
                                          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

+  830   10.8  0.0  2.5  UnnamedSequence      1   123  (484) C AluSx    SINE/Alu     (14)    298    179   1

ANNOTATION EVIDENCE:
  830  10.84 0.00 2.50  UnnamedSequence      1   123    237 C AluSx    SINE/Alu      179    298     14    
830 10.84 0.00 2.50 UnnamedSequence 1 123 (237) C AluSx#SINE/Alu (14) 298 179 m_b1s357i0

  UnnamedSequen          1 TTTTTTTTTTTTTTTTGAGGTGGAGTCTCACTCTGTCACTTAGCAGGCTG 50
                                              ii        i       i i---       
C AluSx#SINE/Al        298 TTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCC---CAGGCTG 252

  UnnamedSequen         51 GAGTGCAGTGGCCCAGTCTTGGCTCACTGCAACCTCCGCCTCCTGGGTTT 100
                                       v ii   i                       i     i
C AluSx#SINE/Al        251 GAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTC 202

  UnnamedSequen        101 AAATGATTCTCCTGCCTCAGCCT 123
                             ii                   
C AluSx#SINE/Al        201 AAGCGATTCTCCTGCCTCAGCCT 179

Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 5.87
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.02 (3 / 122), avg. gap size = 1.00 (3 / 3)

+ 1750   12.7  0.0  1.6  UnnamedSequence    126   373  (234) + AluSx    SINE/Alu       54    297   (15)   2

ANNOTATION EVIDENCE:
 1750  12.71 0.00 1.64  UnnamedSequence    126   373    234 + AluSx    SINE/Alu       54    297     15    
1750 12.71 0.00 1.64 UnnamedSequence 126 373 (234) AluSx#SINE/Alu 54 297 (15) c_b1s352i0

  UnnamedSequen        126 GGGCGGATCACCTGACATCAGGAGTTTGAGACCAGCCTGGCCAATATGGC 175
                                          vi         i                 i    i
  AluSx#SINE/Al         54 GGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGT 103

  UnnamedSequen        176 GAAACCCCATCTCTACTAAAAATACTAAAAAAAATTAGCCAGGCATGGTG 225
                                   i                ----           i   i     
  AluSx#SINE/Al        104 GAAACCCCGTCTCTACTAAAAATAC----AAAAATTAGCCGGGCGTGGTG 149

  UnnamedSequen        226 GCACGCACTTGTAGTCCCAGCTACTTGGGAGACTGAGGCAGGAGAATCGC 275
                             i   i i    i           i     i                  
  AluSx#SINE/Al        150 GCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGC 199

  UnnamedSequen        276 TTGAACCCAGGATGTTGAGGTTGCAGTGAGCTGAGATCACACCATCACAA 325
                                   i   v iv               i      i i   iii  v
  AluSx#SINE/Al        200 TTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAC 249

  UnnamedSequen        326 TCCAGCCTGAGTGACAGAGTGAGACTCCATCTGAAAAAAAAGAAAAAA 373
                                    i i       i        i   v        i      
  AluSx#SINE/Al        250 TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 297

Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 7.61
Transitions / transversions = 5.20 (26/5)
Gap_init rate = 0.02 (4 / 247), avg. gap size = 1.00 (4 / 4)

+ 1346   10.0  0.0  0.6  UnnamedSequence    374   551   (56) + AluSx    SINE/Alu      130    306    (6)   3

ANNOTATION EVIDENCE:
 1346  10.00 0.00 0.56  UnnamedSequence    374   551     56 + AluSx    SINE/Alu      130    306      6    
1346 10.00 0.00 0.56 UnnamedSequence 374 551 (56) AluSx#SINE/Alu 130 306 (6) m_b1s356i0

  UnnamedSequen        374 CAATTAGCCTGGCATGGTGGCAGGCACCTGTAATCCCTGCTACTTGGGAG 423
                           v        v   i       iv  i           v      i     
  AluSx#SINE/Al        130 AAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAG 179

  UnnamedSequen        424 GCTGAGGCAGGAGAATTGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGC 473
                                           i                i                
  AluSx#SINE/Al        180 GCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGC 229

  UnnamedSequen        474 TGAGATCGTGCCATTGCATTCCAGGCTGAGCAACAAGAGCAAGACTCCGT 523
                           i       i    i    i     v   i  i  -     i         
  AluSx#SINE/Al        230 CGAGATCGCGCCACTGCACTCCAGCCTGGGCGAC-AGAGCGAGACTCCGT 278

  UnnamedSequen        524 CTCAAAAAAAAAAAAAAAAAAAAAAAAA 551
                                                       
  AluSx#SINE/Al        279 CTCAAAAAAAAAAAAAAAAAAAAAAAAA 306

Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.21
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.01 (1 / 177), avg. gap size = 1.00 (1 / 1)

+  426    8.9  0.0  0.0  UnnamedSequence    552   607    (0) + AluSx    SINE/Alu        1     56  (256)   4

ANNOTATION EVIDENCE:
  426   8.93 0.00 0.00  UnnamedSequence    552   607      0 + AluSx    SINE/Alu        1     56    256    
426 8.93 0.00 0.00 UnnamedSequence 552 607 (0) AluSx#SINE/Alu 1 56 (256) m_b1s357i1

  UnnamedSequen        552 GGCCAGGTGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAA 601
                               i  i  i                                     i 
  AluSx#SINE/Al          1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50

  UnnamedSequen        602 GGTGGG 607
                             i   
  AluSx#SINE/Al         51 GGCGGG 56

Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 0.90
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)