New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1552327	NA (NA)	4 (0.110)	4/272	4.8	NA	noncoding (79/97 nt)	RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913_3_pae_tpiA	2549473 =	NA (NA)					noncoding (8/98 nt)	RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
Rejected: Coverage evenness skew score above cutoff.

TCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGACACATCCACTGTTTTTTCTGCCTCTGCCAGACTCCAGGCGTTT  >  NC_000913_3_pae_tpiA/1552184‑1552470                                                                                                                                                 |                                                                                                                                                ttaGTTTCAAATGGCGCGGTAAAAGGCGTCATTTTCATATTGTAGAAAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGc                                                                                                                                             <  2:495800/147‑1 (MQ=255)                      aaaGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGGAGGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGc                                                                                                                       >  1:184174/1‑149 (MQ=17)                          gCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGttt                                                                                                                   <  1:910/149‑1 (MQ=32)                                     atatTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTc                                                                                                        <  1:208935/149‑1 (MQ=11)                                         tGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTaaa                                                                                                    <  2:565536/149‑1 (MQ=33)                                           tAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGACTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCATAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATg                                                                                                  <  1:214882/149‑1 (MQ=25)                                            aGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGACTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATgg                                                                                                 <  1:425939/149‑1 (MQ=25)                                                               cATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCACTTTATAAAGCGCCAtt                                                                              <  2:94867/149‑1 (MQ=255)                                                                 tGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCAtttt                                                                            >  2:512978/1‑149 (MQ=255)                                                                   ccGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGCTTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCAtttttt                                                                          >  1:176138/1‑149 (MQ=255)                                                                   ccGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCAtttttt                                                                          >  2:510671/1‑149 (MQ=255)                                                                    cGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCAttttttt                                                                         <  1:510671/149‑1 (MQ=255)                                                                     ggAAGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTa                                                                        <  2:600161/149‑1 (MQ=255)                                                                          cggcgTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCCAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCg                                                                   >  1:538715/1‑149 (MQ=255)                                                                              gggAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAAc                                                               <  2:282740/147‑1 (MQ=255)                                                                                    gCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAAACg                                                         >  2:259023/1‑149 (MQ=255)                                                                                       ttATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCg                                                      <  1:223340/149‑1 (MQ=255)                                                                                            cGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTAtt                                                                      >  1:183803/1‑128 (MQ=255)                                                                                            cGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTAtt                                                                      <  2:183803/128‑1 (MQ=255)                                                                                                aTGAAAACCCTTC‑AACACCAATAGATTCCAGTCAACGTGTAAGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATACAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGa                                             <  1:536206/149‑1 (MQ=21)                                                                                                     aaCCCTTT‑AAAGCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTGATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGACACAt                                        <  2:421605/149‑1 (MQ=255)                                                                                                      aCCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGACACATc                                       <  1:534411/149‑1 (MQ=255)                                                                                                                 tCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGacac                                          >  1:63458/1‑136 (MQ=255)                                                                                                                 tCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGacac                                          <  2:63458/136‑1 (MQ=255)                                                                                                                   cAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGAAGCGCATCAGACAATGTTGCGTTTGTCATCGGTTCTAAATGGCGCTTTATAAAGCTCCATTTTTTTATTGCGTAACCACACGGCCTAATCGGCACACTTCCACTGTTTTTtc                           >  2:313022/1‑149 (MQ=21)                                                                                                                    aaTAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGATTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGACACATCCACTGTTTTTtct                          >  1:59879/1‑149 (MQ=255)                                                                                                                               gTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGGCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGACACATCCACTGTTTTTTCTGCCTCTGCCAg               >  1:449886/1‑149 (MQ=255)                                                                                                                                tGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCCAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGACACATCCACTGTTTTTTCTGCCTCTGCCAGa              <  2:538715/149‑1 (MQ=255)                                                                                                                                            ccTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGACACATCCACTGTTTTTTCTGCCTCTGCCAGACTCCAGGCGttt  >  2:294554/1‑149 (MQ=255)                                                                                                                                                aTAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGACACATCCACTGTTTTTTCTGCCTCTGCCAGACTCCAGGc      >  1:615797/1‑141 (MQ=255)                                                                                                                                                aTAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGACACATCCACTGTTTTTTCTGCCTCTGCCAGACTCCAGGc      <  2:615797/141‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                TCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTC‑AAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGCGACACATCCACTGTTTTTTCTGCCTCTGCCAGACTCCAGGCGTTT  >  NC_000913_3_pae_tpiA/1552184‑1552470

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.