New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	= 1135979	35 (0.880)	4 (0.110)	4/314	NT	10.7%	coding (996/1509 nt)	PP_0997	Sigma‑54 dependent transcriptional regulator/sensory box protein
	?	AE015451	= 1136013	34 (0.910)					coding (962/1509 nt)	PP_0997	Sigma‑54 dependent transcriptional regulator/sensory box protein

GGGCGCTGGATCTGCGTGCACGCCTGCTGCATGAAGAAGTGCGCCAGCATCAGGATGTCCTGGCCACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCGGTAAAGGCCCCGGGCGCGTAGCCGAACAGCTCGCTTTCGGCCAGGCTCTCGGGCAGCGCGGCGCAGTTCAGGGCCAG  >  AE015451/1135806‑1136239                                                                                                                                                                                                                |                                                                                                                                                                                                                                   gggCGCTGGATCTGCGTGCACGCCTGCTGCATGAAGAAGTGCGCCAGCATCAGGATGTCCTGGCCACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCAt                                                                                                                                                                                                         <  1:276031/235‑1 (MQ=255)    cgcTGGATCTGCGTGCACGCCTGCTGCATGAAGAAGTGCGCCAGCATCAGGATGTCCTGGCCACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGc                                                                                                                                                                                                      >  1:679634/1‑235 (MQ=255)             tGCGTGCACGCCTGCTGCATGAAGAAGTGCGCCAGCATCAGGATGTCCTGGCCACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAAc                                                                                                                                                                                             <  1:95904/235‑1 (MQ=255)                      gCCTGCTGCATGAAGAAGTGCGCCAGCATCAGGATGTCCTGGCCACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGcagcag                                                                                                                                                                                      >  2:702630/1‑233 (MQ=255)                                             cAGCATCAGGATGTCCTGGCCACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACAttt                                                                                                                                                            >  2:582926/1‑236 (MQ=255)                                                    aGGATGTCCTGGCCACGGTCGCGAAGCGGCGGTCCCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTcgccacccaccgcgatctggagcgcatggtcgccgaaggcagctttcgcgaagacctgttctaccgtctgaacgtg                                                                                                                                                        >  1:204501‑M2/1‑157 (MQ=255)                                                       aTGTCCTGGCCACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTc                                                                                                                                                  <  1:582927/236‑1 (MQ=255)                                                              ggCCACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGCGaa                                                                                                                                                                                                >  1:99696/1‑183 (MQ=255)                                                                ccACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGaa                                                                                                                                         <  1:604911/236‑1 (MQ=255)                                                                 cACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAac                                                                                                                                        <  1:382498/236‑1 (MQ=255)                                                                    tttCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAACGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGaa                                                                                                                                                                                                >  2:453586/3‑177 (MQ=255)                                                                              cggcggTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGt                                                                                                                           <  1:333365/236‑1 (MQ=255)                                                                                       cTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTcgccacccaccgcgatctggagcgcatggtcgccgaaggcagctttcgcgaagacctgttctaccgtct                                                                                                                                                               >  2:457820‑M2/1‑122 (MQ=255)                                                                                          cAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGt                                                                                                                           <  1:672386/224‑1 (MQ=255)                                                                                               tAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCa                                                                                                            >  2:452544/1‑234 (MQ=255)                                                                                                   cACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCCTCGCTGAGAAAACGCAGCAGCTCGGCCTGCAg                                                                                                                                                                          >  2:190804/1‑168 (MQ=255)                                                                                                          aGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTcgccacccaccgcgatctggagcgcatggtcgcc                                                                                                                                                                                                  >  2:15712‑M2/1‑103 (MQ=255)                                                                                                          aGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGc                                                                                                >  1:387264/1‑235 (MQ=255)                                                                                                          aGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGGTGGCCAGTGCCATCCGCCCAGGCCTGc                                                                                                >  2:257099/1‑235 (MQ=255)                                                                                                                     cAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAAtt                                                                                                                                                    <  2:742021/172‑1 (MQ=255)                                                                                                                      aGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACAGCAACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGGGACAACgca                                                                                                                                                                                          >  2:238484/1‑133 (MQ=255)                                                                                                                           ttCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAGGCTGCCATCGCTGAGaaa                                                                                                                                                                                               >  2:282469/1‑123 (MQ=255)                                                                                                                           ttCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCgccc                                                                                                                                                               >  2:122987/1‑152 (MQ=255)                                                                                                                           ttCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCg                                                                               >  1:451917/1‑235 (MQ=255)                                                                                                                           ttCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTGCATCGAGGAacac                                                                                                                                      >  2:308306/1‑180 (MQ=255)                                                                                                                                gAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCCGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTCCGCGCCGGTaa                                                                           >  1:360636/1‑234 (MQ=255)                                                                                                                                    gCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCCCATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGccc                                                                                                                               <  2:112994/178‑1 (MQ=255)                                                                                                                                     cTGCCGTCGGCGCCCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTcgccacccaccgcgatctggagcgcatggtcgccgaaggcagctttcgcgaagacctgttctac                                                                                                                                                                    >  2:72880‑M2/1‑76 (MQ=255)                                                                                                                                      tGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAAc                                                                                                                                                                                             >  2:228317/1‑114 (MQ=255)                                                                                                                                      tGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAAc                                                                                                                                                                                             <  1:228317/114‑1 (MQ=255)                                                                                                                                          ttCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCTCTGATGCTGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGtt                                                                                                                  <  2:205628/185‑1 (MQ=255)                                                                                                                                             ggCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCGGTAAAGGCCCCGGGcgcg                                                             <  1:696975/235‑1 (MQ=255)                                                                                                                                              gCGACCATGCGCTCCAGAGCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCGGTAAAGGCCCCgg                                                                  <  1:124890/229‑1 (MQ=255)                                                                                                                                                                         gtggCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCGGTAAAGGCCCCGGGCGCGTCGCCGACCCGCCCGCt                                            >  2:197163/1‑224 (MQ=255)                                                                                                                                                                                  atgatgCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCGGTAAAGGCCCCGGGCGCGTAGCCGAACAGCTCGCTTTCgg                                       >  1:657956/1‑220 (MQ=255)                                                                                                                                                                                  atgatgCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCGGTAAAGGCCCCGGGCGCGTAGCCGAACAGCTCGCTTTCgg                                       <  2:657955/220‑1 (MQ=255)                                                                                                                                                                                   tgatgCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCGGTAAAGTCCCCGGGCGCGTAGCCGAACAGCTCGCTTTCGGCCAGGCTCTCggg                          >  1:75879/1‑232 (MQ=255)                                                                                                                                                                                                       acttcacGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCGGTAAAGGCCCCGGGCGCGTAGCCGAACAGCTCGCTTTCGGCCAGGCTCTCGGGCAGCGCGGCGCAGTTCAGGGCCAg  <  1:716205/236‑1 (MQ=255)                                                                                                                                                                                                                tCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCAACAATTTCATCGAGGAACACGGTGCCCTGGTTCGCCAGATCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCGGTAAAGGCCCCGGGCGCGTAGCCGAACAGccc                                               >  2:606167/1‑180 (MQ=255)                                                                                                                                                                                                                |                                                                                                                                                                                                                                   GGGCGCTGGATCTGCGTGCACGCCTGCTGCATGAAGAAGTGCGCCAGCATCAGGATGTCCTGGCCACGGTCGCGAAGCGGCGGTACCTCCAGGTTAAGCACGTTCAGACGGTAGAACAGGTCTTCGCGAAAGCTGCCTTCGGCGACCATGCGCTCCAGATCGCGGTGGGTGGCGCTGATGATGCGCACATCCACCTTCACTTCACGGTCGCCACCCACCCGGCGGAAGCTGCCATCGCTGAGAAAACGCAGCAGCTTGGCCTGCAGGTAGGGCGACATTTCACCAATTTCATCGAGGAACACGGTGCCCTGGTTGGCCAGTTCCATCAGCCCAGGCTTGCCACCGCGTTGCGCGCCGGTAAAGGCCCCGGGCGCGTAGCCGAACAGCTCGCTTTCGGCCAGGCTCTCGGGCAGCGCGGCGCAGTTCAGGGCCAG  >  AE015451/1135806‑1136239

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ 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.