New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 1299498	0 (0.000)	54 (0.900)	42/272	0.5	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913_3_pae_pgi	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

CTTCTCAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/1299350‑1299498 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  NC_000913_3_pae_pgi/1300698‑1300843                                                                                                                                                                                                                                                                                                           CTTCTCAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAA                                                                                                                                                    <  1:106760/149‑1       AAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCATCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATA                                                                                                                                              <  2:486881/149‑1       AAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTATACTCACCATAATGTTATTTTCGCCACATCATAATCCTGGACTTGATGAAGAATAATTGAAATGATATTATTAATTCCACTGCATTTA‑‑GTAAAGGAAAGTGGTAACTAATA                                                                                                                                              >  2:381169/1‑149         ATTACATTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACTTCGTAATCCTGGGCTTGCTGAATAATAATTGAAATTATACTATTAATTCCACTGCATTTG‑‑GTAGAGGACACTGCTAAATAATAAT                                                                                                                                            <  2:975026/149‑1                    TTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAA                                                                                                                                 >  1:856225/1‑149                    TTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAA                                                                                                                                 <  1:349301/149‑1                       TAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGCAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGATAGTGCTAAATAATAATCACTTGTTTAATTA                                                                                                                              >  2:439202/1‑149                       TAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATCATCAATTGTTAATTTA                                                                                                                              >  2:985455/1‑149                       TAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTA                                                                                                                              >  2:166477/1‑149                          GGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGACATATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTG                                                                                                                           <  2:389682/149‑1                              TTCCTTAATTGCTTCTCCTCCCCATCATGTTATTTTCGCAACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTTCACTGCCTTTG‑‑GTTGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCA                                                                                                                       <  2:455098/149‑1                                 CTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTACTACGACTTCCATCGCAGTAGTGG‑‑TGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTT                                                                                                                    <  1:1060891/149‑1                                     ACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACT                                                                                                                >  2:105105/1‑149                                             TCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAAC                                                                                                        >  1:774980/1‑149                                             TCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTAATGGAAC                                                                                                        >  1:682604/1‑149                                                  ACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAA                                                                                                   <  1:394579/149‑1                                                    CATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATC                                                                                                 >  2:1069779/1‑149                                                          GTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAA                                                                                                                                         >  1:613913/1‑103                                                          GTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAA                                                                                                                                         <  2:613913/103‑1                                                                       CATCATAATCCTGGGCTTGCTGAAGAATAATTGAGATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTT                                                                              >  2:701952/1‑149                                                                               TCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATC                                                                      <  1:358409/149‑1                                                                                 CTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTC                                                                    >  2:895595/1‑149                                                                                          CTGAAGAATAATTGAAACGATAGTCTTCATTCCACTGCCTTTG‑‑GTTGAGGAAAGTGCTAAATAATAATCACTCGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTCAGCCAATCTCTATTTGATT                                                           <  2:911442/149‑1                                                                                            GAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGATGAAAGTGCGAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGA                                                         >  2:259839/1‑149                                                                                              gGAATAAGTGAAAGGATATACATAATTTAACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATGATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAAT                                                       <  2:174410/148‑1                                                                                               GAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGGTAAATAATAATCAATTGTTAAATTATTGTGTATTTAACTATTGGAAATGTGATCAGGAAAGATAGAAATGCTTAGCTAATTTCTAGTTGGTTTAATT                                                      >  2:1069463/1‑149                                                                                               GAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAATTAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATT                                                      >  1:1016106/1‑149                                                                                               GAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGAATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGACAATCTCTATTTGATTGCATT                                                      >  1:1028142/1‑149                                                                                                        AAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATT                                                                                                                            <  1:576649/70‑1                                                                                                        AAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATT                                                                                                                            >  2:576649/1‑70                                                                                                          ATGAGATTATTAATTCCACTGCCTTTG‑‑GGAGAGGAAAGTGGTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTT                                           <  2:524559/149‑1                                                                                                             ATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTT                                        <  1:105105/149‑1                                                                                                               ATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAA                                      <  1:439202/149‑1                                                                                                                TTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTATTCTGAAAAGATAGAAATGCTTAGCCAATCTCTATTTGATTGAATTGAACGATGTTTGTTAAG                                     >  2:555706/1‑149                                                                                                                TTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCA                                                                                                                       >  2:931060/1‑67                                                                                                                TTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGCTAAATTATTGTGCA                                                                                                                       <  1:931060/67‑1                                                                                                                 TATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATCGAAAGATGTTTGTTAAGG                                    >  2:735611/1‑149                                                                                                                   TTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATA                                                                                       >  2:21161/1‑96                                                                                                                   TTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATA                                                                                       <  1:21161/96‑1                                                                                                                        TCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGAT                             <  1:701952/149‑1                                                                                                                        TCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGAT                             <  1:166477/149‑1                                                                                                                           ACTGCCTTTG‑‑GTAGAGGAAAGTGCTGAATAATAATCAATTGTTAAAATATTGTGCATTTCACTACTATAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGATAGATGTTTGTTAAGGCATGGATGCA                          >  1:975800/1‑149                                                                                                                             TGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAG                        >  1:207924/1‑149                                                                                                                             TGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAG                        >  2:289806/1‑149                                                                                                                             TGCCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAG                        <  2:207924/149‑1                                                                                                                               CCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGC                                                                           >  2:424018/1‑96                                                                                                                               CCTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGC                                                                           <  1:424018/96‑1                                                                                                                                gTTTG‑‑GTAGAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTA                     <  2:517264/148‑1                                                                                                                                          GAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGCACTCGGGCGAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCT             <  1:1056746/149‑1                                                                                                                                          GAGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCT             <  1:895595/149‑1                                                                                                                                           AGGAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTG            >  2:582537/1‑149                                                                                                                                             GAAAGTGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGAT          >  1:478447/1‑149                                                                                                                                                  gGCTAAAGAATAATCAAGTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACAGGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGT     <  2:81079/148‑1                                                                                                                                                  TGCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGT     <  2:856225/149‑1                                                                                                                                                  TGCTAAATAAGAACAAATTGTTCAATTATTGGGCATTTCACTCCTGGAACGGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGT     <  1:175529/149‑1                                                                                                                                                     TAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  1:804264/1‑149                                                                                                                                                                                                                                                                                                           CTTCTCAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTG‑‑GTAGAGGAAAGTGCTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/1299350‑1299498 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  NC_000913_3_pae_pgi/1300698‑1300843

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.