New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 2679952 =329 (0.900)6 (0.020) 5/230 NT 2.2% intergenic (+4/+756) ssaA2_4/USA300HOU_RS13810 Staphylococcal secretory antigen ssaA2/hypothetical protein
?USA300TCH1516_ALE 2680007 = 245 (0.760)intergenic (+59/+701) ssaA2_4/USA300HOU_RS13810 Staphylococcal secretory antigen ssaA2/hypothetical protein
Rejected: Frequency below/above cutoff threshold.

Only 100 of 373 total aligned reads displayed.

ATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTAAATAATTCGCTATAACT  >  USA300TCH1516_ALE/2679867‑2680147
                                                                                                                                            |                                                                                                                                            
aTACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATACGAGTGATAGAAGTtttta                                                                                                                                              >  2:4177202/1‑141 (MQ=255)
 aaCAACTTTTATCGCCCATCAAACTTCAATACACGTGTACTAAGCCTAAAGGCCGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTttttat                                                                                                                                             <  1:597500/140‑1 (MQ=21)
     aCTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAACTCCCTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTttttatttta                                                                                                                                         <  1:635205/141‑1 (MQ=255)
     aCTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTttttatttta                                                                                                                                         <  1:284702/141‑1 (MQ=255)
       ttttATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATACTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATg                                                                                                                                       >  1:2317433/1‑141 (MQ=255)
        tttATCGTCCATTAAAATATATTACACGTGTAATAAGCAAAAAAGCAGCACGTAACTTTAACTATTGTTACTAATCAAAAAGCTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGa                                                                                                                                      <  2:3079848/141‑1 (MQ=21)
        tttATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGa                                                                                                                                      <  1:793074/141‑1 (MQ=255)
        tttATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGa                                                                                                                                      <  1:2011582/141‑1 (MQ=255)
        ttaaTCGCCAATTAAAATACAATACACGTTTAATAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGa                                                                                                                                      <  2:1720222/138‑1 (MQ=255)
           aTCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAat                                                                                                                                   <  1:434495/141‑1 (MQ=255)
            tCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATCAGTGTTAAAGAAGTTTTTATTTTATGATatt                                                                                                                                  >  2:2881110/1‑141 (MQ=37)
             cGCCCATTAAAATACAATACACGTGTACTAAGGAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGATCGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAatta                                                                                                                                 <  2:4343689/141‑1 (MQ=255)
             cGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAatta                                                                                                                                 <  1:940927/141‑1 (MQ=255)
                ccATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAattatat                                                                                                                              <  1:1132435/141‑1 (MQ=255)
                  aTTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAattatatta                                                                                                                            <  1:3168974/141‑1 (MQ=255)
                   ttAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATTAAattatatttt                                                                                                                           >  1:2602508/1‑139 (MQ=255)
                      aaaTACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTAc                                                                                                                        <  1:324983/141‑1 (MQ=255)
                         tacaatacaCGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTc                                                                                                                     >  2:1168653/1‑141 (MQ=255)
                         aacaataaaCGTGTACTAAGCAAAAAGGCAGCCCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATCGAAGTTTTTATTTTATGAAATTATATTATTACTTc                                                                                                                     <  2:2470104/140‑1 (MQ=255)
                                 acGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATGGAAGACATCATTTTATGAAATTATATTATTACTTCTACAAAtt                                                                                                             >  2:3119358/1‑141 (MQ=37)
                                 acGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGATTTTATTTTATGAAATTATATTATTACTTCTACAAAtt                                                                                                             >  2:213298/1‑141 (MQ=255)
                                  cGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGTACTGTTTATTTTATGAACTTATATTATTACTTCTACACAttt                                                                                                            >  1:149049/1‑141 (MQ=25)
                                  cGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAAttt                                                                                                            <  1:2492284/141‑1 (MQ=255)
                                    tgtACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCa                                                                                                          >  1:2222794/1‑141 (MQ=255)
                                      tACTAAGCAAAAAGGCAGCTCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCaaa                                                                                                        <  1:2465653/141‑1 (MQ=255)
                                      tACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCaaa                                                                                                        <  1:1325235/141‑1 (MQ=255)
                                           aGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGcc                                                                                                   <  1:3533965/141‑1 (MQ=255)
                                            cgaaaaaGGCAGCACGTAACTTTAACTATATTTACTAATCAAGAAACTTCTATCACTATCGCTTCAATTTCCTGTATGCGTTTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCg                                                                                                  <  2:601445/139‑1 (MQ=255)
                                              aaaaaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTGTATGAGCTTCTATTATTACTTTTACCAATTCCTCATTTCCGTa                                                                                                >  1:1736099/1‑141 (MQ=18)
                                               aaaaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTaa                                                                                               <  2:1998029/141‑1 (MQ=255)
                                                aaaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAAt                                                                                              <  1:873448/141‑1 (MQ=255)
                                                 aaGGCAGCATGTAACTTTAACTATAATTACTAATCAAAAACTTTTTATCACGAACGCTTCAACTTCCTGTATGTGTGTGATACAAGTTTTTATTTTATGAAATTATATTATGACTTCTACAAATTTCAAATTGCCGTAAtt                                                                                             <  2:2334403/141‑1 (MQ=255)
                                                 aaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAAtt                                                                                             >  2:4061569/1‑141 (MQ=255)
                                                 aaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAAtt                                                                                             >  2:1458438/1‑141 (MQ=255)
                                                 aaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAAtt                                                                                             >  1:2902778/1‑141 (MQ=255)
                                                  aGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTg                                                                                            >  2:2066583/1‑141 (MQ=255)
                                                    gcagcaCGTAACTTTAACTATATTTACTAATCAAAAATCTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTACTACTTCTACAAATTTCAAATTGCCGTAATTGaa                                                                                          >  2:1010238/1‑141 (MQ=255)
                                                    gcagcaCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGaa                                                                                          >  2:665633/1‑141 (MQ=255)
                                                     ccacaCGTAACTTTACCTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAAc                                                                                         <  1:4131433/138‑1 (MQ=255)
                                                       gcaCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTCCAATTTCCTGTATGCGTGTGATAGAATTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGt                                                                                       <  1:704256/141‑1 (MQ=255)
                                                        caCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTCCTTATTTCAAATTGCCGTAATTGAACGta                                                                                      <  1:3051262/141‑1 (MQ=255)
                                                           atAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTatat                                                                                   <  1:194883/140‑1 (MQ=255)
                                                              aCTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATttc                                                                                <  2:2238164/141‑1 (MQ=255)
                                                                     cTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCa                                                                         >  1:533968/1‑141 (MQ=255)
                                                                      tataTTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTTAACGTATATTTCTTCTTCaa                                                                        >  2:343151/1‑141 (MQ=255)
                                                                          tttACTAATCAAAAAACTTCTATCACGTACGCTTCAATTTCCTGTAGGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACtat                                                                    <  1:2175147/141‑1 (MQ=255)
                                                                           ttACTAATCGAAAAGCTTCTATCACGAACGCTTCAATTTTCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACtatt                                                                   <  2:1101263/141‑1 (MQ=255)
                                                                             aCTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTGTGAAATTATATTATTACTTCTACAAATTTCAAATTGCCATAATTGAACGTATATTTCTTCTTCAACtattat                                                                 >  2:588751/1‑141 (MQ=255)
                                                                              cTAATCAAAAAACTTCTATCACGCACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt                                                                <  1:131263/141‑1 (MQ=255)
                                                                              cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt                                                                >  2:4281602/1‑141 (MQ=255)
                                                                              cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt                                                                <  1:1680804/141‑1 (MQ=255)
                                                                              cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt                                                                >  2:2817723/1‑141 (MQ=255)
                                                                              cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTAGGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt                                                                >  2:1353495/1‑141 (MQ=255)
                                                                              attaaataaaaacttctattatatgcataaaggaaattgaagcgttcgtgatagaagtttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt                                                                <  2:204701‑M2/79‑1 (MQ=255)
                                                                              ataaaataaaaacttctatcaaacttatactggaaattgaagcgttcgtgatngaagtttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt                                                                <  2:2521195‑M2/79‑1 (MQ=255)
                                                                                aaTCAAAAGACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTc                                                              <  1:4296531/141‑1 (MQ=255)
                                                                                 aTCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTAAAATTGCCGTAATTTAACGTATATTTCTTCTTCAACTATTATTTCa                                                             >  1:3677409/1‑141 (MQ=255)
                                                                                     AAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTCATTGAACGTATATTTCTTCTTGAACTATTATTTAATCtt                                                         <  2:2385166‑M1/141‑1 (MQ=255)
                                                                                     AAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTtcatttt                                                         <  2:1270779‑M1/141‑4 (MQ=255)
                                                                                      AAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTGTATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACCTATATTTCTTCTTCAACTATTATTTCATCttt                                                        >  2:3900019‑M1/1‑141 (MQ=255)
                                                                                      AAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCttt                                                        >  1:3802707‑M1/1‑141 (MQ=255)
                                                                                       aaccTTCTATCACGAACTCTTCAATTTCCTGTATTCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTa                                                       <  1:2739745/138‑1 (MQ=255)
                                                                                       AAACTTCTATCACGAACGTTTCTATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTa                                                       >  2:2644891‑M1/1‑141 (MQ=255)
                                                                                       AAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTa                                                       >  2:3266665‑M1/1‑141 (MQ=255)
                                                                                       AAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTa                                                       >  1:666716‑M1/1‑141 (MQ=255)
                                                                                        AACTTCTATCACGAACGCTTTAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAg                                                      >  2:2768016‑M1/1‑141 (MQ=255)
                                                                                        AACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAg                                                      >  1:3895271‑M1/1‑141 (MQ=255)
                                                                                        AACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAg                                                      >  1:2106958‑M1/1‑141 (MQ=255)
                                                                                        AACTTCTACCACGAACGCTTCAATTTCCTGTATGCGAGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGTCGTAATTGAAAGTATCTTTCTTCTTCAACTTTTCTTTCATTTTTAg                                                      <  2:3230116‑M1/141‑1 (MQ=255)
                                                                                          CTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTTTTGTTTAgct                                                    <  1:2035192‑M1/141‑2 (MQ=255)
                                                                                            TCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATa                                                  <  1:3305607‑M1/141‑1 (MQ=255)
                                                                                             CTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTGTCATaa                                                 <  2:379948‑M1/141‑1 (MQ=255)
                                                                                             CTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATaa                                                 <  2:2929808‑M1/141‑1 (MQ=255)
                                                                                                TCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCt                                              <  2:2686223‑M1/141‑1 (MQ=255)
                                                                                                     aaCGCTTCAATTTCCTGTATTCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCTGTAATTTAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCtatata                                         <  2:2564460/141‑1 (MQ=255)
                                                                                                        gCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATaa                                      <  2:2322559/141‑1 (MQ=255)
                                                                                                          ttCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGACGTAATTGGACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATaaaa                                    <  2:3152527/141‑1 (MQ=255)
                                                                                                             aaTTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAAttt                                 <  2:1058487/141‑1 (MQ=255)
                                                                                                             aaTTTCCTGTATGCGTGTGATAGAAGTTTATATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAAttt                                 <  2:3682881/141‑1 (MQ=255)
                                                                                                               tttCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTa                               >  1:1872515/1‑141 (MQ=255)
                                                                                                                ttCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTAt                              <  1:4404504/141‑1 (MQ=255)
                                                                                                                 tCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGCACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTAtt                             >  1:3407908/1‑140 (MQ=255)
                                                                                                                 tCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATg                             >  1:4059882/1‑141 (MQ=255)
                                                                                                                   cTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCt                           >  2:3047821/1‑141 (MQ=255)
                                                                                                                    tGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCta                          <  1:1040415/141‑1 (MQ=255)
                                                                                                                           gtgtGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTa                   <  2:533968/141‑1 (MQ=255)
                                                                                                                            tgtgATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTaa                  <  1:2849590/141‑1 (MQ=255)
                                                                                                                               gatagaagtttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTAaata               <  1:3080070‑M2/128‑1 (MQ=255)
                                                                                                                                atagaagtttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTATCATAATCTATATATAAAATTTTATGCTATTATTTaactat              >  1:3942996‑M2/13‑140 (MQ=255)
                                                                                                                                 tagaagtttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTAaataat             >  2:3520264‑M2/12‑141 (MQ=255)
                                                                                                                                  agaagtttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTAAATAAtt            <  2:1864527‑M2/131‑1 (MQ=255)
                                                                                                                                   gtatgttttCTTTTTTGTCATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTAAATAATTc           <  2:4009705‑M2/132‑1 (MQ=255)
                                                                                                                                   gaagtttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTAAATAATTc           >  1:1238338‑M2/10‑141 (MQ=255)
                                                                                                                                     agtttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATCTAAAATTTTATTCTTTTATTTAATTAAttctt         >  2:861291‑M2/8‑139 (MQ=255)
                                                                                                                                      gtttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTAAATAATTCGCt        <  1:1817301‑M2/135‑1 (MQ=255)
                                                                                                                                       tttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCTGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTAAATAATTCGCta       <  2:3477452‑M2/136‑1 (MQ=255)
                                                                                                                                       tttttATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTAAATAATTCGCta       <  1:2662126‑M2/136‑1 (MQ=255)
                                                                                                                                       tgtgtATTGTATGAAATTATATGATTACTTCTACAAATTTCAAATTGTCGTAATTGAATGTATATTTCTTATTCAACTATTGTGTCATCTTTGGCATAATCTAGATATAAAATTTTATGCTATTATTTAAATAATTCGCta       <  2:1597047‑M2/136‑1 (MQ=255)
                                                                                                                                            attttatGAAATTATATTATTACTTCTACAAATTTCATATTGCTGTAATTGAACGTATATTTCTTATTCAACTATTATTTCATCTTTAGCATAATCTATATATATAATTTTATGCTATTTTTTAAATAATTCGCTATATCt  >  2:332455/1‑141 (MQ=255)
                                                                                                                                            attttatGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCCTTAGCAGAATCTATATATAAAATTTTATGCTATTATTTAAATAATTCGCTATAACt  >  1:4172062/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                            
ATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTTTAGCATAATCTATATATAAAATTTTATGCTATTATTTAAATAATTCGCTATAACT  >  USA300TCH1516_ALE/2679867‑2680147

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.