New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	489979 =	NA (NA)	6 (0.200)	6/272	3.1	19.4%	noncoding (21/98 nt)	RIP43 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP43 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913_3_pae_tpiA	490042 =	25 (0.840)					noncoding (84/98 nt)	RIP43 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP43 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AGGTGACGGAAGTAAAACGCGACTACAAAGGCGATGACCCGACGCCAGCGGTAGGGTAAAAACGAAAGGGGGCAACATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTTAGGGGACATTTAGCGACCCCATTTATTTCTCACTTTTCCGCCTC  >  NC_000913_3_pae_tpiA/489840‑490124                                                                                                                                            |                                                                                                                                                  aGGTGACGGAAGTAAAACGCGACTACAAAGGCGATGACCCGACGCCAGCGGTAGGGTAAAAACGAAAGGGGGCAACATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGc                                                                                                                                          <  1:2212/149‑1 (MQ=255)         gAAGTAAAACGCGACTACAAAGGCGAGGAGCCGACGCCAGCGGTAGGGTAAAAACGAAAGGGGGCAACATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGTGGCGTGACCGCCTTATCCGGCCTACGaaa                                                                                                                                  <  2:227456/149‑1 (MQ=255)                   gcgACTAAAAAGGAGATGACCGGACGACAGGTGTAGGGTAAAAACGAAAGGGGGCAACATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAAt                                                                                                                        <  2:523619/149‑1 (MQ=37)                       cTACAAAGGCGATGACCCGACGCCAGCGGTAGGGTAAAAACGAAAGGGGGCAACATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATTGCGTATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCaa                                                                                                                    <  1:382854/149‑1 (MQ=255)                                       ccGACGCCAGCGGTAGGGTAAAAACGAAAGTGGGCAACATTTAGTTGCCCCGGGGTTGCTAACAAAGTGCGCGTTTTTCATGCCGGCCGCGGCGTGACCGCCTTATCCGGCCTACGACACCGCATGCATTCCATATATTGCCGGCGCgg                                                                                                    >  2:512385/1‑149 (MQ=255)                                         gACGCCAGCGGTAGGGTAAAAACGAAAGGGGGCAACATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGgtg                                                                                                  <  1:492967/149‑1 (MQ=255)                                           cGCCAGCGGTAGGGTAAAAACGAAAGGGGGCAACATTTAGTTGCCCCGAGAATGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTa                                                                                                <  1:155501/149‑1 (MQ=255)                                                      gggAAAAAACGAAAGGGGGCAACATTTAGTTGCCTCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTAGCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAg                                                                                     <  2:438424/149‑1 (MQ=255)                                                         tAAAAACGAAAGGGGGCAACATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCACGAGCGGTGTAGGCCTGATACGCGt                                                                                  >  1:355447/1‑149 (MQ=255)                                                            agaCGAAGGGGGGCAACATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGTAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAgc                                                                               <  1:222332/147‑1 (MQ=255)                                                                  aaGGGGGCAACATTTAGTTGCCCCGCGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGTCCGCCTTATCCGGCCTACGAAACCGCAAGAAGTCAATATATTGCAGGAGCGGTGTAGGCCGGATAAGCGTAGCGCATCa                                                                         >  1:418501/1‑149 (MQ=255)                                                                       ggCAACATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATAAGGCAg                                                                    >  1:135606/1‑149 (MQ=255)                                                                            cATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTg                                                               <  2:311283/149‑1 (MQ=255)                                                                                               tGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAATCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTTAg                                            <  1:490739/149‑1 (MQ=255)                                                                                                  tcaCAAAGTGCTCGTCTCTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAACAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTTAgggg                                         <  1:275623/147‑1 (MQ=21)                                                                                                  tAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTTAgggg                                         >  1:135131/1‑149 (MQ=255)                                                                                                       gatggcgcGTTGTACATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTGAGGGGACAtt                                    <  1:535338/145‑1 (MQ=255)                                                                                                               gttgttCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTTAGGGGACATTTAGCGAcc                            >  2:54103/1‑149 (MQ=255)                                                                                                                      aTGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTCTAGGCCTGATAAGCGCACCCAACCAGTCAGTTTTGCGTTTGCCCGCAACCGTAGGGGACATTTAGCGCCCCCattca                     >  1:265854/1‑147 (MQ=25)                                                                                                                       tGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATACGGCAGTTTTGCGTTTGCCCGCAACCTTAAGGGCCATTTAGCGACCCCatttat                    >  1:114423/1‑149 (MQ=255)                                                                                                                             aTGCGGCGTGACCGCGTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTTAGGGGACATTTAGCGACCCCATTTATTTCTCa              <  2:538049/149‑1 (MQ=255)                                                                                                                                        ccGGCTTATCCGGCCTACGAAACCGCAAGAATTGAATATATTGCAGGAGCTGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTTAGGGGACATTTAGCGACCCCATTTATTTCTCACTTTTCCGCCt   <  2:547110/149‑1 (MQ=255)                                                                                                                                         cggcTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTTAGGGGACATTTAGCGACCCCATTTATTTCTCACTTTTCCGCCtc  <  1:245103/146‑1 (MQ=255)                                                                                                                                         cGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTTAGGGGACATTTAGCGACCCCATTTATTTCTCACTTTTCCGCCtc  >  1:287931/1‑149 (MQ=255)                                                                                                                                            |                                                                                                                                                  AGGTGACGGAAGTAAAACGCGACTACAAAGGCGATGACCCGACGCCAGCGGTAGGGTAAAAACGAAAGGGGGCAACATTTAGTTGCCCCGAGATTGCTAACAAAGTGCGCGTTGTTCATGCCGGATGCGGCGTGACCGCCTTATCCGGCCTACGAAACCGCAAGAATTCAATATATTGCAGGAGCGGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAGTTTTGCGTTTGCCCGCAACCTTAGGGGACATTTAGCGACCCCATTTATTTCTCACTTTTCCGCCTC  >  NC_000913_3_pae_tpiA/489840‑490124

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.