New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 743324	NA (NA)	4 (0.080)	4/252	NT	NA	intergenic (+3/+271)	PP_0635/PP_0636	group II intron‑encoding maturase/cold shock DNA‑binding domain‑containing protein
	?	NC_002947	= 743350	NA (NA)					intergenic (+29/+245)	PP_0635/PP_0636	group II intron‑encoding maturase/cold shock DNA‑binding domain‑containing protein

CAAAGAAACTGTGGGACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTT  >  NC_002947/743248‑743494                                                                                                       |                                                                                                                                                     cAAAGAAACTGTGGGACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTgcg                                                                                                     <  1:285630/149‑1 (MQ=11) cAAAGAAACTGTGGGACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTgcg                                                                                                     <  2:151403/149‑1 (MQ=11)  aaaGAAACTGTGGGACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTgcgc                                                                                                    >  8:106335/1‑149 (MQ=31)  aaaGAAACTGTGGGACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTgcgc                                                                                                    >  5:238832/1‑149 (MQ=31)       aaCTGTGGGACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAAt                                                                                               <  5:305186/149‑1 (MQ=35)         cTGTGGGACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAAt                                                                                               >  8:12385/1‑147 (MQ=35)            tgGGACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGa                                                                                           <  7:106335/148‑1 (MQ=38)            tgGGACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGAc                                                                                          <  6:203198/149‑1 (MQ=39)              ggACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCt                                                                                        <  6:144358/149‑1 (MQ=40)                 ccGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGaaa                                                                                                <  3:95414/138‑1 (MQ=34)                 ccGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGaaa                                                                                                >  4:95414/1‑138 (MQ=34)                 ccGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGcc                                                                                     >  8:252631/1‑149 (MQ=255)                   ggCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCtt                                                                                   <  6:55381/149‑1 (MQ=255)                          gCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGcc                                                                            >  5:295358/1‑149 (MQ=255)                           cTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGccc                                                                           <  1:13884/149‑1 (MQ=255)                              gTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGc                                                                         <  7:12385/148‑1 (MQ=255)                                   gATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTAtgt                                                                    <  6:295358/148‑1 (MQ=255)                                          gATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGAGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAAc                                                           >  3:271570/1‑149 (MQ=255)                                               gATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑TGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCg                                                      >  2:111041/1‑149 (MQ=255)                                               gATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑Gaa                                                                >  5:26107/1‑139 (MQ=255)                                               gATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑Gaa                                                                <  6:26107/139‑1 (MQ=255)                                                    aCCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAGTCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGc                                                 <  6:158869/149‑1 (MQ=255)                                                     ccGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCg                                                <  1:156378/149‑1 (MQ=255)                                                      cGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGt                                               >  8:65436/1‑149 (MQ=255)                                                        gCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTa                                             >  3:223687/1‑149 (MQ=255)                                                             gCCTCGTAACCTGAACCTCCGTGTACGGAACCGGAGGGACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCGTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCGAAGGTTGCTTCACATa                                         <  4:226963/148‑1 (MQ=18)                                                              ccGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGc                                       <  4:271570/149‑1 (MQ=255)                                                               cgcgTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCg                                      <  6:246054/149‑1 (MQ=255)                                                               cgcgTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCg                                      <  3:276242/149‑1 (MQ=255)                                                                 cgTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGAACTGCCTTGTGTGTCCGCTATGT‑AACGCAACCGAAGGTTGCTTCACATAGCggg                                    <  7:188223/149‑2 (MQ=18)                                                                       cTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGacaca                                >  4:108736/1‑147 (MQ=255)                                                                       cTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGacaca                                >  1:235645/1‑147 (MQ=255)                                                                       cTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGAcacaca                              <  6:238832/149‑1 (MQ=255)                                                                         gAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGc                            >  8:57667/1‑149 (MQ=255)                                                                             cgccgTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTAGAAGCAACCTTCGGTTGCGTTACATAGCg                                      <  1:24900/136‑1 (MQ=255)                                                                             cgccgTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCg                                      >  2:24900/1‑135 (MQ=255)                                                                              gccgTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGcgtcgt                       <  4:223687/149‑1 (MQ=255)                                                                               ccgTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGcgtcgt                       >  1:95401/1‑148 (MQ=255)                                                                                cgTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGa                     <  4:185161/149‑1 (MQ=255)                                                                                 gtgtACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGAc                    >  5:173646/1‑149 (MQ=255)                                                                                 gtgtACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGAc                    >  4:125521/1‑149 (MQ=255)                                                                                  tgtACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGTGGAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTTTGCCCGCTATGT‑GAAGCAACATTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGa                     >  1:67172/1‑148 (MQ=255)                                                                                  tgtACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACTAGAGATTGCGCGAAATCAGACCTGCCTTGTTTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTAAATAGCGGACACACAGCGTCGTg                      >  1:253761/1‑148 (MQ=37)                                                                                  tgtACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGtt                                              <  4:254145/122‑1 (MQ=255)                                                                                  tgtACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGtt                                              >  3:254145/1‑122 (MQ=255)                                                                                  tgtACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGa                     <  2:67172/147‑1 (MQ=255)                                                                                  tgtACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACt                   >  5:256160/1‑149 (MQ=255)                                                                                      cGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGcc               >  4:234999/1‑149 (MQ=255)                                                                                       ggAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCg              >  7:65506/1‑149 (MQ=255)                                                                                       ggAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCg              >  8:230112/1‑149 (MQ=255)                                                                                            cGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGa          <  4:43836/148‑1 (MQ=255)                                                                                            cGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGa          >  3:43836/1‑148 (MQ=255)                                                                                                 gCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAactac    <  7:65436/149‑1 (MQ=255)                                                                                                  cACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTAt                                                                      <  5:284836/83‑1 (MQ=255)                                                                                                  cACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTAt                                                                      >  6:284836/1‑83 (MQ=255)                                                                                                   aCGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACtt  <  8:65506/149‑1 (MQ=255)                                                                                                       |                                                                                                                                                     CAAAGAAACTGTGGGACCGGCTCGGGCTGGTCTCGATACTGGATACGATTAACCGGCTTAGCCGCGTAACCTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGT‑GAATCCGCCTCCTACT‑‑CGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGT‑GAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTT  >  NC_002947/743248‑743494

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.