# Smith-Waterman GST matches
#
# sample tag        alignment
1 ACACGCATATTGCTGGT ACACGCATATTGCTGGT   1                   # no. times sampled
                     *                  
                    AAACGCATATTGCTGGT   f 1  446    263   1 #d,seq,frag,off,rnk

1 ACATAAGCTATCCGCCA ACATAAGCTATCCGCCA   1 
                          *
                    ACATAAACTATCCGCCA   f 1  462     96   1  

1 ACCGTGCAATTTATTGA ACCGTGCAATTTATTGA   1 
                                    *
                    ACCGTGCAATTTATTGG   r 1  627     50   1  

1 ACGAAGGATCGGGCCAA ACGAAGGATCGGGCCAA   1 
                      *
                    ACAAAGGATCGGGCCAA   f 1  621    144   1  

1 ACGACACGCACCAACGG ACGACACGCACCAACGG   2 
                     *
                    ATGACACGCACCAACGG   r 1    4    299   1  

1 ACGCACTGTTTGTCAGC ACGCACTGTTTGTCAGC   1 
                                    *
                    ACGCACTGTTTGTCAGT   f 1  174    122   1  

1 ACGGGGGCTTTTGTCTT ACGGGGGCTTTTGTCTT   1 
                    *
                    GCGGGGGCTTTTGTCTT   r 1  273    253   1  

1 ACTCTGATAACGGCCAC ACTCTGATAACGGCCAC   1 
                                    *
                    ACTCTGATAACGGCCAT   r 1  140    105   1  

1 AGCGGTAAAGTCCCACG AGCGGTAAAGTCCCACG   1 
                                    *
                    AGCGGTAAAGTCCCACT   r 1   40    437   1  

1 AGGCCATCCGCCCATCA AGGCCATCCGCCCATCA   1 
                                 *
                    AGGCCATCCGCCCTTCA   f 1  363    727   1  

1 AGGGTTCAAGGTCTTCA AGGGTTCAAGGTCTTCA   1 
                    *
                    TGGGTTCAAGGTCTTCA   r 1    9     64   1  

1 AGTTAATGCTCCGCGCA AGTTAATGCTCCGCGCA   1 
                           *
                    AGTTAATTCTCCGCGCA   f 1  695     35   1  

1 AGTTTTGGTGGCTTGCT AGTTTTGGTGGCTTGCT   1 
                                    *
                    AGTTTTGGTGGCTTGCC   f 1   56    240   1  

1 ATAAACATTTGTAGCAG ATAAACATTTGTAGCAG   1 
                      *
                    ATTAACATTTGTAGCAG   r 3    1    143   1  

1 ATCAAAAAGGCCGGGAA ATCAAAAAGGCCGGGAA   1 
                                 *
                    ATCAAAAAGGCCGCGAA   f 1  680    288   1  

1 ATCGGCCGTAAACGCGA ATCGGCCGTAAACGCGA   1 
                                    *
                    ATCGGCCGTAAACGCGC   r 1   57    442   1  

1 ATCGGCCGTAAACGCGT ATCGGCCGTAAACGCGT   2 
                                    *
                    ATCGGCCGTAAACGCGC   r 1   57    442   1  

1 ATGACCAACGGCAAGCC ATGACCAACGGCAAGCC   2 
                           *
                    ATGACCAGCGGCAAGCC   r 1  548    777   1  

1 ATGCCGAGGGTGGTGAC ATGCCGAGGGTGGTGAC   1 
                                    *
                    ATGCCGAGGGTGGTGAT   f 1   27     92   1  

1 ATGCCGATACAGGCCGT ATGCCGATACAGGCCGT   1 
                      *
                    ATACCGATACAGGCCGT   f 1  369    414   1  

1 ATGCTATCCGGCCCACT ATGCTATCCGGCCCACT   1 
                                    *
                    ATGCTATCCGGCCCACC   r 1  224    335   1  

1 ATTAAAAAGGCCGCGAA ATTAAAAAGGCCGCGAA   2 
                      *
                    ATCAAAAAGGCCGCGAA   f 1  680    288   1  

1 ATTAACATTTGTAGCAC ATTAACATTTGTAGCAC   1 
                                    *
                    ATTAACATTTGTAGCAG   r 3    1    143   1  

1 ATTATCGGGCGTTTTGG ATTATCGGGCGTTTTGG   2 
                          *
                    ATTATCAGGCGTTTTGG   r 1  151    347   1  

1 ATTCAGCGTTGAGGGCG ATTCAGCGTTGAGGGCG   1 
                                    *
                    ATTCAGCGTTGAGGGCT   r 1  113    618   1  

1 CAATTTGGTTTCTGCTA CAATTTGGTTTCTGCTA   1 
                       *
                    CAACTTGGTTTCTGCTA   f 1  658  27141  97  

1 CAGGCGAGTTCCAGATT CAGGCGAGTTCCAGATT   1 
                        *
                    CAGGTGAGTTCCAGATT   r 1  667    295   1  

1 CAGGGCCAATATTACGG CAGGGCCAATATTACGG   1 
                                    *
                    CAGGGCCAATATTACGA   r 1  124    156   1  

1 CATTCGGCGGGCGCTTT CATTCGGCGGGCGCTTT   1 
                         *
                    CATTCAGCGGGCGCTTT   r 1  561    418   1  

1 CCAACTTTCTCAAGCCC CCAACTTTCTCAAGCCC   1 
                                   *
                    CCAACTTTCTCAAGCGC   f 1  507   1480   1  

1 CCAGATTTCCCAACTTT CCAGATTTCCCAACTTT   1 
                            *
                    CCAGATTTTCCAACTTT   r 1  469    799   1  

1 CCAGCCAGGACATTACT CCAGCCAGGACATTACT   1 
                                    *
                    CCAGCCAGGACATTACC   f 1   13    198   1  

1 CCAGTCAGGACATTACC CCAGTCAGGACATTACC   2 
                        *
                    CCAGCCAGGACATTACC   f 1   13    198   1  

1 CCATCCCTGTATTACGT CCATCCCTGTATTACGT   1 
                                    *
                    CCATCCCTGTATTACGC   f 1  241    136   1  

1 CCCCTTCGGATTCCCCT CCCCTTCGGATTCCCCT   1 
                                    *
                    CCCCTTCGGATTCCCCC   f 1  215    167   1  

1 CCCTGCGGTGCGGGAGC CCCTGCGGTGCGGGAGC   1 
                             *
                    CCCTGCGGTACGGGAGC   r 1  277    915   1 f 1  128    915   1 f 1   42    915   1  

1 CCCTTGCAGAGGTTCCA CCCTTGCAGAGGTTCCA   1 
                                    *
                    CCCTTGCAGAGGTTCCC   r 1  369    461   1  

1 CCCTTGTGCCGTGTCTG CCCTTGTGCCGTGTCTG   1 
                          *
                    CCCTTGCGCCGTGTCTG   f 1  125    185   1  

1 CCGCTCGGGATGCTGGG CCGCTCGGGATGCTGGG   1 
                     *
                    CTGCTCGGGATGCTGGG   f 1  291    477   1  

1 CCGGAACAACCCGAAGG CCGGAACAACCCGAAGG   1 
                                    *
                    CCGGAACAACCCGAAGT   f 1  481    220   1  

1 CCGTCAAACACAAACTC CCGTCAAACACAAACTC   1 
                        *
                    CCGTTAAACACAAACTC   r 1  616    434   1  

1 CCTCTATGGCCCCTCGG CCTCTATGGCCCCTCGG   1 
                    *
                    TCTCTATGGCCCCTCGG   r 1  675    646   1  

1 CCTGGAATGCCACCCAC CCTGGAATGCCACCCAC   1 
                                    *
                    CCTGGAATGCCACCCAT   r 1  111    363   1  

1 CCTTGGTATTGCGCAGC CCTTGGTATTGCGCAGC   2 
                                   *
                    CCTTGGTATTGCGCAAC   f 1  133    152   1  

1 CGTCACCTCGCTGAACG CGTCACCTCGCTGAACG   1 
                         *
                    CGTCATCTCGCTGAACG   r 1  686    282   1 r 1  680    282   1 r 1  659    282   1 r 1  631  12871  44 f 1  586    282   1 r 1  173    282   1 r 1  123    282   1 f 1   12    282   1  

1 CTAATCCCAAGCCCCCC CTAATCCCAAGCCCCCC   1 
                                  *
                    CTAATCCCAAGCCCTCC   r 1   86    137   1  

1 CTACAGGCCATCGTCTC CTACAGGCCATCGTCTC   1 
                                   *
                    CTACAGGCCATCGTCCC   f 1  576     92   1  

1 CTGCTGTGGATCAACCA CTGCTGTGGATCAACCA   2 
                                    *
                    CTGCTGTGGATCAACCC   r 1  268    140   1  

1 CTGTTAGGTCTGGGAGG CTGTTAGGTCTGGGAGG   1 
                         *
                    CTGTTCGGTCTGGGAGG   r 1   99    196   1  

1 CTTCGTTTCCCTCACTT CTTCGTTTCCCTCACTT   1 
                     *
                    CCTCGTTTCCCTCACTT   r 1  238    421   1  

1 GAGGGGTTGNTACAAGC GAGGGGTTGNTACAAGC   1 
                             |
                    GAGGGGTTGCTACAAGC   r 1  662     47   1  

1 GATAGAAATACCGCATC GATAGAAATACCGCATC   1 
                                    *
                    GATAGAAATACCGCATT   r 1   69    244   1  

1 GCAAACCGAAACTCTAG GCAAACCGAAACTCTAG   1 
                           *
                    GCAAACCAAAACTCTAG   f 1  650    240   1  

1 GCAACTTCTGTTGCGTG GCAACTTCTGTTGCGTG   1 
                                    *
                    GCAACTTCTGTTGCGTT   r 1    6    118   1  

1 GCACTGAGCTGCACGGG GCACTGAGCTGCACGGG   1 
                                    *
                    GCACTGAGCTGCACGGA   r 1  555     75   1  

1 GCAGCGGCGCGCGTTGC GCAGCGGCGCGCGTTGC   1 
                                *
                    GCAGCGGCGCGCATTGC   f 1  539    175   1  

1 GCAGCGTTAATTCTGTC GCAGCGTTAATTCTGTC   1 
                                   *
                    GCAGCGTTAATTCTGGC   r 1  581    678   1  

1 GCATATACACCCGGTGG GCATATACACCCGGTGG   1 
                          *
                    GCATATGCACCCGGTGG   f 1   51    285   1  

1 GCCAGCGCGCGCCAGGG GCCAGCGCGCGCCAGGG   2 
                                    *
                    GCCAGCGCGCGCCAGGA   r 1  362    618   1  

1 GCCCATCCCACGAATAC GCCCATCCCACGAATAC   1 
                           *
                    GCCCATCTCACGAATAC   f 1  648    140   1  

1 GCCGGCGATACCGATGC GCCGGCGATACCGATGC   1 
                    *
                    ACCGGCGATACCGATGC   f 1  247    642   1  

1 GCCTCATTCACACTCTA GCCTCATTCACACTCTA   1 
                                    *
                    GCCTCATTCACACTCTG   r 1  412     70   1  

1 GCGGCAGTATTGATGTT GCGGCAGTATTGATGTT   1 
                    *
                    ACGGCAGTATTGATGTT   f 1  389    500   1  

1 GCGGGGCATATTTTGGT GCGGGGCATATTTTGGT   1 
                             *
                    GCGGGGCATTTTTTGGT   f 1  379    281   1  

1 GCGTTCCTTTCAGGTAC GCGTTCCTTTCAGGTAC   1 
                           *
                    GCGTTCCCTTCAGGTAC   f 1  335    279   1  

1 GCTGCACTGCACGGCGT GCTGCACTGCACGGCGT   1 
                                    *
                    GCTGCACTGCACGGCGG   f 1  613    128   1  

1 GCTTGCTTTGTTTTGCC GCTTGCTTTGTTTTGCC   1 
                                    *
                    GCTTGCTTTGTTTTGCT   r 1  579    135   1  

1 GGCACCTTGATTAACCA GGCACCTTGATTAACCA   1 
                        *
                    GGCATCTTGATTAACCA   f 1  380     77   1  

1 GGCGCGTTGTGCGTCAA GGCGCGTTGTGCGTCAA   1 
                                    *
                    GGCGCGTTGTGCGTCAC   f 1   44    412   1  

1 GGCGTAATTTGGCGGGA GGCGTAATTTGGCGGGA   1 
                                    *
                    GGCGTAATTTGGCGGGG   f 1   67    174   1  

1 GGGGTGCTGTATCACCA GGGGTGCTGTATCACCA   1 
                                    *
                    GGGGTGCTGTATCACCG   r 1  338   1098   2  

1 GGGTAGAGATTACCAGC GGGTAGAGATTACCAGC   1 
                                *
                    GGGTAGAGATTAACAGC   r 1  535    443   1  

1 GTCAGGTAGAAGCGATG GTCAGGTAGAAGCGATG   1 
                    *
                    ATCAGGTAGAAGCGATG   f 1  313    267   1  

1 GTCGATGGCACCGTCCG GTCGATGGCACCGTCCG   1 
                      *
                    GTTGATGGCACCGTCCG   r 1  338    380   1  

1 GTCGCGCGCACACCTGC GTCGCGCGCACACCTGC   1 
                              *
                    GTCGCGCGCATACCTGC   f 1   17    268   1  

1 GTGCTGTACCAAAGCCA GTGCTGTACCAAAGCCA   1 
                                    *
                    GTGCTGTACCAAAGCCT   r 1  455     62   1  

1 GTGGCGAGTACCGTAAG GTGGCGAGTACCGTAAG   1 
                                    *
                    GTGGCGAGTACCGTAAA   r 1  689    218   1  

1 GTGGCTTGCAGCAACCC GTGGCTTGCAGCAACCC   1 
                              *
                    GTGGCTTGCAACAACCC   f 1  388    416   1  

1 GTGGGCCGCGCCCCTAG GTGGGCCGCGCCCCTAG   1 
                                    *
                    GTGGGCCGCGCCCCTAT   r 1   28    857   1  

1 GTGTGGTGAATGACTGG GTGTGGTGAATGACTGG   1 
                    *
                    CTGTGGTGAATGACTGG   f 1  226    116   1  

1 GTNTCTTTACCTTATGC GTNTCTTTACCTTATGC   1 
                      |
                    GTGTCTTTACCTTATGC   f 1  218    326   1  

1 GTTAGCAGCATCATAAG GTTAGCAGCATCATAAG   1 
                                    *
                    GTTAGCAGCATCATAAT   f 1  232    431   1  

1 GTTAGCCGCATCCTACC GTTAGCCGCATCCTACC   1 
                       *
                    GTTTGCCGCATCCTACC   r 1  157    341   1  

1 GTTTCGATGCGGCAGGC GTTTCGATGCGGCAGGC   1 
                        *
                    GTTTTGATGCGGCAGGC   r 1  545    202   1  

1 GTTTGGTCCTGTGTATA GTTTGGTCCTGTGTATA   1 
                                *
                    GTTTGGTCCTGTCTATA   f 1  103   1283   1  

1 TAGAGACCCGTGCGACA TAGAGACCCGTGCGACA   1 
                        *
                    TAGAAACCCGTGCGACA   f 1  541    107   1  

1 TAGGAAGGTGAGGGGTT TAGGAAGGTGAGGGGTT   1 
                       *
                    TAGAAAGGTGAGGGGTT   r 2    1    352   1  

1 TCACGGATCGCGCCACC TCACGGATCGCGCCACC   1 
                              *
                    TCACGGATCGTGCCACC   r 1  564     61   1  

1 TCTCTATTTTGGCGACG TCTCTATTTTGGCGACG   1 
                                   *
                    TCTCTATTTTGGCGATG   r 1  513    254   1  

1 TCTCTCCTCAGCTTTGC TCTCTCCTCAGCTTTGC   1 
                     *
                    TTTCTCCTCAGCTTTGC   r 1  614    211   1  

1 TCTGGAGCCTGGATGTC TCTGGAGCCTGGATGTC   2 
                                *
                    TCTGGAGCCTGGCTGTC   f 1  233    315   1  

1 TGATGCTCCCTTACTAA TGATGCTCCCTTACTAA   1 
                                   *
                    TGATGCTCCCTTACTTA   r 1  143    140   1  

1 TGATTGCGGCTATCCCC TGATTGCGGCTATCCCC   1 
                      *
                    TGGTTGCGGCTATCCCC   f 1  515    374   1  

1 TGGCCGTCATTGTTGGC TGGCCGTCATTGTTGGC   2 
                    *
                    CGGCCGTCATTGTTGGC   f 1  649    212   1  

1 TGGGTTATGCAGCGCTG TGGGTTATGCAGCGCTG   1 
                               *
                    TGGGTTATGCAACGCTG   f 1  683    199   1  

1 TGGTATGCGATTCAATC TGGTATGCGATTCAATC   1 
                    *
                    GGGTATGCGATTCAATC   f 1  200    141   1  

1 TGTAGCTAAAAAATCAC TGTAGCTAAAAAATCAC   1 
                     *
                    TTTAGCTAAAAAATCAC   f 1  535    454   1  

1 TTGATCGAAACAGGCGA TTGATCGAAACAGGCGA   2 
                                   *
                    TTGATCGAAACAGGCAA   f 1  390    413   1  

2 ACGGAAAAAAAAGGCAC ACGGAAAAAAAAGGCAC   1 
                               -     -
                    ACGGAAAAAAA GGCACC   r 1  668    171   1  

2 ATTATCGGGCGTTTTGG ATTATCGGGCGTTTTGG   2 
                    *          *
                    TTTATCGGGCGCTTTGG   r 1  436    393   1  

2 CACGCACTTCGCCACTG  CACGCACTTCGCCACTG   1
                    -                -
                    GCACGCACTTCGCCACT   f 1  569    130   1  

2 CGAGACTGCTGAGCAGT CGA GACTGCTGAGCAGT   1
                       -             -
                    CGATGACTGCTGAGCAG   r 1  405    125   1  

2 CTCCTGTCATTACATTG CTCCTGTCATTACA TTG   1
                                  -  -
                    CTCCTGTCATTACAATT   r 1  525     78   1  

2 GCAGCGGGGGGGGGCGG GCAGCGGGGGGGGGCGG   1 
                                 -   -
                    GCAGCGGGGGGGG CGGT   r 1  467    171   1  

2 GCTGGTAGTATTCGGTC GCTGGTAGTATTCGGTC   1 
                    -                -
                     CTGGTAGTATTCGGTCT   r 1  523    378   1  

2 GGGATGGCGGTCGCCGC GGGATGGCGGTCGCCGC   1 
                                  * *
                    GGGATGGCGGTCGCGGT   r 1  475     43   1  

2 GGTATGCGATTCAATCA  GGTATGCGATTCAATCA   1
                    -                -
                    GGGTATGCGATTCAATC   f 1  200    141   1  

2 TACCCCATCCACTTTAC TACCCCATCCACTTT AC   1
                                   - -
                    TACCCCATCCACTTTTA   r 1  431     35   1  

2 TCAGAGCGAAGAAGCGG  TCAGAGCGAAGAAGCGG   1
                    -                -
                    GTCAGAGCGAAGAAGCG   f 1   85    169   1  

2 TTGTCGGACAGGATTTC TTGTCGG ACAGGATTTC   1
                           -         -
                    TTGTCGGTACAGGATTT   r 1  504     27   1