New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_012417 961 =1497 (1.170)5 (0.000) 5/250 NT 0.36% pseudogene (682/709 nt) USA300HOU_RS14890 replication protein
?NC_012417 980 = 1340 (1.090)pseudogene (701/709 nt) USA300HOU_RS14890 replication protein
Rejected: Frequency below/above cutoff threshold.

Only 100 of 1551 total aligned reads displayed.

TAAACAAAAACATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGAC  >  NC_012417/840‑1120
                                                                                                                                            |                                                                                                                                            
 taaCAAGAACTTAAAATTTTAAACTGAGACGATGTCGAATCTGGTAATTTGATTAATTCAAGTGATGAACATAAAGCTACAGACGAAGACGAACAAGCACATTCAATTACCGCAATTTCGAATTTCGAAACGCAAAattat                                                                                                                                             <  2:365703/140‑1 (MQ=14)
 aaaCAAAAACATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAattat                                                                                                                                             <  2:586339/141‑1 (MQ=255)
 aaaCAAAAACATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAattat                                                                                                                                             <  1:540609/141‑1 (MQ=255)
      aaaaCATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTAttt                                                                                                                                        >  1:167523/1‑141 (MQ=255)
        aaCATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGCAAAGCAAAATTATTATTTaa                                                                                                                                      <  1:570047/141‑1 (MQ=255)
        aaCATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTaa                                                                                                                                      >  1:240117/1‑141 (MQ=255)
        aaCATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTaa                                                                                                                                      >  1:274238/1‑141 (MQ=255)
          aaTAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTTATGCAAATCACGAAAAGAAAAAACCATTCGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGa                                                                                                                                    <  1:178579/140‑1 (MQ=14)
           aTAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGAc                                                                                                                                   <  2:752682/141‑1 (MQ=255)
           aTAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGAc                                                                                                                                   >  1:640619/1‑141 (MQ=255)
           aTAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGAc                                                                                                                                   >  1:493674/1‑141 (MQ=255)
           aTAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGAc                                                                                                                                   <  1:128975/141‑1 (MQ=255)
           aTAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGAc                                                                                                                                   >  1:78817/1‑141 (MQ=255)
           aTAAAATTTTAAACTTAGACGATGTCGAAAATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACAGCAATTTGGAATTTCGAAAAGCAAAACTATTATTTAAGAc                                                                                                                                   >  2:380195/1‑141 (MQ=255)
              aaaTTTTAAACTTAGACGGTGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGCATTTCGAAAAGCAAAATTATTATTTaaaccctt                                                                                                                                >  2:712690/1‑135 (MQ=255)
              aaaTTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAAGTTCGAAAAGCAAAATTATTATTTAAGACAtt                                                                                                                                >  1:255438/1‑141 (MQ=255)
               aaTTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTa                                                                                                                               <  2:352310/141‑1 (MQ=255)
                    tAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGtt                                                                                                                          >  1:526821/1‑141 (MQ=255)
                     aaagtgagaagaGGTCGAAGATGGGAATTGGATTAATGCAAGGGATGAAGAGAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTg                                                                                                                         <  2:507920/135‑1 (MQ=14)
                     aaaCTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTg                                                                                                                         >  2:936466/1‑141 (MQ=255)
                        cTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGCAGGAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGCCt                                                                                                                      >  1:437262/1‑141 (MQ=255)
                         ttAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTa                                                                                                                     <  2:18299/141‑1 (MQ=255)
                                    ggAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTCAACACTAATGTCttaaat                                                                                                          <  2:691153/140‑5 (MQ=14)
                                     gAAGATGGTAATTTGATTAATGCAAGTGATGAATATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTAGAATTTCGAAAAGCAAAATGATTATTTAAGACATTAGTGTTGACTAATGTCttttttt                                                                                                         >  2:621923/1‑140 (MQ=255)
                                      aaGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTttgt                                                                                                        <  1:558506/141‑1 (MQ=255)
                                            gTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAAACATTAGTGTTGACTAATGTCTTTTTTGTTGAttt                                                                                                  >  2:396594/1‑141 (MQ=255)
                                             tAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAAACATTAGTGTTGACTAATGTCTTTTTTGTTGAtttt                                                                                                 >  2:538405/1‑141 (MQ=255)
                                              aaTTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGAttttt                                                                                                <  1:418363/141‑1 (MQ=255)
                                              aaTTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGAttttt                                                                                                >  2:786886/1‑141 (MQ=255)
                                                tttGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAGGACATTAGTGTTGACTAATGTCTTTTTTGTTGAttttttt                                                                                              >  1:83837/1‑140 (MQ=255)
                                                tttGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTta                                                                                              >  2:320258/1‑141 (MQ=255)
                                                tttGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTta                                                                                              <  2:159961/141‑1 (MQ=255)
                                                tttGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTta                                                                                              >  1:100286/1‑141 (MQ=255)
                                                       aaTGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTCGATTTTTTATaaaaaa                                                                                       <  1:470436/141‑1 (MQ=255)
                                                         tGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGt                                                                                     <  1:114693/141‑1 (MQ=255)
                                                         tGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGt                                                                                     <  1:332351/141‑1 (MQ=255)
                                                          gCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTa                                                                                    >  2:897173/1‑141 (MQ=255)
                                                               tgatgaAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTc                                                                               <  2:145169/141‑1 (MQ=255)
                                                                gatgaAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCt                                                                              >  1:291703/1‑141 (MQ=255)
                                                                gatgaAGATAAAAAAACAGACGAAAAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATATAATATAAAAAAGTACTGTCt                                                                              <  2:639569/141‑1 (MQ=18)
                                                                 atgaAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCtt                                                                             >  1:855184/1‑141 (MQ=255)
                                                                 atgaAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCtt                                                                             <  2:859028/141‑1 (MQ=255)
                                                                  tgaAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATACAAAAGTACTGTCTTa                                                                            <  1:700611/141‑1 (MQ=255)
                                                                  tgaAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTATTGTTGATTTTTTATAAAAAAGTACTGTCttt                                                                            >  2:654573/1‑140 (MQ=255)
                                                                  agaAAATAAAACACAGGAGGAAGAAGAAAAAGCACATACAAGTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAACACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTa                                                                            <  2:553321/140‑1 (MQ=18)
                                                                   gaAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTAt                                                                           <  1:721308/141‑1 (MQ=255)
                                                                   atacaaaaaaCAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTAt                                                                           <  1:677392/135‑1 (MQ=255)
                                                                     aGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTAttt                                                                         >  2:215463/1‑141 (MQ=255)
                                                                     aGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTAttt                                                                         >  2:111578/1‑141 (MQ=255)
                                                                      gATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTAtttt                                                                        >  2:475096/1‑141 (MQ=255)
                                                                        tAAAACAACAGACGAAGAAGAACAAGCTCATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTtg                                                                      <  1:775428/141‑1 (MQ=255)
                                                                        tAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTtg                                                                      <  1:399163/141‑1 (MQ=255)
                                                                         aaaaCAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTtgt                                                                     <  1:807572/141‑1 (MQ=255)
                                                                          aaaCAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTtgtg                                                                    <  1:822232/141‑1 (MQ=255)
                                                                          aaaCAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTtgtg                                                                    <  1:515151/141‑1 (MQ=255)
                                                                           aacaacAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGa                                                                   >  2:126043/1‑141 (MQ=255)
                                                                           aacaacAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGa                                                                   <  1:582980/141‑1 (MQ=255)
                                                                           aacaacAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGa                                                                   <  2:872039/141‑1 (MQ=255)
                                                                           aacaacAGACGAAGAAGAAAAAGCACATTCAATGACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGa                                                                   <  1:91008/141‑1 (MQ=255)
                                                                           aacaacAGACGAAGAAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGa                                                                   <  2:33332/141‑1 (MQ=255)
                                                                               acaGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACaaa                                                               >  1:21109/1‑141 (MQ=255)
                                                                               acaGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGGGTACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACaaa                                                               >  1:927856/1‑141 (MQ=255)
                                                                                caGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAAt                                                              >  2:492664/1‑141 (MQ=255)
                                                                                 aGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATg                                                             >  1:377442/1‑141 (MQ=255)
                                                                                   aCGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCt                                                           <  1:617939/141‑1 (MQ=255)
                                                                                     gaagaagaaAAAGCACATTCAATTCACGAAAGCTCGATTTTCGATATGTAAAAGTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTTATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCtgt                                                         <  2:196320/141‑1 (MQ=18)
                                                                                     caagaagaaAAAGCCCAATCCATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGGCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCtgt                                                         <  1:22756/140‑1 (MQ=255)
                                                                                        aaagaccaaGCACACTCAATGACCGCAACTTGGAATTTCGAAAAGCAATATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCtgtatg                                                      <  1:343655/134‑1 (MQ=18)
                                                                                           gaaACAGCACATTCAATTAACGTAAATTCGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAg                                                   <  2:43932/141‑1 (MQ=17)
                                                                                             aaaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAgtg                                                 <  2:766550/141‑1 (MQ=255)
                                                                                              aaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAgtgt                                                <  2:68194/141‑1 (MQ=255)
                                                                                              aaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAgtgt                                                <  1:868668/141‑1 (MQ=255)
                                                                                              aaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTACTTAAGACAGTAGTGTTGACTAATGTCTTCTCTGTTGATTTATTATAAAAACGTCCTGTCTTATTTTTGTGAGAAATGCTGTATGTAgtgt                                                >  1:152900/1‑141 (MQ=17)
                                                                                                 gCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTcac                                             >  2:277695/1‑141 (MQ=255)
                                                                                                  cacaTTCAATTACCGCAATTTGTAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTCGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTcaca                                            <  1:198629/141‑1 (MQ=255)
                                                                                                         aaTTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATaa                                     >  2:831211/1‑141 (MQ=255)
                                                                                                          aTTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAg                                    <  2:844365/141‑1 (MQ=255)
                                                                                                           ttAGCGCAATTTGGAATTTCGATAAGCAAAATTATTATTTAAGACATTAGTGTTGTCTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGa                                   <  2:26198/141‑1 (MQ=255)
                                                                                                           ttACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGa                                   <  2:456251/141‑1 (MQ=255)
                                                                                                           ttACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGa                                   <  2:607184/141‑1 (MQ=255)
                                                                                                           ttACCGCAATTGGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACGAATTCTGTATGTAGTGTCACAAAAATAAGa                                   <  2:244147/141‑1 (MQ=255)
                                                                                                            tACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTTTCACAAAAATAAGAc                                  <  1:739675/141‑1 (MQ=255)
                                                                                                             aCCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACa                                 <  2:570775/141‑1 (MQ=255)
                                                                                                               cGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGCTTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACaaa                               >  1:449136/1‑141 (MQ=255)
                                                                                                                gCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAAc                              <  1:629275/141‑1 (MQ=255)
                                                                                                                     ttGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAATGTTGACTAATGTCTTTTTTGTTTATTTTTTATAAAAAAATACTGTCTTATTTTTGTGACAGATGCTGTATGTAGTGTCACAAAAATAAGCCAAAAGCaac                         >  2:80719/1‑140 (MQ=18)
                                                                                                                        gAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAatata                      >  1:95861/1‑141 (MQ=255)
                                                                                                                        gAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAatata                      <  2:732248/141‑1 (MQ=255)
                                                                                                                           TTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAACTGATGTATGTAGTGTCACAAAAATAAGACAAAAGCAATATattt                   <  1:658314‑M1/141‑2 (MQ=255)
                                                                                                                             TCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATtgtg                 >  1:884092‑M1/1‑141 (MQ=255)
                                                                                                                              cGAAAAGCAATATTATTATTTAAGACATTCGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTgtgt                <  1:755257/141‑1 (MQ=255)
                                                                                                                                  aaGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTcaca            <  2:226766/141‑1 (MQ=255)
                                                                                                                                    gCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTAACAAAAATAAGGCCAACGCAGTATATTATGTcgtcaa          >  2:922460/1‑136 (MQ=21)
                                                                                                                                    gCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTNTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTNACAAAAATACGACAAACGCAATCGATTGGNTCACcaa          >  2:666600/1‑141 (MQ=21)
                                                                                                                                        aattATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACATATGCTGTATGTAGTGTCACAAAAATAAGACAAAAGCAATATATTGTGTCaccaaaaaa      >  2:416803‑M2/5‑139 (MQ=255)
                                                                                                                                        aattATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATa      >  2:300123‑M2/5‑141 (MQ=255)
                                                                                                                                         attATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAACAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATaa     >  1:363497‑M2/4‑141 (MQ=255)
                                                                                                                                         attATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTTTCACAAAAATaa     >  2:523298‑M2/4‑141 (MQ=255)
                                                                                                                                          ttATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAACAATAAGACAAACGTAATATATTGTGTCACAAAAATAAg    <  1:605056‑M2/139‑1 (MQ=255)
                                                                                                                                           tATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGa   <  1:310150‑M2/140‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                            
TAAACAAAAACATAAAATTTTAAACTTAGACGATGTCGAAGATGGTAATTTGATTAATGCAAGTGATGAAGATAAAACAACAGACGAAGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTGTTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGAC  >  NC_012417/840‑1120

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: 
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.