (10 / 74), avg. gap size = 1.00 (10 / 10)

+ 1236   18.5  0.9  0.9  UnnamedSequence   2837  3060    (0) + AluJb    SINE/Alu            1    224   (88)   7

ANNOTATION EVIDENCE:
 1236  18.46 0.89 0.89  UnnamedSequence   2837  3060      0 + AluJb    SINE/Alu            1    224     88    
1236 18.46 0.89 0.89 UnnamedSequence 2837 3060 (0) AluJb#SINE/Alu 1 224 (88) m_b1s356i0

  UnnamedSequen       2837 GGCCAGGCATAGTGACTCCTGCGTGTAATCCCAGCACTTTGGGAGTCCGA 2886
                               i   iii   i   vi  v                      v    
  AluJb#SINE/Al          1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50

  UnnamedSequen       2887 GGTGAGAGGATAGTTTGAGGCCTTGAGTTTGAGACCAGCCTGGGCAGCAC 2936
                             i i ?    v i     v  vv     i                i  i
  AluJb#SINE/Al         51 GGCGGGNGGATCGCTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACAT 100

  UnnamedSequen       2937 AGTGAGACTCCATCTCTTAAAAAAAAAAAAAAAAATTAGCCAGGCGTGGT 2986
                           i i  i  i  i     -- v      v v           i        
  AluJb#SINE/Al        101 GGCGAAACCCCGTCTCT--ACAAAAAATACAAAAATTAGCCGGGCGTGGT 148

  UnnamedSequen       2987 GGCCCATGCCTGTGGTCCCAGCTGCTTGG--GGCTGAGGTAGGAGGATCA 3034
                              v ii      i         i  i  --        ii        i
  AluJb#SINE/Al        149 GGCGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCGGGAGGATCG 198

  UnnamedSequen       3035 TTTGAGCCCAGAAAGTCGAGGCTGCA 3060
                           i        i i i            
  AluJb#SINE/Al        199 CTTGAGCCCGGGAGGTCGAGGCTGCA 224

Matrix = 14p53g.matrix
Kimura (with divCpGMod) = 13.61
Transitions / transversions = 2.73 (30/11)
Gap_init rate = 0.01 (3 / 223), avg. gap size = 1.33 (4 / 3)