New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 3203173	48 (1.640)	3 (0.110)	3/268	4.0	6.2%	noncoding (30/125 nt)	REP225 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP225 (repetitive extragenic palindromic) element; contains 3 REP sequences
	?	NC_000913_3_pae_tpiA	4285252 =	NA (NA)					noncoding (35/77 nt)	REP320 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP320 (repetitive extragenic palindromic) element; contains 2 REP sequences
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GTTGAAGCGGGATTTAAAGGTGTGGAGATTCGCGAGGAGCTGACCCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGACACTATTCCTCAATTAAAAGAACA  >  NC_000913_3_pae_tpiA/3203025‑3203320                                                                                                                                                     |                                                                                                                                                    gtTGAAGCGGGATTTAAAGGTGTGGGGATTCGCGAGGGGCCGACCCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGc                                                                                                                                                     <  2:429766/149‑1 (MQ=255)  ttGAAGCGGGATTTAAAGGTGTGGAGATTCGCGAGGAGCTGACCCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGca                                                                                                                                                    >  1:9495/1‑148 (MQ=255)   tGAAGCGGGATTTAAAGGTGTGGAGATTCGCGAGGAGCTGACCCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTa                                                                                                                                                   <  1:405782/149‑1 (MQ=255)     aaGCGGGATTTAAAGGTGTGGAGATTCGCGAGGAGCTGACCCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACa                                                                                                                                                 <  1:314199/149‑1 (MQ=255)     aaGCGGGATTTAAAGGTGTGGAGATTCGCGAGGAGCTGACCCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACa                                                                                                                                                 >  1:349740/1‑149 (MQ=255)                 aaGGTGTGGAGATTCGCGAGGAGCTGACCCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAg                                                                                                                                     >  1:375370/1‑149 (MQ=255)                      gtgGAGATTCGCGAGGAGCTGACCCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTa                                                                                                                                <  1:201040/149‑1 (MQ=255)                           gagtCGCGAGGAGCTGACGCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCt                                                                                                                           <  2:178938/146‑1 (MQ=255)                                gcgAGGGGGTGACCCGACGGCGGATTGCGGCGGGAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATaa                                                                                                                      <  1:5277/149‑1 (MQ=255)                                gcgAGGAGCTGAGCCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGCATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAGCGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATaa                                                                                                                      >  1:391864/1‑149 (MQ=255)                                             ccGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGGGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCCCCAGCGt                                                                                                         >  1:50368/1‑149 (MQ=255)                                                aCGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGc                                                                                                      <  2:356519/149‑1 (MQ=255)                                                  ggcggATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCAt                                                                                                    <  1:444560/149‑1 (MQ=255)                                                                    ccAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGa                                                                                  >  1:92676/1‑149 (MQ=255)                                                                           gaaggaaCAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCTTCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATgcggcg                                                                           >  1:359041/1‑149 (MQ=255)                                                                            aaggaaCAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGt                                                                          <  2:375370/149‑1 (MQ=255)                                                                                 acaacGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACg                                                                     <  1:416969/149‑1 (MQ=255)                                                                                      gTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCGGGAGGCGGCGTGAACGCCTTa                                                                >  1:156618/1‑149 (MQ=255)                                                                                           ccAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCgg                                                           >  1:513582/1‑149 (MQ=255)                                                                                            cAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGc                                                          >  2:3344/1‑149 (MQ=255)                                                                                                gCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTAc                                                      <  1:213380/149‑1 (MQ=255)                                                                                                     aaTGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAAt                                                 >  1:324640/1‑149 (MQ=255)                                                                                                      aTGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATc                                                <  1:181148/149‑1 (MQ=255)                                                                                                        gAGTTTTGGGCAGTTTCCGTGATGCGGCGTAATCCCCGTATCCGGCTACATGTCAACGTCAGTTGTAGGCCTGATCAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGt                                              <  2:102000/149‑1 (MQ=21)                                                                                                        gAGTATTGGGCAGTTTGCCGGATGCGGCATAAACGCCTTACCCGCCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGt                                              <  2:102001/149‑1 (MQ=255)                                                                                                         agtaggggggATATTGCCGGATGCGGCGTAAACGGCTTATCCGTCTACAGGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGtt                                             <  2:478419/143‑1 (MQ=21)                                                                                                         aGTATTGGGCATTTGGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGtt                                             <  1:99524/149‑1 (MQ=255)                                                                                                           tATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGa                                           >  1:161922/1‑149 (MQ=255)                                                                                                           tATTGGGCATTTGGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGa                                           <  1:156531/149‑1 (MQ=255)                                                                                                               gggCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAAc                                       >  2:405535/1‑149 (MQ=255)                                                                                                               gggCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAAc                                       >  1:451549/1‑149 (MQ=255)                                                                                                               gggCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGACTGATAGGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAAc                                       >  1:169096/1‑149 (MQ=255)                                                                                                                 gCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGcc                                                                   <  2:156707/119‑1 (MQ=255)                                                                                                                 gCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGcc                                                                   >  1:156707/1‑119 (MQ=255)                                                                                                                    ttttGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCaa                                  >  2:494698/1‑149 (MQ=255)                                                                                                                         ccGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGCCCTACGCAATCGTTGACCACCCCAAGCaac                             >  2:157839/1‑147 (MQ=255)                                                                                                                              tGCGGCGTAAACGCCTTATCCGGCTACGTGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGTCAACGCCAAGCATCCGaca                        <  1:452486/149‑1 (MQ=255)                                                                                                                              tGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGaca                        <  1:3344/149‑1 (MQ=255)                                                                                                                              tGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGaca                        <  2:426923/149‑1 (MQ=255)                                                                                                                                 ggcgTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGGGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGccacca                     >  1:333505/1‑147 (MQ=255)                                                                                                                                   cgTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATCCGAAGCTCGGTCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGACACTAtt                   <  1:505054/149‑1 (MQ=38)                                                                                                                                    ctaaaacccTTATCCGGGTACATGTCCACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCTTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCGACGCAATCGTTGACAACGCCAAGCATCCGACACTATTc                  <  2:156618/142‑1 (MQ=25)                                                                                                                                     ccaccGCTTTCTCCGCCTACCTGTCATCGCCAGTTGTAGCCCTCATACGACGCGCCAGCGCCCCCTCACGCGTTTACTCCCGTTTGCCGCTTGATACCATCCCTCGCCCTACGCAATCGTTGACAACGCCATGCATCCGACACTACTcc                 <  2:250543/145‑1 (MQ=255)                                                                                                                                      aaaaaacTTGTCCGGCTAAATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGACACTATTCCt                <  2:184431/143‑1 (MQ=255)                                                                                                                                        aCGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCCGGCGTCGCAACAAGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACCCAATCGTTGACAACACCAAGCATCCCACACTATTCCTCa              >  1:303835/1‑149 (MQ=37)                                                                                                                                        aCGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTTGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACTCCAAGCATCGGCGTCTATTccata              >  1:418324/1‑146 (MQ=25)                                                                                                                                        aCGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGACACAAATCCTCa              >  1:302745/1‑149 (MQ=255)                                                                                                                                            cTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGACACTATTCCTCAATTa          >  1:253562/1‑149 (MQ=255)                                                                                                                                                  cGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGACACTATTCCTCAATTAAAAGaa    <  1:236950/149‑1 (MQ=255)                                                                                                                                                    gCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGACACTATTCCTCAATTAAAAGAaca  >  1:83775/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                    GTTGAAGCGGGATTTAAAGGTGTGGAGATTCGCGAGGAGCTGACCCGACGGCGGATTGCGGCGGTAGCCAGCTGGAAGGAACAACGTTGCCCAAAGCCTGAATGAGTATTGGGCATTTTGCCGGATGCGGCGTAAACGCCTTATCCGGCTACATGTCAACGACAGTTGTAGGCCTGATAAGACGCGCAAGCGTCGCATCAGGCGTTGATTGCCGGATGCGGCGTGAACGCCTTATTCGGCCTACGCAATCGTTGACAACGCCAAGCATCCGACACTATTCCTCAATTAAAAGAACA  >  NC_000913_3_pae_tpiA/3203025‑3203320

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.