New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 2561201 =398 (1.090)4 (0.010) 5/232 NT 1.2% intergenic (+30/+33) USA300HOU_RS13195/cpdA hypothetical protein/3',5'‑cyclic adenosine monophosphate phosphodiesterase CpdA
?USA300TCH1516_ALE 2561237 = 330 (1.020)coding (804/807 nt) cpdA 3',5'‑cyclic adenosine monophosphate phosphodiesterase CpdA
Rejected: Frequency below/above cutoff threshold.

Only 100 of 458 total aligned reads displayed.

CCAGGAAGAAAGTGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAACATGGCCCATAAT  >  USA300TCH1516_ALE/2561097‑2561377
                                                                                                                                             |                                                                                                                                             
ccAGGAGCAAAGTGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTaa                                                                                                                                               <  2:1776080/141‑1 (MQ=255)
ccAGGAAGAAAGTGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACACGGTCAGGTCTGCGCATTTTaa                                                                                                                                               >  2:1863271/1‑141 (MQ=255)
    gaagaaAGTGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAAttt                                                                                                                                           >  1:2969233/1‑141 (MQ=255)
    gaagaaAGTGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAAttt                                                                                                                                           <  1:3935203/141‑1 (MQ=255)
    gaagaaAGTGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAAttt                                                                                                                                           <  1:1769100/141‑1 (MQ=255)
       gaaAGTGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCta                                                                                                                                        >  2:3749762/1‑141 (MQ=255)
         aggTGAATTTATGTGCAACAACATTTATATAGAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACATATTTCTCGCGTGTGTAAAACATAAATTGCGCAAACTTGGTCAGGTTTTCGTATTTTAAATTTCtatt                                                                                                                                      <  2:342664/139‑1 (MQ=255)
           gTGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCtattat                                                                                                                                    <  1:434456/141‑1 (MQ=255)
           gTGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGAGTCAGGTTTGCGCATTTTAAATTTCtattat                                                                                                                                    >  2:2417535/1‑141 (MQ=255)
            tGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTattatt                                                                                                                                   <  2:3550102/141‑1 (MQ=255)
                 ttATGTGCAAACACAATCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTAt                                                                                                                              <  2:3097366/141‑1 (MQ=255)
                         aaacacaTTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCat                                                                                                                      <  2:4064500/138‑1 (MQ=255)
                         aaCCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCat                                                                                                                      <  1:1384682/141‑1 (MQ=255)
                         aaCCACACTCATATACAATTGAAAATCAGCGACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACGTAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCat                                                                                                                      <  2:3351458/141‑1 (MQ=255)
                           ccACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCattt                                                                                                                    <  1:4189389/141‑1 (MQ=255)
                           cagaaTTCATATGAAAGTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCattt                                                                                                                    <  2:394224/137‑1 (MQ=255)
                               aTTCATATACAATCGAAAATCAGCAACAAAATAAACAAA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCatttattt                                                                                                                <  2:1074531/141‑1 (MQ=255)
                                  cATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCt                                                                                                             <  1:3576999/141‑1 (MQ=255)
                                    tataCAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTgg                                                                                                           <  1:2398616/141‑1 (MQ=255)
                                     ataCAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGt                                                                                                          <  2:3457616/141‑1 (MQ=255)
                                      taCAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATAGTCTTATTTATTTCGTGGTa                                                                                                         >  1:3859382/1‑141 (MQ=255)
                                             gAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATAtct                                                                                                 <  2:1040593/141‑1 (MQ=255)
                                              aaaaTCAGCAACAAAATAAACACA‑CGGGAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATAtctt                                                                                                >  1:2119749/1‑141 (MQ=255)
                                              aaaaGCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATAtctt                                                                                                <  1:3988601/141‑1 (MQ=255)
                                               aaaTCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCCAACTGAGACAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATAtcttc                                                                                               >  2:2675886/1‑141 (MQ=255)
                                                 aTCAGAAACAAAAAAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAATCATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTg                                                                                             <  2:1634322/141‑1 (MQ=255)
                                                  tCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑GATATCTTCTGa                                                                                            >  1:310641/1‑141 (MQ=255)
                                                  tCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGa                                                                                            >  1:1592965/1‑141 (MQ=255)
                                                  tCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATACGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGa                                                                                            >  1:2828526/1‑141 (MQ=255)
                                                    aGCAACAAAATAAACACA‑CGTAATTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAAc                                                                                          <  2:2637588/141‑1 (MQ=255)
                                                    aGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAAc                                                                                          <  1:1662825/141‑1 (MQ=255)
                                                    aGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAAc                                                                                          >  1:1280796/1‑141 (MQ=255)
                                                    aGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTCCATGGTA‑AATATCTTCTGaaa                                                                                          >  2:2135984/1‑140 (MQ=255)
                                                      aaacaaAATAAA‑ACATCGTAATTAAGCACATTTTTAGTGTTTGTAAAACATAAAATGCTCAAGCTGTGTTAGGTTTGCTCATTTTAAATTTCTATTATTTGTATCTTCTCATTTATTTCCTTGTA‑AATATCTTCTGAACGc                                                                                        <  2:3971148/140‑1 (MQ=255)
                                                        acaaAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAACACATAAAATGCGCAAACTGGGTCCTGTTTGCGCATTTTAAATTTCTATAATTTTTATCATCTCATTTATTTCCTGCTA‑AATCTCTTCTGAACGCCa                                                                                      >  2:476310/1‑141 (MQ=255)
                                                         taaaaTAAACAAA‑CGTAAGTAAACACATTACTGGCGTGTGTAAAACATAACATGAAGTCGAGGGGGCTGGATTTTGCATCTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCAt                                                                                     <  2:2003920/140‑1 (MQ=255)
                                                             aTAAACCCA‑CGTAAGCAAACACATTACCCGCTTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTCGTA‑AATATCTTCTGAACGCCATTGTc                                                                                 <  1:365960/141‑1 (MQ=255)
                                                              tAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCt                                                                                <  1:1103825/141‑1 (MQ=255)
                                                              tAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCt                                                                                <  2:793493/141‑1 (MQ=255)
                                                              tAAACACA‑CGTAAGCAAACACATTACTGGCGTGTGTAAAACATAACATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCt                                                                                <  2:1412067/141‑1 (MQ=255)
                                                              tAAACACA‑AGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGGACGCCATTGTCt                                                                                <  2:2335886/141‑1 (MQ=255)
                                                                aaCACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTg                                                                              >  1:3804575/1‑141 (MQ=255)
                                                                aaCACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTg                                                                              >  1:254811/1‑141 (MQ=255)
                                                                       cGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGc                                                                        <  1:2750452/141‑1 (MQ=255)
                                                                          aagtaaACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTa                                                                     <  1:2026731/141‑1 (MQ=255)
                                                                          aagtaaACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTa                                                                     >  2:3242928/1‑141 (MQ=255)
                                                                          aagtaaACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATGTATTTCCTGGCA‑AATATCTTCTGAACGCCCTTGTCTTGCATAGCCTa                                                                     >  2:2453871/1‑141 (MQ=255)
                                                                           agtaaACACATTACTCGCGTGTGTAGAACAGAAAATTCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAg                                                                    >  1:861954/1‑141 (MQ=255)
                                                                           agtaaACACATTACTCGCGTGTGTAAAACATAACATGCGCAAACTGTGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAg                                                                    <  1:3007262/141‑1 (MQ=255)
                                                                             taaACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTT‑AATATCTTCTGAACGCCATTGTTTTGTATTGCCTAgca                                                                  >  2:1439439/1‑139 (MQ=255)
                                                                                  acaATACTCCGGTGTGCAAAACAGAAAATGCGGAAAATGGGTCAGGTTTGTTAATTATAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGa                                                             <  2:1351229/141‑1 (MQ=255)
                                                                                   caTTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGAc                                                            >  1:2438366/1‑141 (MQ=255)
                                                                                    aTTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACa                                                           <  1:458347/141‑1 (MQ=255)
                                                                                     ttACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACag                                                          >  1:3300616/1‑141 (MQ=255)
                                                                                      tACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACaga                                                         >  1:1831540/1‑141 (MQ=255)
                                                                                        cTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAgaga                                                       >  2:3670002/1‑141 (MQ=255)
                                                                                        cTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAgaga                                                       >  1:3500051/1‑141 (MQ=255)
                                                                                         tCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATCGCCCCGACACGTACagagct                                                      >  1:1433300/1‑139 (MQ=255)
                                                                                          cgcgTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAgagaga                                                     >  1:280620/1‑139 (MQ=255)
                                                                                           gcgTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTTTATCGTGTTTTCTTTTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATaa                                                    >  1:3230392/1‑141 (MQ=255)
                                                                                           gcgTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATaa                                                    >  1:3375694/1‑141 (MQ=255)
                                                                                               gtgtAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATc                                                <  1:2662705/141‑1 (MQ=255)
                                                                                               gtgtAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCACGCCAAATTGCGATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATc                                                <  1:1882787/141‑1 (MQ=255)
                                                                                                tgtAAAACATAAAATGCGCAAACTGGGTTAGGTTTGCGCATTTTAAATTTATCTACACTATGGCTTCCCCTTTATGTATTGTCA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCt                                               <  2:4290267/141‑1 (MQ=255)
                                                                                                tgtAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGGCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCt                                               >  1:2283258/1‑141 (MQ=255)
                                                                                                tgtAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCt                                               <  2:203739/141‑1 (MQ=255)
                                                                                                tgtAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCt                                               <  1:1996490/141‑1 (MQ=255)
                                                                                                tgtAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCt                                               <  2:2529104/141‑1 (MQ=255)
                                                                                                tgtAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCt                                               <  2:4241577/141‑1 (MQ=255)
                                                                                                tgtAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCt                                               <  2:1211992/141‑1 (MQ=255)
                                                                                                tgtAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCt                                               <  2:1241010/141‑1 (MQ=255)
                                                                                                  tAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGc                                             >  1:3037257/1‑141 (MQ=255)
                                                                                                       cATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCcatca                                        <  1:1484769/141‑1 (MQ=255)
                                                                                                        aTAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCcatcat                                       >  1:922404/1‑141 (MQ=255)
                                                                                                         TAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATCACCTGGCAGAATCT‑TTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCatcatc                                      <  1:4377263‑M1/141‑1 (MQ=255)
                                                                                                          AAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCt                                     >  1:706309‑M1/1‑141 (MQ=255)
                                                                                                             ATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATc                                  <  1:2223023‑M1/141‑1 (MQ=255)
                                                                                                             ATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATc                                  <  1:538682‑M1/141‑1 (MQ=255)
                                                                                                                  CAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACt                             <  1:3157323‑M1/141‑1 (MQ=255)
                                                                                                                   aagcTGGGTCATGTTTGTGCATTTTAAATTTCTTTTATTTGTATCGTCTCATTTATTTACTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGCTAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACtt                            <  2:74618/138‑1 (MQ=255)
                                                                                                                   AAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCTTTTATTTCCTGTCA‑AATATCTTCTGAACGCCATTTTCTTGGACAGCCTAGACACGGACAGAGCTAACATCTGCCATCATctatcactctc                            <  2:1519142‑M1/141‑5 (MQ=255)
                                                                                                                    AACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACttt                           <  1:4290985‑M1/141‑1 (MQ=255)
                                                                                                                    AACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACttt                           <  2:4371371‑M1/141‑1 (MQ=255)
                                                                                                                    AACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACttt                           >  1:3722619‑M1/1‑141 (MQ=255)
                                                                                                                       tGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACCGACAGAGATAACATCTGCCATCATCTATCACACTTTTAc                        >  2:1569495/1‑141 (MQ=255)
                                                                                                                        gggTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACg                       <  2:566287/141‑1 (MQ=255)
                                                                                                                         ggTCAGGTTTGCGCATTTTAAATTTCTATTATGTGTATCGTCTCATTTAGTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGa                      <  1:247598/141‑1 (MQ=255)
                                                                                                                             agttttgcgcattttaAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAAt                  <  1:2171569‑M2/125‑1 (MQ=255)
                                                                                                                             aGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAAt                  <  2:37196/141‑1 (MQ=255)
                                                                                                                              ggTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATg                 <  1:3752327/141‑1 (MQ=255)
                                                                                                                               gtacgcgcattttaAATTTCTAGTAGTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCGTTGTGTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGa                <  2:4108785‑M2/127‑1 (MQ=255)
                                                                                                                                 ttgcgcattttaAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAAc              <  2:4168918‑M2/129‑1 (MQ=255)
                                                                                                                                 ttgcgcattttaAATTTCTATTATTCGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAAc              <  1:762271‑M2/129‑1 (MQ=255)
                                                                                                                                   gcgcattttaAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAACAt            >  1:4034333‑M2/11‑141 (MQ=255)
                                                                                                                                     gcattttaAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTTTGGAGCAAATAGGCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAACATgg          <  1:1024981‑M2/133‑1 (MQ=255)
                                                                                                                                      tattttaAATTTATATTATTTGTATTGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAACATGGc         <  2:304033‑M2/134‑1 (MQ=255)
                                                                                                                                       attttaAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAACATGGcc        <  1:4086535‑M2/135‑1 (MQ=255)
                                                                                                                                       attttaAATTTCTATTATTTGCATCGGCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCATAGACACGTACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAACTTGGcc        <  2:2547775‑M2/135‑1 (MQ=255)
                                                                                                                                             aaTTTGTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAACATGGCCCataat  <  2:2938978/141‑1 (MQ=255)
                                                                                                                                             aaTTTCTATTATTTGTATCGGCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAACATGGCCCataat  <  2:2269664/141‑1 (MQ=255)
                                                                                                                                             |                                                                                                                                             
CCAGGAAGAAAGTGCATTTATGTGCAACCACATTCATATACAATTGAAAATCAGCAACAAAATAAACACA‑CGTAAGTAAACACATTACTCGCGTGTGTAAAACATAAAATGCGCAAACTGGGTCAGGTTTGCGCATTTTAAATTTCTATTATTTGTATCGTCTCATTTATTTCCTGGTA‑AATATCTTCTGAACGCCATTGTCTTGGATAGCCTAGACACGGACAGAGATAACATCTGCCATCATCTATCACACTTTTACGAAAATGAACATGGCCCATAAT  >  USA300TCH1516_ALE/2561097‑2561377

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.