New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 2579070 (0.000)58 (0.970) 47/266 0.2 100% intergenic (+8/+16) crl/insB9 RNA polymerase holoenzyme assembly factor Crl/IS1 transposase B
?NC_000913 258684 = 0 (0.000)pseudogene (9/331 nt) crl RNA polymerase holoenzyme assembly factor Crl

GTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTG  >  NC_000913/258542‑258824
                                                                                                                                              |                                                                                                                                             
tgttaaaaatttgctaaattgtgccaatttggtaaaacagttgcaccacaacaggagatagcaatgacgtggccgaggggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaa                                                                                                                                               <  1:664121‑M2/1‑1 (MQ=255)
tgttaaaaattggcgaaattttgccaacaaggtatattgtgttcatctcaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaa                                                                                                                                               <  1:482139‑M2/1‑1 (MQ=255)
  ttaaaaatttgctaaattttgccaatttggtaaaacagttgcatcacaacaggtgttagcaatgacgttcacgagctgacacccgaagaccagattgatcaaaaaatttaccgcactaggcccgcataattgtgaatgtaaat                                                                                                                                             >  2:1128360‑M2/141‑141 (MQ=255)
  ttaaaaatttgctaaattttgccaatttggtaaaacaggggcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                                                                                                             >  1:221451‑M2/141‑143 (MQ=255)
    aaaaatttgctaaattttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGc                                                                                                                                           >  1:980432‑M2/139‑143 (MQ=255)
            tctaaatgttgcgaatgtgggaatacagttgcatctgaacaggagatagcaatgacggtaccgagtggtcactcgaagagcagattgatcaaaaaatttacctcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                                                                                                   <  2:984521‑M2/13‑1 (MQ=255)
              taaattttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATc                                                                                                                                 >  1:378158‑M2/129‑143 (MQ=255)
                   tttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTc                                                                                                                            <  2:210466‑M2/20‑1 (MQ=255)
                   tttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTc                                                                                                                            <  1:508139‑M2/20‑1 (MQ=255)
                    ttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtcAGTGCAAAGATAATCGATTCt                                                                                                                           >  2:487099‑M2/123‑143 (MQ=255)
                         aatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaacaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTc                                                                                                                      >  1:643189‑M2/118‑143 (MQ=255)
                                 aaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCt                                                                                                              >  1:678541‑M2/110‑143 (MQ=255)
                                  aaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTg                                                                                                             >  1:412240‑M2/109‑143 (MQ=255)
                                   aacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttatcgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTgg                                                                                                            <  1:925877‑M2/36‑1 (MQ=255)
                                   aacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGGTTCTTTTTCGATTGTCTgg                                                                                                            <  1:1123657‑M2/36‑1 (MQ=255)
                                        ttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTa                                                                                                       <  1:1122072‑M2/41‑1 (MQ=255)
                                         tgcatcacaacaggagatagcagtgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTAt                                                                                                      <  2:689768‑M2/42‑1 (MQ=255)
                                           catcacaatatgaattagcaataatattactgagtagacaacagaagagcagacagaacaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGc                                                                                                    <  1:16836‑M2/44‑1 (MQ=255)
                                                 aacaggagagagcagtgacgtgagcgagtggacacccgaagagcagattgatcaaaaaatttaccgcgctgtgcccgtacattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAAc                                                                                              <  1:664322‑M2/50‑1 (MQ=255)
                                                    aggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTg                                                                                           >  1:402593‑M2/91‑143 (MQ=255)
                                                    aggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccggatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGAGTGTCTGGCTGTATGCGTCAACGTg                                                                                           >  1:53695‑M2/91‑143 (MQ=255)
                                                      tagagagcaatgacgttaccgagtggacaccctaagagcagagttatcaaaaaatttaccgcactaggctcgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGaa                                                                                         <  2:107891‑M2/55‑1 (MQ=255)
                                                       agatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGaaa                                                                                        <  1:797755‑M2/56‑1 (MQ=255)
                                                              aatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGACTGTCTGGCTTTATGCGTCAACGTGAAACCGGCAc                                                                                 >  2:967450‑M2/81‑143 (MQ=255)
                                                              aatgacgttaccgagtggacacccgaagagcagaatgatcaaaaaatttaccgcactaggcccgaatggccgtgaaggcaAGTGCAAAGATAATCGATTCTTTTTCGCTTGTCTGGCTGTACGCGCCACCGTGAaaccgcccc                                                                                 >  2:462157‑M2/81‑139 (MQ=255)
                                                                tgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCg                                                                               <  1:208160‑M2/65‑1 (MQ=255)
                                                                 gacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCgg                                                                              >  1:552620‑M2/78‑143 (MQ=255)
                                                                 aactgtaccgagtcgacacgcgaatggcagagtggtcaaaaaatttaccgcactaggcccgtatagtcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCgg                                                                              <  1:1020546‑M2/66‑1 (MQ=255)
                                                                   cgtcaccgaggggacacccgaagagcagatggatcacaaaatttaccgcactaggcccgtatattcgggaaggtaCGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTTTGCTTCAACGTGAAACCGGCACCGGaa                                                                            <  2:969131‑M2/68‑1 (MQ=255)
                                                                    gttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGCTTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAg                                                                           >  1:687293‑M2/75‑143 (MQ=255)
                                                                     ttaccgagtggatacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGt                                                                          <  1:277019‑M2/70‑1 (MQ=255)
                                                                       accgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAAACGGCACAGGAAGTGc                                                                        >  2:444387‑M2/72‑143 (MQ=255)
                                                                       acagagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGc                                                                        <  1:1085694‑M2/72‑1 (MQ=255)
                                                                         cgagtggacacccgaagagcagattgatcaaaaaatttacggcactaggcccgtatattcgtgaaggtaAGTGCAAACATAATCGATTCTTTTTGGATTGTATGGCGGTAGGCGTCAAGGTGAAACAGACGACGGACGTGCGt                                                                      >  2:345298‑M2/70‑143 (MQ=255)
                                                                         cgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTGTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGt                                                                      <  2:368657‑M2/74‑1 (MQ=255)
                                                                           agtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATGGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGa                                                                    >  1:967415‑M2/68‑143 (MQ=255)
                                                                              ggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAAtt                                                                >  1:642819‑M2/65‑143 (MQ=255)
                                                                                 gtggcgtagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTg                                                             <  1:418935‑M2/82‑1 (MQ=255)
                                                                                 cacccgacgagcagatgggtcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTg                                                             <  1:423511‑M2/82‑1 (MQ=255)
                                                                                   cccgaagagcagattgagcaaaaaatgtaccgcactaggcccgtatattcgtgaaggtaAGTGCAAACAAAATCAATAAATTTTTGCTGGTGTGGGTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTggg                                                           <  1:487099‑M2/84‑1 (MQ=255)
                                                                                    ccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATACTCGATGCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTgggg                                                          <  1:1097676‑M2/85‑1 (MQ=255)
                                                                                    ccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggaaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGACAACATGAAAACGACACCGGAAGTGCGTgaaatcaaggg                                                          >  2:90236‑M2/59‑138 (MQ=255)
                                                                                                   atcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGACACCGGCCACGCAGGTGCGTGAATTCTGGGGCTGGTGGATGGAGCt                                           >  1:1092072‑M2/44‑143 (MQ=255)
                                                                                                     agttaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTgg                                         <  1:205861‑M2/102‑1 (MQ=255)
                                                                                                      aaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGa                                        >  1:682241‑M2/41‑143 (MQ=255)
                                                                                                      aaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCGGGa                                        >  1:125705‑M2/41‑143 (MQ=255)
                                                                                                      aaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCAACGGAAGTGCGTGAATTCTGgggctgggggagggcgacaga                                        >  2:769742‑M2/41‑136 (MQ=255)
                                                                                                       aaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCGGGTGGATGGCGCGGGaa                                       >  2:909406‑M2/40‑143 (MQ=255)
                                                                                                            tttaccgccctaggcctgtgtattcgtgagggtgAGGGCAAAGATAATGGAGTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCTGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCa                                  <  1:841636‑M2/109‑1 (MQ=255)
                                                                                                            tgcaccgcactagggccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCa                                  <  1:935655‑M2/109‑1 (MQ=255)
                                                                                                             ttgccgcactatgctcgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAg                                 <  2:797655‑M2/110‑1 (MQ=255)
                                                                                                              taccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAgg                                <  1:861412‑M2/111‑1 (MQ=255)
                                                                                                                       aggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGGTTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAACCCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGtt                       <  2:208838‑M2/120‑1 (MQ=255)
                                                                                                                           ccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGTTGGTGCTGGTAGCGCAGCAATCCCGTTTTAc                   >  1:530703‑M2/20‑143 (MQ=255)
                                                                                                                                tattcgttaaggtaAGTGCCAGGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCTGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACa              <  2:980432‑M2/129‑1 (MQ=255)
                                                                                                                                 attcgtGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGCTTGTCTGGCTGTATGCGTCAAGGTGAAACCGGCACACGCAGGCCGGGCAGTCCGGGGCCGGCGGACGGAGCGGGGAGCGCAGGGATGCCGGTATACCGACAg             >  2:564826/6‑143 (MQ=255)
                                                                                                                                  ttggtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGt            <  2:378158‑M2/131‑1 (MQ=255)
                                                                                                                                   tcgtgagggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGtt           <  1:462157‑M2/132‑1 (MQ=255)
                                                                                                                                   gcgtgaaggtaAGTGCAAAGATGATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCATGAATCCCGTTTTACCTACAGtt           <  2:414992‑M2/132‑1 (MQ=255)
                                                                                                                                     gtGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGAAAACACTGTTCGTTAATAACCGTGGGTACTGAATGAGATGGAAGCGCAGGAACCCCGTTCTACCTACAGttcc         >  2:243438/2‑141 (MQ=255)
                                                                                                                                          ggtaAGTTCAAAGATTGTCGTGTCTTGTGCGCTTGTCCGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGGGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGtt    <  1:670219‑M2/139‑1 (MQ=255)
                                                                                                                                           gtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTCCCTACAGTTACCCGttt   >  1:36745‑M2/4‑143 (MQ=255)
                                                                                                                                            taAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTg  >  2:637886‑M2/3‑143 (MQ=255)
                                                                                                                                              |                                                                                                                                             
GTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACCTACAGTTACCAGTTTG  >  NC_000913/258542‑258824

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.