New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 257908 =NA (NA)29 (1.370) 25/284 0.0 100% intergenic (+9/‑768) crl/crl pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers
?NC_000913 = 1293039 0 (0.000)intergenic (‑117/‑488) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase

AGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGCCAATAAATATCTTTTCATAAAATTAGCCAGAAAAGACGCGGCATATAGCCCTATTTACACCGATGATTTCGCAGCACGTGAGGTTAAAACTTCCTGATTCATGTCACATTTTATGGGGAGATTATCGTAGGCTGACGACCT  >  NC_000913/1292900‑1293181
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aGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTCCCGggt                                                                                                                                             <  2:339994‑M2/143‑4 (MQ=255)
aGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATAATGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATACCCCGGAATGTAAGGAATTCACAATTGTCCTTGACTCTGTGCCGggt                                                                                                                                             <  2:142576‑M2/143‑4 (MQ=255)
aGAATTTTAAGTGATTCGCTCATTGTAAAAATATCAAACTTATATTGGGGTGGTTTGTTAAGATAATAATACAGCCTTAAATTCAGTGGTGCAATAGCCAGAAATGTAAGGAAATAAAAATTGTCGTATATTTTAGgccggta                                                                                                                                             >  2:118903/1‑140 (MQ=255)
 gAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGACTTAAATTCAGTTGTGAAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggta                                                                                                                                            <  1:103917‑M2/143‑5 (MQ=255)
             cTTCGCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaact                                                                                                                                <  1:238584‑M2/143‑17 (MQ=255)
              ttCGCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGagtaatgactccaactt                                                                                                                               <  1:317811‑M2/143‑18 (MQ=255)
                 gCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTATATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttatt                                                                                                                            >  1:88499‑M2/1‑123 (MQ=255)
                  ttcATTTTAGTTATCTTAATCTTATTTTGGGGTGGTTTGTTTATTTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttattg                                                                                                                           >  1:209405‑M2/2‑122 (MQ=255)
                             attctcaaATTGTTTTTTGGGTTGTTCGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGTACTGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttattgatagtgtttta                                                                                                                >  2:136791‑M2/3‑111 (MQ=255)
                               tctcAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttattgatagtgttttatg                                                                                                              <  1:377661‑M2/143‑35 (MQ=255)
                                ctcAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTACCGggtaatgaatccaaattattgaaagtgtgttatgt                                                                                                             <  1:249763‑M2/143‑36 (MQ=255)
                                                    gtTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgact                                                                                         >  2:238584‑M2/1‑88 (MQ=255)
                                                      ttgttgAGGTAATAATAGAGTCTTAAATTCAGTTGTGCATTAGCCAGGAATGTAAGTAATTCAATATTGTTCTTTATTTTGTGCCGggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgacttt                                                                                       >  1:218403‑M2/1‑86 (MQ=255)
                                                         ttgAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgactttgtc                                                                                    <  2:306352‑M2/143‑61 (MQ=255)
                                                         ttgAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCATTATTTTGTGCCGggtaatgactccaactaattaatagtgttttacgttcagataatgcccgatgactttctc                                                                                    <  2:183990‑M2/143‑61 (MQ=255)
                                                                     taGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAAAGTAAGCAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaactaattgatagtgttttatgatcagataatgcccgatgaccatgtcatgaagctccac                                                                        <  2:104995‑M2/143‑73 (MQ=255)
                                                                         gCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgactttgtcatgcagctccaccgat                                                                    >  1:196090‑M2/1‑67 (MQ=255)
                                                                          ccTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttattgatggtagtcaacgatcagataatgcccgatgactttgtcatgcagctccaccgatt                                                                   <  1:81520‑M2/143‑78 (MQ=255)
                                                                           cTTAAATTCAATTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgactttgtcatgcagctccaccgattt                                                                  >  2:242911‑M2/1‑65 (MQ=255)
                                                                            ttAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAACTTGTTCTTTATTTTGTGCCGggtaatgactccaacttattgatagagttttatgttcagataatgcccgatgactttgtcatgaagctccaccgatttt                                                                 <  1:213002‑M2/143‑80 (MQ=255)
                                                                                  tCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTTTTTTTTGCCTggtaatgactccaactgattgatagtgttttatgttcagataatgcccgatgactttgtcatgcagctccaccgattttgagaac                                                           >  1:23940‑M2/1‑58 (MQ=255)
                                                                                    ttttgtGCGATAGCCAGGAATGTTAGGTATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttatggatagtgttttatgttcagataatgcccgatgactttgtcatgcagctccaccgattttgagaacga                                                         >  2:50917‑M2/3‑56 (MQ=255)
                                                                                          gCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgactttgtcatgcagctccaccgatttttagaacgacagcga                                                   <  1:316581‑M2/143‑94 (MQ=255)
                                                                                                   aGGATTTTAAGTATTTCAAGATTGTTCTTTATTTTGTGCCGggtaatgactccaactgatggatagtgttgtatgttcagataatgcccgatgactttgtcatgcagctccaccgattttgagaacgacagcgacttccgtcc                                          >  1:64201‑M2/1‑41 (MQ=255)
                                                                                                                     aaaTTGTTCTTTATTTTGTGCCGggtaatgactctttcttattgatagttttttatgttcagataatgcccgatgactttgtcatgcagctccaccgattttgagaacgacagcgacttccgtcccagccgtgccaggtgctg                        >  1:93788‑M2/1‑23 (MQ=255)
                                                                                                                           ttCTTTATTTTGTGCCGggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgactttgtcatgcagctccaccgattttgagaacgacagcgacttccgtcccagccgtgccaggtgctgcctcag                  <  1:45610‑M2/143‑127 (MQ=255)
                                                                                                                                         ccGggtaatgactcaaacttatggagagtgttttatgttcagataatgcccgatgactttgtcatgcagctccaccgattttgagaacgacagcgacttccgtcccagccgtgccaggtgctgcctcagattcacgttatgcc    <  2:335996‑M2/143‑141 (MQ=255)
                                                                                                                                          cGggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgactttgtcatgtagctccaccgattttgagaacgacagcgacttccgtcccagccgtgcccggtcctgccacagattcaggtcatgcag   <  2:365921‑M2/143‑142 (MQ=255)
                                                                                                                                          cGggtaatgactccaacttattgatagtgttttatgttcagataatgcccgatgactttgtcatgcagctccaccgattttgagaacgacagcgacttccgtcccagccctgccaggtgctgcctcagattcagggtgtgcgg   <  2:280112‑M2/143‑142 (MQ=255)
                                                                                                                                           gggtaatgactccaacttattgatagtgttttatgtccatataatgcccgatgactttgtcatgcagctccaccgattttgagaacgacagcgacttccgtcccagccgtgccaggtgctgcctcagattcaggttatgccgc  >  1:97052‑M2/1‑1 (MQ=255)
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AGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGCCGCCAATAAATATCTTTTCATAAAATTAGCCAGAAAAGACGCGGCATATAGCCCTATTTACACCGATGATTTCGCAGCACGTGAGGTTAAAACTTCCTGATTCATGTCACATTTTATGGGGAGATTATCGTAGGCTGACGACCT  >  NC_000913/1292900‑1293181

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ 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.