New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	1954429 =	NA (NA)	6 (0.150)	6/272	4.6	10.9%	noncoding (1/98 nt)	RIP139 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP139 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913_3_pae_tpiA	2236680 =	49 (1.250)					noncoding (147/150 nt)	REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCATCAGGCAGCTTTACGTTTGCATAACCTCAGCGCCCGTTTCCGGGCGCTATTCACGT  >  NC_000913_3_pae_tpiA/1954283‑1954576                                                                                                                                                   |                                                                                                                                                    aagaGCAGCGACGCACCGAATGGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGcc                                                                                                                                                   >  1:426806/1‑149 (MQ=255)      cagcGACGCACCGAATTGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCAACTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATg                                                                                                                                              <  2:4228/149‑1 (MQ=255)         cGACGCACCGAATGGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACGTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATgcgg                                                                                                                                           <  2:120108/149‑1 (MQ=255)             gCACCGAATGGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTg                                                                                                                                       >  1:162038/1‑149 (MQ=255)               aCCGAATGGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGaa                                                                                                                                     <  1:101789/149‑1 (MQ=255)               aCCGAATGGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGaa                                                                                                                                     <  2:162038/149‑1 (MQ=255)                  gAATGGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTTAAGGTCTGGTGTTACTGCGGGTTGCGGCGTGAACGc                                                                                                                                  >  1:252892/1‑149 (MQ=255)                        atggTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGCAGGTTATCCGTCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGGAAAGGTCTGGGTTTACTGCCGGTTGCGGCGTGAACGCCTTagc                                                                                                                            >  1:355277/1‑147 (MQ=255)                             tACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATAAGGCGTTCACGCCGCATCCGGca                                                                                                                       <  2:460473/149‑2 (MQ=255)                             tACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCGAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGcc                                                                                                                       >  2:134749/1‑149 (MQ=255)                               ccGGATCTCTGGCCGATTTCCTCGACCCCCATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTa                                                                                                                     <  1:343488/149‑1 (MQ=255)                                cGAATCGGGGGCCGATTTCCTGGACCCACATGATCCGGGTAAAACGGTGGAGGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGTGGCGTGAACGCCGTCTCCGTccgtc                                                                                                                    >  2:577245/1‑146 (MQ=255)                                    tCGCAGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAAAGCGCGGTGCTGATTGCGAGCAAGCCGTAAAGGTCTGCTAATACTGCCGGATGCGCCATGCACGCCTTGTCCGGCCGACaaca                                                                                                                >  2:105752/1‑147 (MQ=255)                                        tGGCCGCTTTCCTCGACCCACATGTTCCGGGTAAAACGGCGGCAGGTTATACGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGACTGGGATTACTGCCGGATGCCGCGTGAACCCCTTATCCGACCTACAACACCtt                                                                                                            >  2:468558/1‑149 (MQ=255)                                        tGGCCGATTTCGTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCtt                                                                                                            >  1:456551/1‑149 (MQ=255)                                          gCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGc                                                                                                                        >  1:299431/1‑135 (MQ=255)                                          gCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGc                                                                                                                        <  2:299431/135‑1 (MQ=255)                                               ttgccTCGACCCAGATTATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAAGCTTGCTAAtt                                                                                                     <  1:701320/146‑1 (MQ=255)                                                    tCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGGCTCCCAAACCTTGCTAATACAata                                                                                                >  2:183158/1‑149 (MQ=255)                                                    tCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAat                                                                                                 >  2:10886/1‑148 (MQ=255)                                                    tCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAat                                                                                                 <  1:10886/148‑1 (MQ=255)                                                       aCCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAatatat                                                                                             >  2:10489/1‑149 (MQ=255)                                                        cccACATGATCCGGGTAAAACGGTGGAAGGTTATACGGCACCTAAACGCGCGGTGCTGAGTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATAtt                                                                                            <  2:348372/149‑1 (MQ=255)                                                         ccACATGATCCGGGTAAAACGGTGGGAGGTTATCCGGCACCTAAACTCGCGGTGCTGATTGCGCGCGAGCCGTAAAGGTCTGGTGTTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTAGAAAACCTTGCTACTTCAAAATATTg                                                                                           >  1:652665/1‑149 (MQ=38)                                                         ccACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTg                                                                                           >  2:394099/1‑149 (MQ=255)                                                         ccACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTg                                                                                           >  1:303859/1‑149 (MQ=255)                                                           acaTGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCa                                                                                         <  1:148696/149‑1 (MQ=255)                                                             atcaTCCGGGTAAAAGGGTTTAAAGTTATCCGGGACCTAAACCGGCGGTGCTTATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGTCCTACAAAACCTTGCTAATTCAATATATTGCAgg                                                                                       <  2:441145/146‑1 (MQ=25)                                                               gATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGa                                                                                     <  2:456551/149‑1 (MQ=255)                                                                aTCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGAc                                                                                    <  1:644815/149‑1 (MQ=255)                                                                 tCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACt                                                                                   >  2:457097/1‑149 (MQ=255)                                                                     ggTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGTGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTCTGt                                                                               >  2:244568/1‑149 (MQ=255)                                                                     ggTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATGTTGTAGGGACTATGt                                                                               <  1:456703/149‑1 (MQ=255)                                                                      gTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTa                                                                              >  1:193321/1‑149 (MQ=255)                                                                          aaCGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGcc                                                                          >  2:94981/1‑149 (MQ=255)                                                                                ggAAGGTTATCCGGCACCTAACCGCGCGGGGATGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATaa                                                                    <  1:183158/149‑1 (MQ=255)                                                                                     gTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCCGGGACTCTGTAGGCCTGTTAACCATa                                                               >  1:72049/1‑149 (MQ=255)                                                                                     gTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATa                                                               >  1:308222/1‑149 (MQ=255)                                                                                        aTCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAgcg                                                            <  1:404218/149‑1 (MQ=255)                                                                                           cGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCAt                                                         >  2:649060/1‑149 (MQ=255)                                                                                                 cTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTCTCCGGCCTACAAAACCTTGCTAGTTCAATATATTTCCGGGACTATGTAGGCCTGATCAGCTTAGCGCCTCAGGcg                                                   >  2:20509/1‑148 (MQ=25)                                                                                                        cgcgGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCATCAGGCAGCTTTAc                                            >  1:259326/1‑149 (MQ=255)                                                                                                            gTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCATCAGGCAGCTTTACGttt                                        >  1:450186/1‑149 (MQ=255)                                                                                                            atgtcgATGGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAGGGCATTATCCGTCCCACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCATCAGGCAGCTTTACGttt                                        <  2:443015/144‑1 (MQ=25)                                                                                                                   ttGCGCGCAAGCCGTAAAGGTCTGGTATTACTAAAAGCGAAGGGGGAAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTAGGTAGGCCTGATAAGCATAACGCATCAGGCAGCTTGACGATTGCATAAc                                 >  1:358498/1‑149 (MQ=18)                                                                                                                       gcgcAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAgcgc                                                           <  1:625213/119‑1 (MQ=255)                                                                                                                       gcgcAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAgcgc                                                           >  2:625213/1‑119 (MQ=255)                                                                                                                         gcAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACACCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTCTGTAGGCCTGATACGCATAGCGGCTCAGGCAGCTTTACGTTTGCATAACCTCAgc                           >  1:318217/1‑149 (MQ=25)                                                                                                                                     ggTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCATCAGGCAGCTTTACGTTTGCATAACCTCAGCGCCCGTTTCCgg               <  2:426806/149‑1 (MQ=255)                                                                                                                                      ggcTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCATCAGGCCGCTTTCCGTTTGCATCACCTCAGCGCCCGTTTCCggg              <  1:331447/147‑1 (MQ=255)                                                                                                                                               tACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCATCAGGCAGCTTTACGTTTGCATAACCTCAGCGCCCGTTTCCGGGCGCTATTCa     <  2:303859/149‑1 (MQ=255)                                                                                                                                                taggCCGGATAAGGCGTTCACGCCGCATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCATCAGGCAGCTTTACGTTTGCATAACCTCAGCGCCCGTTTCCGGGCGCTAt        <  2:106989/142‑1 (MQ=37)                                                                                                                                                  tGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCATCAGGCAGCTTTACGTTTGCATAACCTCAGCGCCCGTTTCCGGGCGCTATTCACGt  >  1:46342/1‑149 (MQ=255)                                                                                                                                                  tGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCATGATAAGCATAGCGCATCAGTCAGCTGTACGTTTGCATAACCTCAGCGCCCGTTTCCGGGCGCTATTCACgc  >  2:263073/1‑148 (MQ=255)                                                                                                                                                   |                                                                                                                                                    AAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAAACCTTGCTAATTCAATATATTGCAGGGACTATGTAGGCCTGATAAGCATAGCGCATCAGGCAGCTTTACGTTTGCATAACCTCAGCGCCCGTTTCCGGGCGCTATTCACGT  >  NC_000913_3_pae_tpiA/1954283‑1954576

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.