New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 4094602	52 (1.770)	5 (0.180)	5/268	3.2	8.8%	noncoding (287/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	NC_000913_3_pae_pgi	= 4094618	54 (1.940)					noncoding (303/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCT  >  NC_000913_3_pae_pgi/4094457‑4094747                                                                                                                                                  |                                                                                                                                                  cGACGGTGTCGCGTCTTATCAGGCCTACAAGTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAg                                                                                                                                                <  2:433870/149‑1 (MQ=255)     gCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCAc                                                                                                                                            <  1:450040/149‑1 (MQ=38)         tCGCGTCTTATCAGGCCTACCACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTtgt                                                                                                                                        >  2:373900/1‑149 (MQ=38)                ttATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATGCGGCACAAGTGccttat                                                                                                                                 <  1:104838/149‑5 (MQ=11)                    cAGGGCTTCAGCTGTGGCCGCCCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTTCAACTATTCCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCgg                                                                                                                             <  2:168663/149‑1 (MQ=11)                      ggCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCCTCCCGcc                                                                                                                           >  2:164957/1‑148 (MQ=255)                        ccTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGcaat                                                                                                                         <  1:265663/149‑1 (MQ=38)                          tACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATCAGGCACTTGTGCCGCATCCGGcaatca                                                                                                                       >  2:129200/1‑149 (MQ=38)                             aaCTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATg                                                                                                                    >  2:366845/1‑149 (MQ=38)                                ggTTGCCGACCTGTAGGCCGGAGAAGGCACTCGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCt                                                                                                                 <  2:121348/148‑1 (MQ=25)                                      cGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCCCATCCGGCAATCAATACCTGATGCg                                                                                                           >  2:83303/1‑149 (MQ=25)                                          cTGTAGGCCGGATAAGGCACTTGTGCCGGATCCGGCAATCAATGCCTGATGAGACGCTGTCGCGTATTATCAGGGCTACAACTATTGCCGACCTGTGGGGCGGATAAGGCAATTGTGCCGCGCCCGTCAGTCCATGCCTGCTGGGACGc                                                                                                       >  1:170284/1‑149 (MQ=11)                                          cTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGc                                                                                                       <  1:1807/149‑1 (MQ=35)                                             tAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGt                                                                                                    >  1:445619/1‑149 (MQ=35)                                                  cGGATAAGGCACTTGCGCCGCAGCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGt                                                                                               <  2:283020/149‑1 (MQ=18)                                                   ggATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTc                                                                                              <  1:467122/149‑1 (MQ=33)                                                    gatgcggCACAAGTGCCTTATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGtat                                                                                             >  2:331521/6‑147 (MQ=11)                                                    gATAAGGCACTTGTGCCGCATCCGGCAATACCTACCTCATGCGACGCTGTCGCGTCTTATCAGGCCTCCAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTCTCGCGCCt                                                                                             >  1:125621/1‑149 (MQ=11)                                                        aGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATc                                                                                         >  1:169978/1‑149 (MQ=32)                                                        aGGCACTTGCGCCGCATCCGGCAATCAATGCCTGATGCGGCGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATACGGATCTTAATGTTTGATGCGACGCTGTCGCGTCTTATc                                                                                         <  1:125719/149‑1 (MQ=11)                                                          ccagctgtgCCGCAACCAGCAATCAAAGCCTGATGCGACGGTGTCGCCTCTTATCAGGCCTACAACTATGCCCGACCTGTAGGCCAGAGAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAg                                                                                       <  2:98125/144‑1 (MQ=11)                                                                   ccGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCATTGCCTGATGCGACGCTGGCCCGTCTTATCAGGCCTACCAc                                                                              >  1:172476/1‑149 (MQ=255)                                                                         ccGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGc                                                                        <  1:373900/149‑1 (MQ=32)                                                                           ggCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCCGTCGCGTCTTATCAGGCCTACAACTGTTGCCg                                                                      >  2:107999/1‑149 (MQ=17)                                                                             caatcaatGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCAGAACCGCAGAGCGGATAAAAAACTCGTGCCGCATCCGGCACTCAATCCCTGATGGGACGCTGTCGCGTCTTATCAGACCTACAACTTTTGCCGag                                                                    >  1:382067/1‑148 (MQ=11)                                                                                   atGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAg                                                              <  1:468429/149‑1 (MQ=34)                                                                                         gATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGcaatcaat                                                                                                                     <  2:215784/88‑1 (MQ=35)                                                                                         gATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGcaatcaat                                                                                                                     >  1:215784/1‑88 (MQ=35)                                                                                             cGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAg                                                    <  1:367211/149‑1 (MQ=35)                                                                                              gACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGCCCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAgg                                                   >  2:453783/1‑149 (MQ=25)                                                                                              gACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCa                                                                                        >  1:303986/1‑112 (MQ=33)                                                                                              gACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCa                                                                                        <  2:303986/112‑1 (MQ=33)                                                                                              gACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGcc                                                           >  1:287160/1‑141 (MQ=35)                                                                                              gACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGcc                                                           <  2:287160/141‑1 (MQ=35)                                                                                              gACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAgg                                                   <  1:197051/149‑1 (MQ=35)                                                                                               aCGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGgc                                                  <  2:181549/149‑1 (MQ=35)                                                                                                 gCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAAGCACTTGTGCCGCCTCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCCAAGGCCGGCTCAGgcgc                                                >  2:355812/1‑149 (MQ=11)                                                                                                      cgcgTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTcgcg                                           <  1:332756/149‑1 (MQ=255)                                                                                                              aTCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGc                                                                                                                                      <  1:369389/50‑1 (MQ=40)                                                                                                               tCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACCACTGTTGCCGACCCGTCGGCCGGATAAGGCGCTCGCGCCCCATCCg                                  >  2:90668/1‑149 (MQ=255)                                                                                                               tCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTCGGCCGGATCAGGCGCCCGCGCCGCCTCCg                                  >  2:368813/1‑149 (MQ=255)                                                                                                               tCAGGCCTACAACTATGGCCGACCTGTAGGCCGGATAAGGCATTAGTGTCGCTTGCTGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCg                                  <  1:146165/149‑1 (MQ=14)                                                                                                                cAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCCGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCgg                                 <  1:107999/149‑1 (MQ=255)                                                                                                                  ggCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCggac                               >  1:338054/1‑147 (MQ=255)                                                                                                                   gCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCCCGCGCCGCATCCGGCAg                              >  1:20468/1‑149 (MQ=255)                                                                                                                            tATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGAGCGGCATCCGGCAGTGCTTAccc                     >  2:285168/1‑149 (MQ=255)                                                                                                                              tggCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCcgc                   <  1:689/147‑1 (MQ=255)                                                                                                                                  cGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGAcc                                                                   <  1:371693/97‑1 (MQ=33)                                                                                                                                   gACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCTCGTCTTATCAGGCCTACAACTGTTGACGAAGCGTGTGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGa              <  1:101456/149‑1 (MQ=18)                                                                                                                                    acttGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGAc             <  2:436543/146‑1 (MQ=255)                                                                                                                                         tAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAg                                                    <  1:136991/105‑1 (MQ=38)                                                                                                                                           ggCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTAGCGTCTTAGCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGCTAAGGCGCTCGCGCCGCATCCGGCAATGTTTACCCGCGGCGACTCAAAAt      >  1:406329/1‑149 (MQ=255)                                                                                                                                               ggATAAGGCACTTGTGCCGCCTCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAAtttct  <  1:164957/149‑1 (MQ=255)                                                                                                                                               ggATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAAtttct  <  2:425540/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                  CGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCT  >  NC_000913_3_pae_pgi/4094457‑4094747

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ 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.