New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_pgi 3583428 =NA (NA)25 (0.470) 25/270 NT 43.1% intergenic (+10/‑55) yrhA/insA pseudogene, interrupted by IS1E/IS1 repressor TnpA
?NC_000913_3_pae_pgi 3665150 = 33 (0.620)coding (661/825 nt) gadX acid resistance regulon transcriptional activator; autoactivator

GTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/3583561‑3583428
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTA  >  NC_000913_3_pae_pgi/3665150‑3665287
                                                                                                                                                                                                                                                                                
ggCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCACCACCCGCTGTGATATCCAC                                                                                                                             <  1:674373/147‑1
                                 CGTCAGTAGCTAAACAGGCGGGACAGCTGATATAACGTGAAGCCCCTGTAGCACCTCAAAACTACCATCATACCCTAGATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCAT                                                                                            <  2:305116/149‑1
                                  GTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATG                                                                                           <  1:537113/149‑1
                                       TAGCTGAACAGGAGGGACAGCTGATAGAAACAGATGCTATTGTAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAA                                                                                      <  1:385550/149‑1
                                             AACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAA                                                                                >  1:750909/1‑149
                                                 GGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACCCGCTTAATTGAAAAACCATGTATAACAATAAGTTG                                                                            <  1:44231/149‑1
                                                                       GAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTCCAAAGCACGTTACATTCTACAC                                                      >  2:597902/1‑149
                                                                        AAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACT                                                     >  2:64723/1‑149
                                                                          GCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCA                                                   <  1:516349/149‑1
                                                                              CTGGAGCACCTCAAAATCACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCACAGCACGTTGCATTCTACACTCAGTAA                                               <  2:902922/149‑1
                                                                                  AGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGAAAAGCACGTTGCATTCTACACTCAGTAAGAAA                                           >  2:648539/1‑149
                                                                                        TCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGA                                     >  1:486001/1‑149
                                                                                          AAAACCACCATCATACACTAAATCAGGAAGTTGGCAGCATCACCCGTTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAAT                                   <  1:413456/149‑1
                                                                                          AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACT                                                                                                                     >  2:310862/1‑67
                                                                                          AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACT                                                                                                                     <  1:310862/67‑1
                                                                                               CACCCTCATATACTAAATCAGAAAGTTGGCACCATCACCGGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGAT                              <  2:328437/149‑1
                                                                                                ACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAGGCAACTGTGAATATTATG                             >  2:206694/1‑149
                                                                                                    TCATACACTAAATCAGTAAGTTGGCAGGATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTC                         <  2:39488/149‑1
                                                                                                    TCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTC                         >  1:592806/1‑149
                                                                                                       tcCACTAAATCAGGAAGTACGCAGCATCACCCGCTGGGAGATCCCCAGGATACTGCAACTCGCTTAATTGAAAATCCATGTATAACAAGAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTC                      <  1:480355/147‑1
                                                                                                       TACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTC                      >  1:14248/1‑149
                                                                                                              AATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTAAGTAAGGAACTGTGGTTATGATGTCTCTTATTCGCGC               >  2:843002/1‑149
                                                                                                                     AAGTTGGCAGCATCACCCGGTGTGAGATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTGTCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTT        <  2:309333/149‑1
                                                                                                                         tgggatCATCACCCGCTGTGATATCCACAGGATACTGCATCTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCACATCACGTTGCATTCTACACTCAGTAAGCAACTGTGTATATGATGTCTCTTCTTCGCGCAATTTTTTCTT    <  2:824865/143‑1
                                                                                                                           GCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACACTAATTTGCAAAGCACGTTCGTTGGTACACTCAGTAAGCAACTATGAATATGATGTCTCTTCTTCACGCAATTTTTTCTTTA  >  1:736050/1‑149
                                                                                                                                                                                                                                                                                
GTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/3583561‑3583428
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTA  >  NC_000913_3_pae_pgi/3665150‑3665287

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.