New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE = 2543400115 (0.920)5 (0.040) 5/240 NT 4.3% intergenic (+194/‑373) hlgA/hlgC_2 Gamma‑hemolysin component A/Gamma‑hemolysin component C
?USA300TCH1516_ALE = 2543418 118 (1.020)intergenic (+212/‑355) hlgA/hlgC_2 Gamma‑hemolysin component A/Gamma‑hemolysin component C
Rejected: Frequency below/above cutoff threshold.

Only 100 of 150 total aligned reads displayed.

TTTTAACAAATTGAATCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCGGTTACCTTAA  >  USA300TCH1516_ALE/2543260‑2543539
                                                                                                                                            |                                                                                                                                            
ttttAACAAATTGAATCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA                                                                                                                                              <  2:562599‑M1/141‑1 (MQ=255)
 tttAACAAATTGAATCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGa‑a                                                                                                                                            <  1:631201/141‑1 (MQ=255)
     aCAACTTGAATCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCt                                                                                                                                        >  1:304105/1‑141 (MQ=255)
     aCAAATTGAATCAGCCTTATAACATTAAATTATTTTATCGTACATCAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCAAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCt                                                                                                                                        >  2:1075773/1‑141 (MQ=255)
         aTTGAATCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTtaaa                                                                                                                                    <  1:908062/141‑1 (MQ=255)
         aTTGAATCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTtaaa                                                                                                                                    <  2:634702/141‑1 (MQ=255)
            gAATCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAAAAACTGATTTTGATTAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTtaaataa                                                                                                                                 >  1:44846/1‑141 (MQ=255)
             aaTCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAACAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTtaaataaa                                                                                                                                <  1:616810/141‑1 (MQ=255)
              aTCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTaaataaat                                                                                                                               <  2:453878/141‑1 (MQ=255)
               tCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAaataaata                                                                                                                              >  2:705988/1‑141 (MQ=255)
                cAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAatat                                                                                                                             >  3:454393/1‑141 (MQ=255)
                 aGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAAtatt                                                                                                                            >  1:1042103/1‑141 (MQ=255)
                 aGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAAtatt                                                                                                                            <  1:114876/141‑1 (MQ=255)
                  gCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAAtatta                                                                                                                           >  3:59157/1‑141 (MQ=255)
                   ccTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTAt                                                                                                                          <  1:558346‑M2/141‑2 (MQ=255)
                     ttATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTAtca                                                                                                                        <  2:749245‑M2/141‑4 (MQ=255)
                      tataACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTAtcaa                                                                                                                       <  1:916068‑M2/141‑5 (MQ=255)
                         aaCATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTAtcaagtt                                                                                                                    >  3:261908‑M2/1‑134 (MQ=255)
                           cATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTAtcaagttaa                                                                                                                  <  1:489385‑M2/141‑10 (MQ=255)
                             ttAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTtaata                                                                                                                >  2:788182/1‑141 (MQ=255)
                             ttAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTtaata                                                                                                                <  1:198835/141‑1 (MQ=255)
                              tAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGAtaatatttatttaagctttcaagttaaatt                                                                                                                <  1:773127‑M1/141‑31 (MQ=255)
                               aaaTTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATaaa                                                                                                              <  2:515417/141‑1 (MQ=255)
                               aaaTTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATaaa                                                                                                              <  3:272579/141‑1 (MQ=255)
                                  ttattTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGAtaatatttatttaagctttcaagttaaattgttt                                                                                                            <  2:202186‑M1/141‑35 (MQ=255)
                                       ttATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACaattaat                                                                                                      <  1:38325/141‑1 (MQ=255)
                                        tATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACaattaatt                                                                                                     <  3:342415/141‑1 (MQ=255)
                                         aTCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAAttt                                                                                                    <  2:153650/141‑1 (MQ=255)
                                         aTCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAAttt                                                                                                    <  4:412632/141‑1 (MQ=255)
                                         aTCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAAttt                                                                                                    <  2:398353/141‑1 (MQ=255)
                                          tCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAAtttt                                                                                                   >  1:873251/1‑141 (MQ=255)
                                          tCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAAtttt                                                                                                   >  1:734878/1‑141 (MQ=255)
                                            gTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTa                                                                                                 <  2:180973/141‑1 (MQ=255)
                                              aCATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGa                                                                                               >  1:965585/1‑141 (MQ=255)
                                                aTTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATg                                                                                             >  1:22943/1‑141 (MQ=255)
                                                        taataataaCAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATtcatc                                                                                     <  1:42656/141‑1 (MQ=255)
                                                        taataataaCAACTGATTCTTATAAAAATAAAGTATAGAACCATAGTAAATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTCAAATAAATATTTTCAAGTTAATAAACAATTAATTTTTAGATGGATtcatc                                                                                     <  2:1047716/141‑1 (MQ=255)
                                                         aataataaCAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGATAATATTTATTTAAGCTTcaagttaaattgtttcatttgtattatttgtgtatcta                                                                                      <  2:7630‑M2/141‑39 (MQ=255)
                                                          ataataaCAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCaa                                                                                   <  2:66433/141‑1 (MQ=255)
                                                          ataataaCAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCaa                                                                                   >  4:138524/1‑141 (MQ=255)
                                                          ataataaCAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCaa                                                                                   <  1:572283/141‑1 (MQ=255)
                                                             ataaCAATTGATTTTTATAATAATAAAGTATCGAATCATAGTAGATACACAAATAAAACAAAAAAAACAATCTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTTTTTTTTATATGGATTCATaaaaaa                                                                                <  2:975864/141‑1 (MQ=255)
                                                             ataaCAACTTATTTTTATAAAAATAAAGTATCGAACCATAGTATATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCaaaaa                                                                                <  2:888609/141‑1 (MQ=255)
                                                             ataaCAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCaaaaa                                                                                <  2:656212/141‑1 (MQ=255)
                                                             ataaCAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCaaaaa                                                                                >  1:1034829/1‑141 (MQ=255)
                                                             aaaaccacTGATTTTTATAAGAATAAAGTATCGAACAATAGTAGATACAAAAATAATACAAATACAAGAATTTACCTAGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCaaaaa                                                                                <  3:456176/139‑1 (MQ=255)
                                                               aacaacTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATc                                                                              >  2:478548/1‑141 (MQ=255)
                                                                      gATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTaaaaa                                                                       <  3:144801/141‑1 (MQ=255)
                                                                      gATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTaaaaa                                                                       >  4:135915/1‑141 (MQ=255)
                                                                       aTTTTTATAAGAATAAAGTATAGAACCAGAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAg                                                                      <  4:229911/141‑1 (MQ=255)
                                                                           ttATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGcaca                                                                  >  3:199743/1‑141 (MQ=255)
                                                                            tataAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACaa                                                                 <  2:203882/141‑1 (MQ=255)
                                                                            tataAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACaa                                                                 >  4:212642/1‑141 (MQ=255)
                                                                                aGAATAAAGGATAGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTg                                                             <  2:328640/141‑1 (MQ=255)
                                                                                  aaTAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTa                                                           <  3:96507/141‑1 (MQ=255)
                                                                                  aaTAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTa                                                           <  1:846593/141‑1 (MQ=255)
                                                                                   aTAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTAt                                                          <  2:21515/141‑1 (MQ=255)
                                                                                     aaaGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTAttt                                                        <  2:831834/141‑1 (MQ=255)
                                                                                     aaaGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTAttt                                                        >  3:234721/1‑141 (MQ=255)
                                                                                        gTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTAc                                                     <  1:470427/141‑1 (MQ=255)
                                                                                           tCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACaaa                                                  >  2:830196/1‑141 (MQ=255)
                                                                                           tCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACaaa                                                  >  2:496328/1‑141 (MQ=255)
                                                                                             aaaCCATAGTAGATACACAAATAATACAAATGAAACACTTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACATTTTGTATTTTACAAACa                                                <  1:889845/140‑1 (MQ=255)
                                                                                              aaCCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACat                                               <  3:82235/141‑1 (MQ=255)
                                                                                               aCCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACatt                                              >  2:700475/1‑141 (MQ=255)
                                                                                                      tagATACACAAATAATACAAATGAAACAATTTAACTTGAtaatatttatttaagctttcaagttaaattgtttcatttgtattatttgtgtatctactatggttcgatactttattcttataaaaatcagttgttattatt                                        <  1:7630‑M1/141‑103 (MQ=255)
                                                                                                      tagATACACAAATAATACAAATGAAACAATTTAACTTGAaagcttaaataaatattatcaagttaaattgtttcatttgtattatttgtgtatctactatggttcgatactttattcttataaaaatcagttgttattatt                                        <  2:7630‑M1/141‑103 (MQ=255)
                                                                                                      tagATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGGATTTTACAAACATTAATTaaa                                       <  1:638123/141‑1 (MQ=255)
                                                                                                       agttACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTaaaa                                      <  4:392139/138‑1 (MQ=255)
                                                                                                          tACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTAAAAAAAAAAAATAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAaaag                                   <  2:333636/141‑1 (MQ=255)
                                                                                                            catttataataCAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAaaagaa                                 >  4:428423/6‑141 (MQ=255)
                                                                                                              caAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAaaagaaag                               >  2:922007/1‑141 (MQ=255)
                                                                                                               aaaTAATACAAATGAAACCATTTACCATGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGc                              <  2:861021/141‑1 (MQ=255)
                                                                                                               aaaTAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGc                              <  4:382653/141‑1 (MQ=255)
                                                                                                                 ataataCAAATGAAAAAATTTAACTTGA‑AAACTTAAATAAATATTATCAATTTAATAAACAATTAATTTTTAGAAAAAAAAAAAAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCaa                            <  2:305481/141‑1 (MQ=255)
                                                                                                                  taataCAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTAATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACAGTAATTAAAAAAGAAAGCAAg                           <  4:259296/141‑1 (MQ=255)
                                                                                                                      aCAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGatcc                       >  1:389977/1‑138 (MQ=255)
                                                                                                                      aCAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACAt                       >  1:990032/1‑141 (MQ=255)
                                                                                                                      aCAAATGAAACAATATAACTAGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACAt                       <  2:278780/141‑1 (MQ=255)
                                                                                                                        aaaTGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTc                     >  2:932573/1‑141 (MQ=255)
                                                                                                                            gAAACAATTTAACTTGC‑AAGATTAAATAAATATTATCATGTTAATAACCAAAAACTTTTTAGATCGAAACATCACAAATCGTAAAAAGCACAATTTGTATTTTACAAACCTTAATTAAAAAAGAAAGCAAGACATTCGTGc                 <  3:42299/141‑1 (MQ=255)
                                                                                                                               aCAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAAt              <  1:1046585/141‑1 (MQ=255)
                                                                                                                                 aaTTTAACTTGA‑AGGCATAAATAAATCTTAtcacgttaaattgtttcatttgtattatttgtgtatctactatgtttcaatactttattcttataaaaataagttgttattattaaatttaatgtacgataaaataattta            >  2:770688‑M2/1‑30 (MQ=255)
                                                                                                                                 aaTTTAACTTGA‑AAGCTTAAATAAATATTAtcaagttaaattgtttcatttgtattatttgtgtatctactatggttcgatactttattcttataaaaatcagttgttattattaaatttaatgtacgataaaataattta            <  1:773127‑M2/141‑112 (MQ=255)
                                                                                                                                 aaTTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTTTTTTTTTTTATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCg            >  2:755819/1‑141 (MQ=255)
                                                                                                                                 aaTTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCg            >  1:42916/1‑141 (MQ=255)
                                                                                                                                 aaTTTAACTTGA‑AAGATTAAATAAATATTAACAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCg            <  2:1028832/141‑1 (MQ=255)
                                                                                                                                   tttAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCGGt          <  2:508277/141‑1 (MQ=255)
                                                                                                                                    ttAACTTGAtaatatttatttaagctttcaagttaaattgtttcatttgtattatttgtgtatctactatggttcgatactttattcttataaaaatcagttgttattattaaatttaatgtacgataaaataatttaatg          <  1:489476‑M1/141‑133 (MQ=255)
                                                                                                                                    ttAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCGGtt         <  3:138524/141‑1 (MQ=255)
                                                                                                                                     tAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCGGTTa        >  1:503709/1‑141 (MQ=255)
                                                                                                                                      aagttGA‑AAGCTTAAATAAATATTCTCAAGTTAATAAATAATTAACTTTTAGATGGATTCATCAAAAATCGTAAAAAGAACAATTTGTATTTTACAAACATTAATTAAAAATAAAAGCAAGACATTCGTGCAATCGGTTAc       <  2:970031/138‑1 (MQ=255)
                                                                                                                                      aaCTTGAtaatatttatttaagctttcaagttaaattgtttcatttgtattatttgtgtatctactatggttcgatactttattcttataaaaatcagttgttattattaaatttaatgtacgataaaataatttaatgtt        >  3:261908‑M1/1‑7 (MQ=255)
                                                                                                                                       aCTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCGGTTAcc      >  1:295920/1‑141 (MQ=255)
                                                                                                                                       aCTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCGGTTAcc      >  2:142095/1‑141 (MQ=255)
                                                                                                                                       aCTTAA‑AAGAATAAATAAATATAATCAAGTTAATAAACAATTAATTTTTAGATGGATTAAACAAAAAACATAAAAAGCAAAATTTGTATTTTACAAAAAAAAAAAAAAAAAGAAAGCAAGACATTCGTGCAATCGGTTAcc      <  2:1037912/141‑1 (MQ=255)
                                                                                                                                        cTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCGGTTACCt     <  1:501356/141‑1 (MQ=255)
                                                                                                                                         ttGAtaatatttatttaagctttcaagttaaattgtttcatttgtattatttgtgtatctactatggttcgatactttattcttataaaaatcagttgttattattaaatttaatgtacgataaaataatttaatgttata     <  1:916068‑M1/141‑138 (MQ=255)
                                                                                                                                          tGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATTGATTCATCAAAAAAAAAAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCGGTTACCTTa   <  4:285684/141‑1 (MQ=255)
                                                                                                                                            ataatatttatttaagctttcaagttaaattgtttcatttgtattatttgtgtatctactatggttcgatactttattcttataaaaatcagttgttattattaaatttaatgtacgataaaataatttaatgttataagg  <  1:558346‑M1/141‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                            
TTTTAACAAATTGAATCAGCCTTATAACATTAAATTATTTTATCGTACATTAAATTTAATAATAACAACTGATTTTTATAAGAATAAAGTATCGAACCATAGTAGATACACAAATAATACAAATGAAACAATTTAACTTGA‑AAGCTTAAATAAATATTATCAAGTTAATAAACAATTAATTTTTAGATGGATTCATCAAAAATCGTAAAAAGCACAATTTGTATTTTACAAACATTAATTAAAAAAGAAAGCAAGACATTCGTGCAATCGGTTACCTTAA  >  USA300TCH1516_ALE/2543260‑2543539

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.