New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 743469	25 (1.460)	5 (0.330) +AGGCAGGTCTGATTTCGC	4/242	1.5	18.7%	intergenic (+145/+129)	PP_0635/PP_0636	group II intron‑encoding maturase/cold shock DNA‑binding domain‑containing protein
	?	NC_002947	= 1431465	NA (NA)					intergenic (+74/+78)	PP_1252/PP_1253	group II intron‑encoding maturase/ArsR family transcriptional regulator
Rejected: Frequency below/above cutoff threshold.

CTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGTGAATCCGCCTCCTACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCAAGCTAGCTTGGCGGTCACGCTAAGCCGAGTGAGGCATTCGATCCTGCTAGCGACGCATTTGCT  >  NC_002947/743321‑743614                                                                                                                                                     |                                                                                                                                                    cTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGACGGGTGTGAATCCGCCTCCTACTCGATTGCGCGAAATCAGACGTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGGTACATAGCGGACACACAg                                                                                                                                                    >  1:355382/1‑150 (MQ=255)                     cggTACGCACGGTGGTGTGAGAGGACGGCGGGTGTGAATCCGCCTCCTACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGaa                                                                                                                                >  2:214227/3‑150 (MQ=255)                      cGTACGCACGGTGGTGTGAGAGGACGGCGGGTGTGAATCCGCCTCCTACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGaaa                                                                                                                               >  2:356869/1‑150 (MQ=255)                             aCGGTGGTGTGAGAGGACGGCGGGTGTGAATCCGCCTCCTACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTg                                                                                                                        <  2:108656/150‑1 (MQ=255)                                gtggtgTGAGAGGACGGCGGGTGTGAATCCGCCTCCTACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑Tc                                                                                                                   >  2:19767/1‑150 (MQ=255)                                   gtgtGAGAGGACGGCGGGTGTGAATCCGCCTCCTACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑Tcgcg                                                                                                                >  2:347739/1‑150 (MQ=255)                                                   ggTGTGAATCCGCCTCCTACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAgaga                                                                                                <  2:252391/150‑1 (MQ=255)                                                           tCCGCCTCCTACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCaga                                                                                                  >  1:203920/1‑140 (MQ=255)                                                           tCCGCCTCCTACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCaga                                                                                                  <  2:203920/140‑1 (MQ=255)                                                               cctcctACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGc                                                                                    >  2:93600/1‑150 (MQ=255)                                                                  cctACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGtt                                                                                 <  2:355382/150‑1 (MQ=255)                                                                           ttGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGtgtg                                                                                                         <  1:377727/117‑1 (MQ=255)                                                                           ttGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGtgtg                                                                                                         >  2:377727/1‑117 (MQ=255)                                                                            tGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCg                                                                       <  1:214227/150‑1 (MQ=255)                                                                                  aaaTCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCa                                                                 <  1:356869/150‑1 (MQ=255)                                                                                    aTCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCAag                                                               <  1:111531/150‑1 (MQ=255)                                                                                         aCCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCAagctagc                                                          >  2:213426/1‑150 (MQ=255)                                                                                                ttGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAaggcaggtctgatttcgcgcaatcgagtaggaggcggattcacacccgccgtccaataacagcaccgtgcgtacggttccgtacacggcggttcaa                                                     >  1:21572‑M1/1‑54 (MQ=255)                                                                                                       tccGCTATGTAACGCAACCGAAGGTTGCTTCACATAGCGGGCACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCaa                                                                <  1:62436/129‑1 (MQ=25)                                                                                                       tccGCTATGTAACGCAACCGAAGGTTGCTTCACATAGCGGGCACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCaa                                                                >  2:62436/2‑130 (MQ=25)                                                                                                       tccGCTATGTAACGCAACCGAAGGTTGCTTCACATAGCGGGCACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCAAGCTAGCTTGGCGGTCACGCt                                            >  2:61014/2‑150 (MQ=37)                                                                                                                 gAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAaggcaggtctgatttcgcgcaatcgagtaggaggcggattcacacccgccgtcctctcacaccaccgtgcgtacggttccgtacacggcggttcaggttacgcggctaagccg                                    >  1:336672‑M1/1‑37 (MQ=255)                                                                                                                  aaGCAACCTTCGGTTGCGTTACATAGCGGGCACACAaggcaggtctgatttcgcgcaatcgagtaggaggcggattcacacccgccgtcctctcacaccaccgtgcgtacggttccgtacacggcg                                                           >  1:125130‑M1/1‑36 (MQ=255)                                                                                                                  aaGCAACCTTCGGTTGCGTTACATAGCGGGCACACAaggcaggtctgatttcgcgcaatcgagtaggaggcggattcacacccgccgtcctctcacaccaccgtgcgtacggttccgtacacggcg                                                           <  2:125130‑M1/126‑91 (MQ=255)                                                                                                                      aaCCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCAAGCTAGCTTGGCGGTCACGCTAAGCCGAGTGAGGCa                             <  1:213426/150‑1 (MQ=255)                                                                                                                          ttCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGa                                                                                      <  2:170398/89‑1 (MQ=255)                                                                                                                          ttCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGa                                                                                      >  1:170398/1‑89 (MQ=255)                                                                                                                              gTTGCGTTACATAGCGGACACACAGCGTAGTG‑CAT‑CACGGTAATCAGCAGGGTTTCGCGGCGTGTGGAGCAGTGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCAAGCTAGCTTGGCGGTCACGCTAAGCCGAGTGAGGCATTCGATcc                     <  1:93600/150‑1 (MQ=255)                                                                                                                                    ttACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCAAGCTAGCTTGGCGGTCACGCTAAGCCGAGTGAGGCATTCGATCCTGCTAg               >  2:231534/1‑150 (MQ=255)                                                                                                                                                   acaaggcaggtctgatttcgcgcaatcgagtaggaggcggattcacacccgccgtcctctcacaccaccgtgcgtacggttccgtacacggcggttcaggttacgcggctaagccggttaatcgtatccagtatcgagaccagcccgagc  <  2:336672‑M1/150‑148 (MQ=255)                                                                                                                                                     |                                                                                                                                                    CTGAACCGCCGTGTACGGAACCGTACGCACGGTGGTGTGAGAGGACGGCGGGTGTGAATCCGCCTCCTACTCGATTGCGCGAAATCAGACCTGCCTTGTGTGCCCGCTATGTGAAGCAACCTTCGGTTGCGTTACATAGCGGACACACAGCGTCGTGACTTGCCGGGGAAACTACTTGG‑‑TCGCGGCGTGTGGAGCAGAGACTGTAGGGGAGCGTTGACAGTGGCGGTTTCAAGCTAGCTTGGCGGTCACGCTAAGCCGAGTGAGGCATTCGATCCTGCTAGCGACGCATTTGCT  >  NC_002947/743321‑743614

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.