New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	2549484 =	NA (NA)	5 (0.130)	5/272	5.0	NA	noncoding (19/98 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
	?	NC_000913_3_pae_tpiA	3676128 =	NA (NA)					noncoding (8/161 nt)	RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site	RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site
Rejected: Coverage evenness skew score above cutoff.

GTCAGTTGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAAT  >  NC_000913_3_pae_tpiA/2549339‑2549632                                                                                                                                                  |                                                                                                                                                     gTCAGTTGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCa                                                                                                                                                   <  1:648245/149‑1 (MQ=255)      ttGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCt                                                                                                                                              >  2:212637/1‑149 (MQ=255)        gCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTAc                                                                                                                                            >  1:45261/1‑149 (MQ=255)          cGATTGTAACTTATGGATGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGt                                                                                                                                          <  2:31047/149‑1 (MQ=255)             ttGCAACTTCTGGTTGGGGAGTTGATCAGGTTTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGCTCTGAGAGTGCTGACAAACGCAGAAATGCCTGATCCGCTACGCTTATCGGGCCTGCGTgca                                                                                                                                       >  2:250595/1‑147 (MQ=255)                cAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGACTGTTGCGTTACGCTTATCAGGCCTACGTGGAGcc                                                                                                                                    <  1:713473/149‑1 (MQ=255)                   cTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCcac                                                                                                                                 >  1:150209/1‑149 (MQ=255)                        ggTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAatat                                                                                                                            <  1:686266/149‑1 (MQ=255)                              ggaGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGaa                                                                                                                      <  1:332859/147‑1 (MQ=255)                                 gTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAATCCCCCCGATTCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTa                                                                                                                   >  1:500709/1‑149 (MQ=39)                                                   gggtgaaaGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCg                                                                                                 <  1:190066/144‑1 (MQ=255)                                                           gCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGc                                                                                         >  1:488684/1‑149 (MQ=255)                                                           gCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGc                                                                                         >  1:488688/1‑149 (MQ=255)                                                           gCAGAAGTAATAAAAAGGCCAATACGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGAGCTACGCTTATCAGGCCTACGCGGAGCACACAATATATTGAACTAACACGATTTCGCAGGCCCGATACGGc                                                                                         >  2:413018/1‑149 (MQ=25)                                                            cAGAAGTAATAAAAAGACCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGCCg                                                                                        >  2:712872/1‑149 (MQ=255)                                                                    ataaAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCAcccc                                                                                >  2:293023/1‑149 (MQ=255)                                                                               agtcagtAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCGCGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCgt                                                                     <  2:45261/149‑1 (MQ=255)                                                                               agtcagtAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCgt                                                                     <  2:257508/149‑1 (MQ=255)                                                                                          ttACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTACCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAAAATATTAAATTAGCACGATTTCGTAGGCCGGCTAAAGCCTTCACGCCGCCTCCGGCGTGTACACCccgc                                                          >  2:307345/1‑149 (MQ=21)                                                                                              tggctggTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACtt                                                      >  1:46234/1‑149 (MQ=255)                                                                                                 ctggGCTGAGAGTGCTGACAAACGCAAAACTGTCTTGTGCGCTAGGCTTATCAGGACTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGt                                                   <  1:212637/149‑1 (MQ=21)                                                                                                  tggTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTgg                                                    >  2:448068/1‑147 (MQ=255)                                                                                                  tggTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTgg                                                    <  1:448068/147‑1 (MQ=255)                                                                                                     tCTGAGAGTGCTGCCAAACGCAAAACCGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCAGCCGGCGTGTACAACGCGCAGTTGGTcatc                                               >  1:592311/1‑147 (MQ=255)                                                                                                             tGCTGATAAACGCAAAACTGCCGGATTGGTTAGGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAg                                       <  1:258724/149‑1 (MQ=21)                                                                                                               cTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTTAGGc                                     >  1:39220/1‑149 (MQ=255)                                                                                                               cTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGc                                     >  1:101238/1‑149 (MQ=255)                                                                                                                tGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACACGCACTTGGTCAACACTCTGAGGcc                                    >  1:708264/1‑149 (MQ=255)                                                                                                                  aCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGGCGCATCCGGCGTGTACATCGCGCACTGGGGCAACAATCTGAGGCcag                                  >  1:636254/1‑149 (MQ=255)                                                                                                                    aaaCGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCcagtc                                >  1:58268/1‑149 (MQ=255)                                                                                                                    aaaCGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCcagtc                                >  2:391683/1‑149 (MQ=255)                                                                                                                      ccGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGTATTAGCACGATTTCGTAGGTCGGATAACGCGTTATCGCCGCATCAGGCGTGTACAACGCGCACTTGGTAAACAATATGAGGCcaggaag                              >  2:549057/2‑145 (MQ=21)                                                                                                                        gCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTa                            >  1:642729/1‑149 (MQ=255)                                                                                                                        gCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGACGTTCAAGCCGCATCCGGCGTGTCCAACCCGCCCTTGGTCAACAATCCGAGGCCAGCCAGTa                            >  2:133441/1‑149 (MQ=21)                                                                                                                            aaCTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTTAGGCCAGTCAGTAATGt                        <  2:39220/149‑1 (MQ=255)                                                                                                                                  cTGAAGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGc                  <  1:177967/149‑1 (MQ=255)                                                                                                                                    gATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCACCAATc                                           <  2:626803/122‑1 (MQ=255)                                                                                                                                    gATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATc                                           >  1:626803/1‑122 (MQ=255)                                                                                                                                              tcTTATCAGGCTCACGGGGAGCCCACAATTGTTTGAATTAGCGCGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGTACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAAt      <  2:500709/148‑1 (MQ=37)                                                                                                                                              gCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGAGCACTTGGGCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAAt      >  2:656406/1‑149 (MQ=255)                                                                                                                                                  aTCAGGCGTAGGTGGAGCCCACAAAATAGTTAATTGGGAGGATTTCGGAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAAt  <  2:150209/149‑1 (MQ=37)                                                                                                                                                  aTCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGc                                                                                         >  1:150910/1‑62 (MQ=255)                                                                                                                                                  aTCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGc                                                                                         <  2:150910/62‑1 (MQ=255)                                                                                                                                                  aTCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAAt  <  2:642729/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                     GTCAGTTGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAAT  >  NC_000913_3_pae_tpiA/2549339‑2549632

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.