New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4135844 =	46 (0.910)	4 (0.090)	4/240	NT	9.1%	coding (53/921 nt)	PP_3640	AraC family transcriptional regulator
	?	NC_002947	4135888 =	37 (0.790)					coding (97/921 nt)	PP_3640	AraC family transcriptional regulator

CTCCATATTCGTCAGTCGCCTTTCCTTGCTCCTGAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATGCCGTGTTCCTGCTGCGTGACCTGGCCTATCGCTTG  >  NC_002947/4135744‑4136031                                                                                                                                                  |                                                                                                                                                 cTCCATATTCGTCAGTCGCCTTTCCTTGCTCCTGAGTCTTTGCATTAGATGATTTCGTCCCGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAg                                                                                                                                              >  7:79158/1‑149 (MQ=255) cTCCATATTCGTCAGTCGCCTTTCCTTGCTCCTGAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTAGCATGCCAg                                                                                                                                              >  7:27986/1‑149 (MQ=255)        ttCGTCAGTCGCCTTTCCTTGCTCCTGAGTCTTTGCATTAGATGATTTCGTCCAGACCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTAccc                                                                                                                                         >  6:181847/1‑147 (MQ=255)           gTCAGTCGCCTTTCCTTGCTCCTGAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAgg                                                                                                                                     >  2:157278/1‑148 (MQ=255)           gTCAGTCGCCTTTCCTTGCTCCTGAGTCTTAGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAgg                                                                                                                                     >  1:27302/1‑148 (MQ=255)                 cGCCTTTCCTTGCTCCTGAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTTGCATGCCAGTACCCAAGGCATggg                                                                                                                               <  8:27986/148‑1 (MQ=255)                  gCCTTTCCTTGCTCCTGAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATgggc                                                                                                                              <  2:27302/148‑1 (MQ=255)                          ttGCTCCTGAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGc                                                                                                                                                 >  4:263549/1‑121 (MQ=255)                          ttGCTCCTGAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGc                                                                                                                                                 <  3:263549/121‑1 (MQ=255)                            gCTCCTGAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCtt                                                                                                                   >  6:180716/1‑149 (MQ=255)                               ccTGAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCAAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCa                                                                                                                >  7:73358/1‑149 (MQ=255)                                cTGTGTCTTTGCATTAGTTGTTTTAGTCCAGCCCGCTTGTCGATTGGTTATTTGAATGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCAt                                                                                                               <  8:73358/149‑1 (MQ=255)                                  gAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCGAGCTTTCATCt                                                                                                             >  4:82926/1‑149 (MQ=255)                                   aGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATc                                                                                                              <  3:273471/147‑1 (MQ=255)                                       tttGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCtggtgg                                                                                                        >  4:28587/1‑149 (MQ=255)                                         tGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCAAGGGCCGGGCCAGCTTTCATCtggtgg                                                                                                        <  2:56926/147‑1 (MQ=255)                                           cATTAGATGATTTCGTCGAGCCCGCTTGTCGAGTGGGTATTAGAAAGCCTGGAGCTCGAGGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGc                                                                                                     <  8:79158/148‑1 (MQ=255)                                           cATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGc                                                                                                     <  2:67541/148‑1 (MQ=255)                                            aTTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCaa                                                                                                   <  5:181847/149‑1 (MQ=255)                                                      ttCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTgct                                                                                         >  7:302594/1‑149 (MQ=255)                                                       tCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTgctg                                                                                        >  6:289821/1‑149 (MQ=255)                                                       tCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTgctg                                                                                        >  6:263804/1‑149 (MQ=255)                                                             aGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGca                                                                                  >  5:10006/1‑149 (MQ=255)                                                               cccGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGcaca                                                                                <  1:157278/149‑1 (MQ=255)                                                                    ttGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGAc                                                                          >  2:23981/1‑149 (MQ=255)                                                                       tCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGc                                                                       <  5:289821/149‑1 (MQ=255)                                                                                     gAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATTGGCGCCGCATGCAATGCACTAACCAAAGGAATGGGCC‑GGCCCGCGTTCATAATGTGGTTGAAGGGCATTTCATGCAGCACA‑ATTAACGCCAGCCGCCCGCCaa                                                         >  1:232901/1‑148 (MQ=255)                                                                                     gAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCAt                                                         >  4:251889/1‑149 (MQ=255)                                                                                       aaGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCAttt                                                       >  7:137985/1‑149 (MQ=255)                                                                                              gAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTgctgg                                                                                       >  7:259154/1‑111 (MQ=255)                                                                                              gAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTgctgg                                                                                       <  8:259154/111‑1 (MQ=255)                                                                                                gCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAgg                                                                                                 <  5:193082/99‑1 (MQ=255)                                                                                                gCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAgg                                                                                                 >  6:193082/1‑99 (MQ=255)                                                                                                    gATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAgg                                          >  5:60023/1‑149 (MQ=255)                                                                                                    gATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAg                                           <  3:251889/148‑1 (MQ=255)                                                                                                     ATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGt                                         <  2:146240‑M1/149‑1 (MQ=255)                                                                                                       tgccagccgccgcaatagcggcctacatgaaacaggctggcatGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTg                                        >  3:33260‑M2/44‑149 (MQ=255)                                                                                                       GCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGa                                       <  4:54904‑M1/149‑1 (MQ=255)                                                                                                        gccagccgccgcaatagcggcctacatgaaacaggctggcatGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGAc                                                                          <  4:266875‑M2/72‑1 (MQ=255)                                                                                                        gccagccgccgcaatagcggcctacatgaaacaggctggcatGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGAc                                                                          >  3:266875‑M2/43‑114 (MQ=255)                                                                                                         CAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTggtggt                                                                                                       <  2:281071‑M1/84‑1 (MQ=255)                                                                                                         CAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTggtggt                                                                                                       >  1:281071‑M1/1‑84 (MQ=255)                                                                                                         CAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATg                                     <  8:97742‑M1/149‑1 (MQ=255)                                                                                                                tttCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATGCCGTGtt                              >  1:121043/1‑149 (MQ=255)                                                                                                                  tCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATGCCGTGTTc                             <  7:97742/148‑1 (MQ=255)                                                                                                                  tCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGG‑CATTTGCCTGGAGAAAGGTGATGCCGTGTTCct                           >  1:253182/1‑149 (MQ=255)                                                                                                                    aatagcggcctacatgaaacaggctggcatGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATGCCGTGTTCct                           <  4:33260‑M2/119‑1 (MQ=255)                                                                                                                         ggCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATGCCGTGTTCCtgctgc                      <  5:180716/148‑1 (MQ=255)                                                                                                                            cGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAg                                                              >  8:94968/1‑105 (MQ=255)                                                                                                                                 tt‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATGCCGTGTTCCTGCTGCGTGACCTg              <  3:28587/148‑1 (MQ=255)                                                                                                                                     cggcggCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATGCCGTGTTCCTGCTGCGTGACCTGGcc           <  1:23981/148‑1 (MQ=255)                                                                                                                                             ggcatGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCATGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATGCCGTGTTCCTGCTGCGTGACCTGGCCTATCGCTTg  <  2:232901‑M2/144‑1 (MQ=255)                                                                                                                                              gcatGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATGCCGTGTTCCTGCTGCGTGACCTGGCCTATCGCtt   <  1:146240‑M2/143‑1 (MQ=255)                                                                                                                                               catGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAg                                           <  7:264096‑M2/103‑1 (MQ=255)                                                                                                                                               catGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAg                                           >  8:264096‑M2/4‑106 (MQ=255)                                                                                                                                                 tGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACACTTGACGGCCAGCCGCAGGCCATTTGCCTgg                                                 <  1:192369‑M2/98‑1 (MQ=255)                                                                                                                                                 tGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTgg                                                 >  2:192369‑M2/2‑98 (MQ=255)                                                                                                                                                  |                                                                                                                                                 CTCCATATTCGTCAGTCGCCTTTCCTTGCTCCTGAGTCTTTGCATTAGATGATTTCGTCCAGCCCGCTTGTCGATTGGTTATTAGAAAGCCTGGAGCTCGATGCCAGCCTGTTTCATGTAGGCCGCTATT‑GCGGCGGCTGGCATGCCAGTACCCAAGGCATGGGCCGGGCCAGCTTTCATCTGGTGGTGCAAGGCCATTGCTGGCTGCACA‑TTGACGGCCAGCCGCAGGCCATTTGCCTGGAGAAAGGTGATGCCGTGTTCCTGCTGCGTGACCTGGCCTATCGCTTG  >  NC_002947/4135744‑4136031

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.