New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1483730	3 (0.060)	73 (1.560)	47/282	0.1	96.0%	coding (670/3903 nt)	hrpA	putative ATP‑dependent helicase
	?	NC_000913_3_pae_tpiA	= 2290113	NA (NA)					intergenic (‑32/+1)	insH1/yejO	IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system

AAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGAGTCAGT  >  NC_000913_3_pae_tpiA/2289975‑2290261                                                                                                                                           |                                                                                                                                                      aaaaTCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGt                                                                                                                                             >  2:364970/1‑149 (MQ=38)     tctcTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTACGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGAAAAACATGCTCTCATATAAGGGCCGTGTTCGCACCTCCCACACCGCTGTAAcc                                                                                                                                         >  2:366841/1‑149 (MQ=11)      ctctTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGcca                                                                                                                                        <  1:364970/149‑1 (MQ=255)                gTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGCCAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGGACAGa                                                                                                                              <  2:190089/149‑1 (MQ=255)                     aCGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGATAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAACCACCAGAACAGATATTg                                                                                                                         >  2:586659/1‑149 (MQ=255)                       ggCGCTTACTGCTGAATTCACTGTCGGCGAAGGTACGTCAATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCg                                                                                                                       <  1:561881/149‑1 (MQ=255)                          gcTTACGGCTGAATTCACTGGCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGaa                                                                                                                    <  2:382108/149‑1 (MQ=255)                                tgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACaa                                                                                                              >  1:532690/1‑149 (MQ=255)                                 gctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAAATATTGCGGAACGACaca                                                                                                             >  2:557871/1‑147 (MQ=255)                                     aaTTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAg‑aga                                                                                                        <  1:12109/149‑1 (MQ=255)                                       ttCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGAGCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGaaa                                                                                                      <  1:11875/149‑1 (MQ=255)                                          aCTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAAAAg                                                                                                   >  2:289106/1‑149 (MQ=255)                                                ggCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAg                                                                                             >  1:722871/1‑149 (MQ=255)                                                ggCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAg                                                                                             >  2:295965/1‑149 (MQ=255)                                                   gAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGCAACGACAAAG‑AGAAACAGAACCAGAtt                                                                                          >  1:74459/1‑149 (MQ=255)                                                           gTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGAc                                                                                                                >  2:130327/1‑120 (MQ=255)                                                           gTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGAc                                                                                                                <  1:130327/120‑1 (MQ=255)                                                           gTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATTCAtt                                                                                  >  1:465675/1‑149 (MQ=255)                                                             tgatgaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTCCCATAACGCTGTAGCCCCCAGAACAGATATTGCGG‑ATTACATGGCATTAACAGAACCAGATTGATGCATTGa                                                                                <  2:790604/149‑1 (MQ=18)                                                              gatgaCTCATGATGAACACTGTTCTATGGCTCCAGATGACAAACATGATCCCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAAATTGATGCATTGAg                                                                               >  2:98302/1‑149 (MQ=255)                                                                              cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGaaa                                                               <  1:295965/149‑1 (MQ=255)                                                                              cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGaaa                                                               >  2:243966/1‑149 (MQ=255)                                                                              cccTGTTCTATGGCTCCAGATGACAAACATGATATCATATCAGGAACTTGTTAGCACGTCCTATAACGCTGTAGACAACAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGAATTTAGGTTTCATCCTATGaaa                                                               >  2:299556/1‑149 (MQ=25)                                                                                  gTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAaattaa                                                           >  2:256239/1‑149 (MQ=255)                                                                                       aTGGCTTCAGATTACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCAGAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCt                                                      <  1:557871/149‑1 (MQ=255)                                                                                            tCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTaa                                                 >  2:84990/1‑149 (MQ=255)                                                                                             ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTaaa                                                <  1:428250/149‑1 (MQ=255)                                                                                              cAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTaaaa                                               <  1:674587/149‑1 (MQ=255)                                                                                              cAGATGACAAACATCATCTTATATCAGGGACTTGTTCGCACCCTCCATAGCGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTaaaa                                               <  1:316811/149‑1 (MQ=255)                                                                                                gATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGc                                             >  2:559195/1‑149 (MQ=255)                                                                                                 aTGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAag‑a                                                                                                          >  2:720411/1‑87 (MQ=255)                                                                                                 aTGACAAACATGATCTCATATCAGGGACTTGTTCGCACATTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAag‑a                                                                                                          <  1:720411/87‑1 (MQ=255)                                                                                                      aaaCATGACCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTTCTGTTAAAAGCCTTggg                                       <  2:420691/149‑1 (MQ=255)                                                                                                            gATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATg                                                                                      >  1:688588/1‑96 (MQ=255)                                                                                                            gATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATg                                                                                      <  2:688588/96‑1 (MQ=255)                                                                                                                tcATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTATAGaaa                               <  2:807781/147‑1 (MQ=255)                                                                                                                tcATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTATAGaaa                               >  1:807781/1‑147 (MQ=255)                                                                                                                    atCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATAccc                         <  1:288645/149‑1 (MQ=255)                                                                                                                        gggACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACGGAAAGTAACCATaa                     >  2:259716/1‑148 (MQ=255)                                                                                                                             ttGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGTTACAGAAAATACCCATAGCTCCa                >  1:13962/1‑149 (MQ=255)                                                                                                                                       cTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAACG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGAGt      >  1:737100/1‑149 (MQ=255)                                                                                                                                         tCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGAGTCa    >  1:466710/1‑149 (MQ=255)                                                                                                                                           cATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGAGTCAGt  <  1:256239/149‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                      AAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAG‑AGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGAGTCAGT  >  NC_000913_3_pae_tpiA/2289975‑2290261

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.