New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 707781	52 (0.860)	5 (0.090)	5/266	7.6	9.6%	noncoding (12/165 nt)	RIP63 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site	RIP63 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site
	?	NC_000913_3_pae_tpiA	= 707795	46 (0.820)					noncoding (26/165 nt)	RIP63 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site	RIP63 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GTAAAGCATTCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGT  >  NC_000913_3_pae_tpiA/707633‑707918                                                                                                                                                     |                                                                                                                                          gTAAAGCATTCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGCGTAATTTGGAGGTTCGCTATGCCGGATg                                                                                                                                           >  2:479377/1‑149 (MQ=255)  tAAAGCATTCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCTCCATTCTACGGCGGAAAAACCGGTATTTAACAGCACCGTTGGGCTGCGTGATACCTGCGCGAAAGTAGGCGAGTAGTTTTAAGTTTCGCTATGCCGGATgg                                                                                                                                          <  1:800972/149‑1 (MQ=255)  tAAAGCATTCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTCTGCCGGATgg                                                                                                                                          >  1:738870/1‑149 (MQ=255)   aaaGCATTCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATggg                                                                                                                                         <  2:345966/149‑1 (MQ=255)        aTTCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGtt                                                                                                                                    <  1:485251/149‑1 (MQ=255)         ttCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGttt                                                                                                                                   <  2:590185/149‑1 (MQ=255)          tCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTa                                                                                                                                  >  1:974334/1‑149 (MQ=255)            cAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGAGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACg                                                                                                                                >  2:660399/1‑149 (MQ=255)             aGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGt                                                                                                                               >  1:539352/1‑149 (MQ=255)                        gAAGGTTACTTCTGGCTCGATAGCCGACATTCTACGGCGGAAACAGCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGTCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGCGACGTAAACGCCCCATCCGGCa                                                                                                                    <  1:913369/149‑1 (MQ=255)                         aaGGTTACTTCTGCCTTGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGGTGGGCTGCGTGAGACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCaa                                                                                                                   <  1:479377/149‑1 (MQ=255)                         aaGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCaa                                                                                                                   <  2:382359/149‑1 (MQ=255)                            gTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGCTGGGGCGTTTACGTCGCATCCGGCAAGGa                                                                                                                >  2:241112/1‑149 (MQ=255)                            gTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAggc                                                                                                                >  2:242597/1‑148 (MQ=255)                            gTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTGAAGGTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGa                                                                                                                >  1:871223/1‑149 (MQ=255)                                 ttCTGCCTCGATCGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAAGAACAGa                                                                                                           >  2:915219/1‑149 (MQ=255)                                 ttCTGCCCCGAGCGCCGCGATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGa                                                                                                           >  2:915210/1‑149 (MQ=255)                                    tGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTCGGCTGCGTGATACCTGAGCGGAAGTAGGCGAGTAATTTGAAGTTTCGCTATGCCGGATGGAGAGTTTACGTCCCATCCGGCCAGCAACAGACaa                                                                                                        >  2:143545/1‑149 (MQ=255)                                      ccTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGTTGGGGCGTTTACGTCGCATCCGGCAAGGGACAGACAAAc                                                                                                      >  1:41768/1‑149 (MQ=255)                                      ccTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAAc                                                                                                      >  1:990719/1‑149 (MQ=255)                                       gtCGTTAGCCGCCATTGTACTGCGGAAAACCCGGTATTTAACCTCACCGTTGGGCCCAGCGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTCCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACa                                                                                                     <  2:337755/148‑1 (MQ=255)                                       cTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGTGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGGTTACGTCCCATCCAGCAAAGAACAGCCCAACa                                                                                                     >  2:261161/1‑149 (MQ=255)                                           aTAGGCGCCATTCTACGGCGGAAACACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGttt                                                                                                 <  1:868884/149‑1 (MQ=255)                                           aTAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGttt                                                                                                 >  1:668268/1‑149 (MQ=255)                                           aTAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGttt                                                                                                 <  1:52749/149‑1 (MQ=255)                                               ccgccATTCTGCGGCGGAAAACACGGTATTTAACCGCACCGTTGGGCTGCGTGACGCCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCaaa                                                                                             <  2:958648/149‑1 (MQ=255)                                                cgccAGTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTTGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAAc                                                                                            <  1:130810/149‑1 (MQ=255)                                                 gccATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACg                                                                                           >  2:1047977/1‑149 (MQ=255)                                                         aCGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTg                                                                                   >  1:578198/1‑149 (MQ=255)                                                             cggAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCCAGGAACAGACAAACAGTTTCAAACGCTAAATCGCCTg                                                                               >  2:371515/1‑149 (MQ=255)                                                                     ccGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTa                                                                       <  1:240994/149‑1 (MQ=255)                                                                       ggTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGt                                                                                                                                     <  1:187909/85‑1 (MQ=255)                                                                       ggTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGt                                                                                                                                     >  2:187909/1‑85 (MQ=255)                                                                        gTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACCGACAAACAGTTTCAAAAGCTAAATTGCCTGATTCGCTACGc                                                                    >  2:614915/1‑149 (MQ=255)                                                                             tAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATc                                                               <  2:366510/149‑1 (MQ=255)                                                                              aaCCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCa                                                              <  1:714844/149‑1 (MQ=255)                                                                               aCCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAg                                                             <  1:388983/149‑1 (MQ=255)                                                                                  gtttaggtGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTTTGCCGGATGTGGCGTTTACGTCGCATACGGTAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCGTTTTGCGCTACGCTTTTCAGGcc                                                          >  2:972717/8‑149 (MQ=255)                                                                                  gCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGGAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAACGAACAGACAAACAGTTTCAAACGCTCAACTGCCTGATGCGCTCCGCTTCTCCGGcc                                                          >  2:984553/1‑149 (MQ=255)                                                                                   gaCCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTGAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAGGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCt                                                         >  2:39579/2‑149 (MQ=255)                                                                                   cACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCACTACGCGTATCAGGCCt                                                         >  1:542914/1‑149 (MQ=255)                                                                                          gggCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATggt                                                  >  1:41668/1‑147 (MQ=255)                                                                                              tGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTCCATGATctct                                              >  1:232782/1‑149 (MQ=255)                                                                                                  tGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCaa                                          >  2:664895/1‑149 (MQ=255)                                                                                                  tGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCaa                                          <  2:974334/149‑1 (MQ=255)                                                                                                        cTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTCCATCATCTCTGACACATAtt                                    >  2:254372/1‑149 (MQ=38)                                                                                                        cTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCaa                                          <  1:299246/143‑1 (MQ=255)                                                                                                        cTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCaa                                          >  2:299246/1‑143 (MQ=255)                                                                                                         tGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTg                                   >  1:826196/1‑149 (MQ=255)                                                                                                           ggCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAg                                 <  2:503283/149‑1 (MQ=255)                                                                                                                  gTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATTCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGt                          >  2:657906/1‑149 (MQ=255)                                                                                                                           tAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAGACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATCTATTGAGTTTGCGTGCTTATGTa                 >  1:889133/1‑149 (MQ=255)                                                                                                                           tAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCCCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTa                 <  1:371515/149‑1 (MQ=255)                                                                                                                                          cTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGt  >  1:533471/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                          GTAAAGCATTCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGT  >  NC_000913_3_pae_tpiA/707633‑707918

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.