New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 3595947	31 (1.050)	5 (0.170)	5/238	NT	14.3%	intergenic (‑462/+4)	PP_3172/nemA	group II intron‑encoding maturase/FMN‑linked N‑ethylmaleimide reductase
	?	NC_002947	= 4393488	NA (NA)					intergenic (‑430/+40)	PP_3868/PP_3869	group II intron‑encoding maturase/sheath protein

CCGCGACACCCTTGCCTCCGGCTAACACTTCCCCTTGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCCGGCGGATACAGCACGTTGACCCGGGCGGGGTCGGTAGTCG  >  NC_002947/4393354‑4393637                                                                                                                                       |                                                                                                                                                      ccGCGACACCCTTGCCTCCGGCTAACACTTCCCCTTGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACtt                                                                                                                                        >  1:553294/1‑150 (MQ=33)           cTTGCCTCCGGCTAACACTTCCCCTTGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCtt                                                                                                                              >  1:685147/1‑150 (MQ=255)                           acTTCCCCTTGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGtt                                                                                                              >  1:390324/1‑150 (MQ=255)                             ttCCCCTTGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTAc                                                                                                            >  2:784108/1‑150 (MQ=255)                               ccccTTGCCGGGTGTGTAGAGGACTTTCAGCTCCAAGTGACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGTCTGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGa                                                                                                          >  1:439746/1‑150 (MQ=255)                                 ccTTGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACGAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTc                                                                                                                  <  1:645568/140‑1 (MQ=255)                                 ccTTGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTtggt                                                                                                                           <  1:596328/131‑1 (MQ=255)                                 ccTTGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTtggt                                                                                                                           >  2:596328/1‑131 (MQ=255)                                 ccTTGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTc                                                                                                                  >  2:645568/1‑140 (MQ=255)                                   ttGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTtggt                                                                                                                           >  1:691429/1‑129 (MQ=255)                                   ttGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTtggt                                                                                                                           <  2:691429/129‑1 (MQ=255)                                              gtAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACCACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAg                                                                                           <  2:89663/150‑1 (MQ=255)                                              gtAGAGGACTCTCACCTCCAAGTCACCCCCTTGGCAACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAg                                                                                           <  2:439746/150‑1 (MQ=255)                                               tAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGc                                                                                                                                                <  1:340910/96‑1 (MQ=32)                                               tAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGc                                                                                                                                                >  2:340910/1‑96 (MQ=32)                                                 gagGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCg                                                                                        >  1:157365/1‑150 (MQ=255)                                                       tttCACCTCCAACTCACCCACTTGGCCAGCACAACCAAGCGGGTTGCGCTTCCGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTg                                                                                  >  2:115885/1‑150 (MQ=255)                                                            ccTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTAtt                                                                             >  1:87077/1‑150 (MQ=255)                                                             cTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTagt                                                                             <  2:595395/149‑3 (MQ=255)                                                             cTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTAtt                                                                             >  1:595395/1‑149 (MQ=255)                                                             cTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTg                                                                            >  2:85253/1‑150 (MQ=255)                                                                cAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAg                                                                         >  2:602821/1‑150 (MQ=255)                                                                 aaGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAgg                                                                        <  2:630526/150‑1 (MQ=255)                                                                 aaGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAgg                                                                        <  2:163851/150‑1 (MQ=255)                                                                     cACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGACCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCaa                                                                    <  1:178945/150‑1 (MQ=255)                                                                     aaCCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCaa                                                                    >  2:51728/2‑150 (MQ=255)                                                                       cccACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGc                                                                                                       >  2:521105/1‑113 (MQ=255)                                                                       cccACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGc                                                                                                       <  1:521105/113‑1 (MQ=255)                                                                        ccACTTGGCCACCACAACCAAGCGAGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCa                                                                 >  1:30093/1‑150 (MQ=255)                                                                            ttGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCg                                                             >  2:137395/1‑150 (MQ=255)                                                                                ccaccaCAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGc                                                         <  2:553294/150‑1 (MQ=255)                                                                                  accacAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTTCGATGCCGCGTACTGCAGGCGGGGCTGGTa                                                                               <  2:546839/126‑1 (MQ=255)                                                                                  accacAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTTCGATGCCGCGTACTGCAGGCGGGGCTGGTa                                                                               >  1:546839/1‑126 (MQ=255)                                                                                   ccacAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTgg                                                      <  1:51728/150‑1 (MQ=255)                                                                                        aCCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCAc                                                 <  1:149330/150‑1 (MQ=255)                                                                                         ccAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCAcc                                                <  1:115885/150‑1 (MQ=255)                                                                                           aaGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCAc                                                 >  1:436543/1‑147 (MQ=255)                                                                                           aaGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCAc                                                 <  2:436543/147‑1 (MQ=255)                                                                                               gcgTTGCGCGTAAGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTa                                                           >  1:759146/3‑133 (MQ=255)                                                                                               gcgTTGCGCGTAAGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTa                                                           <  2:759146/131‑1 (MQ=255)                                                                                                 gTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCcgg                                        <  2:685147/150‑1 (MQ=255)                                                                                                  ttGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTgg                                                                                 <  2:371943/108‑1 (MQ=255)                                                                                                  ttGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTgg                                                                                 >  1:371943/1‑108 (MQ=255)                                                                                                  ttGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCcggc                                       <  1:784108/150‑1 (MQ=255)                                                                                                  ttGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCcggc                                       <  1:85253/150‑1 (MQ=255)                                                                                                  ttGCGCTTACGCGCAACGCGCCATGCCTCGAGCACACAAAAATGCCCGCACTTGGCTTGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCcggc                                       <  2:87077/150‑1 (MQ=39)                                                                                                           cgcgCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCCGGCGGATACAGc                              <  2:756933/150‑1 (MQ=255)                                                                                                               cAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCCGGCGGATACAGCACGt                          <  2:462/150‑1 (MQ=255)                                                                                                                aaCGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCCGGCGGATACAGCACGtt                         <  1:137395/150‑1 (MQ=255)                                                                                                                          gCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGc                                                         >  1:499829/1‑108 (MQ=255)                                                                                                                          gCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGc                                                         <  2:499829/108‑1 (MQ=255)                                                                                                                            cTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCCGGCGGATACAGCACGTTGACCcgtgtggg             <  2:157365/150‑1 (MQ=255)                                                                                                                            cTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCCGGCGGATACAGCACGTTGACCcgggcggg             <  1:219514/150‑1 (MQ=255)                                                                                                                               gcgcACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGc                                                         <  1:28848/103‑1 (MQ=255)                                                                                                                               gcgcACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGc                                                         >  2:28848/1‑103 (MQ=255)                                                                                                                                 gcACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTgg                                                                                 <  2:57822/77‑1 (MQ=255)                                                                                                                                 gcACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTgg                                                                                 >  1:57822/1‑77 (MQ=255)                                                                                                                                      caAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCCGGCGGATACAGCACGTTGACCCGGGCGGGGTCGGTAGTc   <  2:390324/150‑1 (MQ=255)                                                                                                                                       aaaaaGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCCGGCGGATACAGCACGTTGACCCGGGCGGGGTCGGTAGTCg  >  1:21810/1‑150 (MQ=255)                                                                                                                                       aaaaaGGCCCGCACTTGGCGGGCCTTCGTGGATGATTAACTCACGATGCCCCGCACTGTAGGCGGGGCTGGGAGTGTAGGGCAAGCACCCGTAGCTGGTTCACCAGATCCGGCGGATACAGCACGTTGACCCGGGCGGGGTCGGTAGTCg  >  2:489622/1‑150 (MQ=255)                                                                                                                                       |                                                                                                                                                      CCGCGACACCCTTGCCTCCGGCTAACACTTCCCCTTGCCGGGTGTGTAGAGGACTTTCACCTCCAAGTCACCCACTTGGCCACCACAACCAAGCGGGTTGCGCTTACGCGCAACGCGCCATGCCTGGCGCACACAAAAAGGCCCGCACTTGGCGGGCCTTGGTGGATGATTCAGTTACGATGCCGCGTACTGCAGGCGGGGCTGGTATTGCAGGGCAAGCACCCGTAGCTGGTTCACCAGATCCGGCGGATACAGCACGTTGACCCGGGCGGGGTCGGTAGTCG  >  NC_002947/4393354‑4393637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.