New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 52495 =282 (0.770)342 (0.950)
+T		 9/258 NT 53.3% intergenic (+105/‑568) USA300HOU_RS00215/USA300HOU_RS00220 hypothetical protein/hypothetical protein
?USA300TCH1516_ALE = 52988 321 (0.880)intergenic (+598/‑75) USA300HOU_RS00215/USA300HOU_RS00220 hypothetical protein/hypothetical protein

Only 100 of 712 total aligned reads displayed.

GTTTTTTAAAGCATTAGATGCCTTAAAGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAAT  >  USA300TCH1516_ALE/52357‑52634
                                                                                                                                          |                                                                                                                                            
gttTTTTAAAGCATTAGATGCCTTAAAGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGt                                                                                                                                            <  1:1433161/141‑1 (MQ=255)
gttTTGTAAAGCATTAGATGCCTTAAAGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGt                                                                                                                                            <  1:3884788/141‑1 (MQ=255)
  tttttAAAGCATTAGATGTCTTAAAGTAATAGTTTTTCACTGAATATATTTATAGATAGTATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGa                                                                                                                                          <  2:193995/141‑1 (MQ=255)
   ttttAAAGCATTAGATGCATTAAAGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGaa                                                                                                                                         <  2:880282/141‑1 (MQ=255)
         aGCATTAGATGCCTTAAAGAAATAGTTTTTTTTTTTTTTTTTTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACTTATAATGTTGTGTAAATCGCGTTAAATAATc                                                                                                                                   >  2:1567465/1‑141 (MQ=255)
           taatcgcgcgaaaatcacgtgaaataatcagaggaatcgtttgaaatcatcgtagtaatcgcgcgaaaatcgcgtgaaataatcagaggaaacgttagaaaacatcgtagtgatcgcgcgaaaatcaCGTGAAAAAATCag                                                                                                                                 <  2:3692098‑M1/14‑1 (MQ=255)
                 aTGCCTGAAAGAAATAGTTTTTCACTGAAAATATGTATAGATATAATTAAAATGAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAAt                                                                                                                           <  2:3269206/141‑1 (MQ=255)
                      ttAAAGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGttt                                                                                                                      >  1:1998288/1‑141 (MQ=255)
                      ttAAAGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGttt                                                                                                                      <  1:2979375/141‑1 (MQ=255)
                      ttAAAGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTGAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGttt                                                                                                                      <  2:1999101/141‑1 (MQ=255)
                      ttAAAGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGCATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGttt                                                                                                                      <  2:3576665/141‑1 (MQ=255)
                         aaGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGaa                                                                                                                   >  1:1546301/1‑141 (MQ=255)
                         aaGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGaa                                                                                                                   >  2:298311/1‑141 (MQ=255)
                         aaGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGaa                                                                                                                   <  1:3523259/141‑1 (MQ=255)
                         aaGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGaa                                                                                                                   >  1:2388466/1‑141 (MQ=255)
                         aaGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTATTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGaa                                                                                                                   >  2:509671/1‑141 (MQ=255)
                                 gTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCgt                                                                                                           <  1:1762542/141‑1 (MQ=255)
                                    tttCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCgtagt                                                                                                        >  1:1072691/1‑141 (MQ=255)
                                                   ttATAGATATAATTAAAATTAATTAATATTAACCCAGGATAATGTAGTCTTAATCGTTATGAAATAAGAAAAATATTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGAAGTAATCGCG‑CGAAAATc                                                                                        >  1:3132331/1‑141 (MQ=37)
                                                     ataGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCAc                                                                                      <  2:1181806/141‑1 (MQ=255)
                                                       aGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGt                                                                                    <  1:2291416/141‑1 (MQ=255)
                                                        gATATAATTAAAATTAATTAATATTAAGCCAGGATATTGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTg                                                                                   <  1:3005485/141‑1 (MQ=255)
                                                           ataATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGaaa                                                                                <  1:3630312/141‑1 (MQ=255)
                                                               ttaaaattaaTTAATAGTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAaataat                                                                            >  1:2821772/1‑141 (MQ=255)
                                                                taattttaatt‑atATTAAGCCCGGATCATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCa                                                                          >  2:2297251/6‑141 (MQ=25)
                                                                    attaattaATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCagag                                                                       >  1:2930782/1‑141 (MQ=255)
                                                                     ttaattaaTATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAgg                                                                      <  1:3789326/141‑1 (MQ=255)
                                                                     ttaattaaTATTAAGACAAGATAATGTAGGCTTAAGCGTTGTGAAATACGGAAAATGTTGTGGAAATCGCGTGAAATAAGCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAgg                                                                      <  2:341219/141‑1 (MQ=21)
                                                                       cctgcacaatcccgtaagatagtgaggggaatcgcgtgaaatcatactaataatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGaa                                                                    >  2:3785765‑M1/68‑141 (MQ=255)
                                                                         ttaatATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATc                                                                  >  1:3351314/1‑141 (MQ=255)
                                                                          taatATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAACTGTTGCGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCg                                                                 <  1:1019039/141‑1 (MQ=255)
                                                                          taatATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCg                                                                 >  1:2435022/1‑141 (MQ=255)
                                                                             aaatcgcgttaaataatcagaggaatcgtttgagatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGttt                                                              >  1:2547967‑M1/62‑141 (MQ=255)
                                                                             aaatcgcgtgaaataatcagatgaatcgtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGttt                                                              >  1:742707‑M1/62‑141 (MQ=255)
                                                                              atTAAGCGAGGATAATGTAGTCTTAATCGTACTGAAATACGAAAAATGGTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCT‑CGAAAATCACTTGAAATAATCAGAGGAATCGTTTg                                                             <  1:48154/141‑1 (MQ=21)
                                                                                 aaGCCAGGATAATGTAGGCTTAATCGTACTGAAATAAGAAAAATGATGTGGAAATCGCGTGAAATAATCAGATGAATCGTTTGAAATCATCGTAGTAATCGTG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGaaa                                                          <  2:631475/141‑1 (MQ=18)
                                                                                         ataatcagaggaatcgtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCgta                                                  <  2:2537540‑M1/92‑1 (MQ=255)
                                                                                         ataatcagaggaatcgtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCgta                                                  <  2:3352122‑M1/92‑1 (MQ=255)
                                                                                          taatcagaggaatcgttttaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCgtag                                                 >  1:4253679‑M1/49‑141 (MQ=255)
                                                                                          taatcagaggaatcgtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCgtag                                                 >  1:3067530‑M1/49‑141 (MQ=255)
                                                                                          tAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCgtag                                                 >  2:2367891/1‑141 (MQ=255)
                                                                                             tcagaggaatcgtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGaaa                                                                                                                  <  1:3921168‑M1/29‑1 (MQ=255)
                                                                                             tcagaggaatcgtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATcgcg‑cg                                                                                              <  1:906544‑M1/48‑1 (MQ=255)
                                                                                              cagaggaatcgtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAACTCATCGTAGTAAt                                             <  1:3728568‑M1/97‑1 (MQ=255)
                                                                                                     atcgtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGaa                                                                                                                   <  2:2094186‑M1/28‑1 (MQ=255)
                                                                                                     atcgtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGaa                                                                                                                   >  1:2094186‑M1/38‑65 (MQ=255)
                                                                                                      aaTCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGaa                                     >  1:854283/1‑141 (MQ=255)
                                                                                                       cgtttgaagtcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGaaa                                    >  1:99628‑M1/36‑141 (MQ=255)
                                                                                                       cgtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGaaa                                                                                                                                        <  2:429293‑M1/7‑1 (MQ=255)
                                                                                                       aTCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGaaa                                    >  1:1823063/1‑141 (MQ=255)
                                                                                                        tCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGaaaa                                   >  1:569873/1‑141 (MQ=255)
                                                                                                        gtttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGttt                                                                                                                      <  1:3661691‑M1/25‑1 (MQ=255)
                                                                                                         tttgaaatcatcgtagtaatcgcgcgaaaatcaCg                                                                                                                                             <  1:3829170‑M1/2‑1 (MQ=255)
                                                                                                         tttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGCAATAATCAGAGTAATCGTTTGAAATCATCGTAGTAATCGCA‑CCACAATCCCGTGACATAATCAGCGGAATCGTTTGAACTCCTCGTAGTAATCGCtcgaacat                                  <  1:160781‑M1/108‑4 (MQ=255)
                                                                                                         tttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACg                                                                                     <  1:232310‑M1/57‑1 (MQ=255)
                                                                                                         tttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGaaa                                                          <  2:3989185‑M1/84‑1 (MQ=255)
                                                                                                         cGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAAt                                  >  1:1168762/1‑141 (MQ=255)
                                                                                                          ttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGaaa                                                                                                                  <  2:2199885‑M1/29‑1 (MQ=255)
                                                                                                          ttgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAatcatc                                                     >  2:4081671‑M1/33‑121 (MQ=255)
                                                                                                           tgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAaataa                                                                                                                                     <  2:1633409‑M1/10‑1 (MQ=255)
                                                                                                           tgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAAt                                                                                         >  2:826471‑M1/32‑84 (MQ=255)
                                                                                                           tgaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAatca                                                       <  2:3873865‑M1/87‑1 (MQ=255)
                                                                                                            gaaatcatcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGaa                                                                                                                   <  1:4157557‑M1/28‑1 (MQ=255)
                                                                                                             cTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACg                              >  1:1520870/1‑141 (MQ=255)
                                                                                                                aaaTACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGACCGTAAGC‑CAACAAAGAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGa                           >  1:3227703/1‑141 (MQ=17)
                                                                                                                aaaTACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGa                           >  1:641319/1‑141 (MQ=255)
                                                                                                                 aattatagaaatggagcaaaaataaCGTGAAATAATCAAAGGAAACGTTTGAAATCATCGTAGTAATCGTG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGaa                          >  2:172459‑M1/26‑141 (MQ=255)
                                                                                                                  atcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGTAATCGTTTGaa                                                                                                                   <  2:1687979‑M1/28‑1 (MQ=255)
                                                                                                                  atcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATcgcg                                                                                                 >  1:2181051‑M1/25‑70 (MQ=255)
                                                                                                                  atcgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGa                                                                                             >  2:2797086‑M1/25‑73 (MQ=255)
                                                                                                                    cgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTg                                                             <  1:3387269‑M1/81‑1 (MQ=255)
                                                                                                                    cgtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTg                                                             <  2:1039480‑M1/81‑1 (MQ=255)
                                                                                                                     gtagtaatcgcgcgaaaatcaCGTGAAATAATCagag                                                                                                                               <  2:3078910‑M1/16‑1 (MQ=255)
                                                                                                                     gtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGaa                                                                                                                   >  1:1340956‑M1/22‑49 (MQ=255)
                                                                                                                     gtagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATcgc                                                                                                  <  1:2753332‑M1/45‑1 (MQ=255)
                                                                                                                      tagtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGaaa                                                                                           <  1:4398971‑M1/51‑1 (MQ=255)
                                                                                                                      tagtaatcgcgcgaaaaacaCGTAAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGAaataat                     >  1:1930014‑M1/21‑141 (MQ=255)
                                                                                                                       agtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATcgcg‑cg                                                                                              <  1:4049691‑M1/48‑1 (MQ=255)
                                                                                                                       agtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATcgc                                          >  2:1875600‑M1/20‑119 (MQ=255)
                                                                                                                       agtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATcgc                                          <  1:1875600‑M1/100‑1 (MQ=255)
                                                                                                                       aaaaaTGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAGACAGGCGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCAGGAGAaaaaata                    >  2:3446933/1‑140 (MQ=14)
                                                                                                                       aaaaaTGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGAAATAATc                    >  1:939600/1‑141 (MQ=255)
                                                                                                                        gtaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGaa                                                                                 <  1:397829‑M1/61‑1 (MQ=255)
                                                                                                                         aaatcgcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGAAATAATCag                  >  1:4304054‑M1/18‑141 (MQ=255)
                                                                                                                         aaaTGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAACATCACGTGAAATAATCag                  >  1:1646088/1‑141 (MQ=255)
                                                                                                                           atcgcactaaaataaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGAAATAATCagag                >  1:4334823‑M1/16‑141 (MQ=255)
                                                                                                                              gcgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCgtag                                                                                                         <  2:2443117‑M1/38‑1 (MQ=255)
                                                                                                                               tgtgGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTGGGAATCATCGTAGTAACCGCGCGCAAATCACGTGAAATCATCAGAGGatg            >  1:2470078/1‑139 (MQ=11)
                                                                                                                               cgcgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGAAATAATCAGAGGAAt            <  1:2870342‑M1/130‑1 (MQ=255)
                                                                                                                                 cgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCgtag                                                                                                         <  2:4375049‑M1/38‑1 (MQ=255)
                                                                                                                                 cgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGaaa                                                          <  1:2643483‑M1/84‑1 (MQ=255)
                                                                                                                                 cgaaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGaa                                     <  1:1212619‑M1/105‑1 (MQ=255)
                                                                                                                                  ggaaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGAAATAATCAGAGGAATCGt         >  1:789217‑M1/9‑141 (MQ=255)
                                                                                                                                    aaatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATAAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGAAATAATAATAGCTATCGttt       <  2:741467‑M1/135‑1 (MQ=255)
                                                                                                                                     aatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGt                                                                >  2:1395032‑M1/6‑83 (MQ=255)
                                                                                                                                     aatcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGt                                                                <  1:1688150‑M1/78‑1 (MQ=255)
                                                                                                                                      atcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGAAATAATCAGAGGAATCGTTTGa     >  1:3446370‑M1/5‑141 (MQ=255)
                                                                                                                                       tcaCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGa                                                                                             >  2:2717954‑M1/4‑52 (MQ=255)
                                                                                                                                        caCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGa                                                                     <  1:1365875‑M1/73‑1 (MQ=255)
                                                                                                                                         aCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATc                                                                                        <  1:3298000‑M1/54‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                            
GTTTTTTAAAGCATTAGATGCCTTAAAGAAATAGTTTTTCACTGAAAATATTTATAGATATAATTAAAATTAATTAATATTAAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCG‑CGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAATCATCGTAGTAATCGCGCGAAAATCACGTGAAATAATCAGAGGAATCGTTTGAAAT  >  USA300TCH1516_ALE/52357‑52634

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.