New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 52495 =41 (0.840)52 (1.070)
+T		 3/258 NT 58.3% intergenic (+105/‑568) USA300HOU_0043/USA300HOU_0044 hypothetical membrane protein/possible transcriptional regulator
?CP000730 = 52988 34 (0.700)intergenic (+598/‑75) USA300HOU_0043/USA300HOU_0044 hypothetical membrane protein/possible transcriptional regulator

ATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/52634‑52495
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTTTCGCGCGATT  <  CP000730/52988‑52864
                                                                                                                                            |                                                                                                                             
ATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGT                                                                                                                               <  1:355005/141‑1
   TCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGAT                                                                                                                            >  1:541963/1‑141
     AAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTT                                                                                                                          >  1:85749/1‑141
        cgttttcccgtATTATTTCACGTTATTTTCGCGCGATTACTCCGATGATTTCAAACGGTTCCTCTGATTATTTCACGTGATTCTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGCTTATTTCACGGGATTTTCG                                                                                                                       <  1:343219/130‑1
           tttCTCTTATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACTATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGC                                                                                                                    <  2:216821/138‑1
             CCTCAGATTATTTCACGTGATTTTCGCGCGATGACTACGAAGATTTCAAACGATTCATCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGTTTCCCTTGATTATTTCCCATGATTTTCGCGCGA                                                                                                                  >  1:408690/1‑141
               TCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATT                                                                                                                >  1:288942/1‑141
                CTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACATGATTTTCACGAGATTt                                                                                                               >  1:411014/1‑140
                       TTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGTTTCCTCTGATTATTTCACGTGATTTTCCCGCAATTtttactat                                                                                                        >  1:308293/1‑133
                        TTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATG                                                                                                       >  1:321003/1‑141
                        TTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATG                                                                                                       <  1:433765/141‑1
                         TCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTTATTTTCACTCCATTACTtttatta                                                                                                      >  2:228529/1‑134
                                ATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAA                                                                                               >  1:519146/1‑141
                                  TTTCGCGCGATTACTACGATGATTTCAAACGATTCCGCTTATTATTCCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACG                                                                                             <  2:177836/141‑1
                                    TCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGAT                                                                                           >  1:457563/1‑141
                                     CGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATT                                                                                          >  1:177836/1‑141
                                         CGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTC                                                                                      <  1:504868/141‑1
                                         CGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTC                                                                                      <  2:321003/141‑1
                                          GATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCACGCAATTTTTAGTATTTTTTCAAACGTTTCCTCT                                                                                     >  2:532454/1‑141
                                            TTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGA                                                                                   <  2:78071/141‑1
                                              ACTACGATGCGTTCAAACGATTCCGCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAGACGATTCCacggagt                                                                                 >  1:418597/1‑134
                                               CTACGATGCTTTCAAACGATTCCCCTGAATATTTCACGTGATTAGCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTACACGCGATTTTTGCGCGATTACTACGATGATTTCAAACGATACCTCTGATTt                                                                                >  2:304304/1‑140
                                                TACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTCCTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTGCTACGATGATTTCAAACGATTCCTCTGATTAT                                                                               >  1:382644/1‑141
                                                     TGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCAC                                                                          <  1:564353/141‑1
                                                        TTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTtatgtg                                                                       >  1:268223/1‑135
                                                          TCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGAT                                                                                                        <  1:88636/106‑1
                                                            AAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTC                                                                                      >  2:473324/1‑122
                                                            AAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTC                                                                                      <  1:473324/122‑1
                                                             AACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCGCGTGATTTTCGC                                                                                                                      >  2:72974/1‑89
                                                             AACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCGCGTGATTTTCGC                                                                                                                      <  1:72974/89‑1
                                                             AACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGC                                                                                                                      <  1:189507/89‑1
                                                             AACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGC                                                                                                                      >  2:189507/1‑89
                                                                               TTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGC                                                                                                                    <  2:426269/73‑1
                                                                                 CACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACG                                                                         <  1:140889/114‑1
                                                                                    GTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTA                                                                                <  1:567286/104‑1
                                                                                        TTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATT                                                                              <  2:492379/102‑1
                                                                                           TCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT                                                                                                     <  2:486350/76‑1
                                                                                           TCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT                                                                                                     >  1:486350/1‑76
                                                                                            CGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAA                                                                                               <  2:183832/81‑1
                                                                                            CGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAA                                                                                               >  1:183832/1‑81
                                                                                                               TTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTTTCACGAGATTATTCCTATTATTTCAAAATATTCACTTGATTATTTagagtg                >  2:281398/1‑135
                                                                                                               TTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATT                                                                                 <  1:522246/76‑1
                                                                                                               TTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATT                                                                                 >  2:522246/1‑76
                                                                                                                  CAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTAT                                                                               <  1:273524/75‑1
                                                                                                                   AAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTA                                                                                <  2:185872/73‑1
                                                                                                                   AAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTA                                                                                >  1:185872/1‑73
                                                                                                                   AAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGAT                                                                                           <  2:348340/62‑1
                                                                                                                          TCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAAC                                                                                              <  2:432612/52‑1
                                                                                                                            CTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAA                                                                                               <  2:308628/49‑1
                                                                                                                            CTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAA                                                                                               >  1:308628/1‑49
                                                                                                                            CTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAA                                                                                               >  2:562476/1‑49
                                                                                                                            CTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAA                                                                                               <  1:562476/49‑1
                                                                                                                             TCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTTTCGCACGATTACTACGATGGTTTCAAAGGATTACTATGATGAGATCACGTGTTCTTCGCGTGATT  >  2:398938/1‑141
                                                                                                                                      TTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCAC                                                                          <  1:240670/60‑1
                                                                                                                                      TTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCAC                                                                          >  2:240670/1‑60
                                                                                                                                            |                                                                                                                             
ATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/52634‑52495
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGATTTTCGCGCGATT  <  CP000730/52988‑52864

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.