New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	= 1552283	24 (0.960)	3 (0.130)	3/262	3.2	11.8%	noncoding (35/97 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_vch_tpiA	3676223 =	23 (1.010)					noncoding (103/161 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.
Rejected: Frequency below/above cutoff threshold.

GCGACATCAGTCGTTGTAATAAGAGTGAAAAGCCTGATGCGCTACGCTTATCAGGCCTGAATTTCCATACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGACACTGATTAGCCTCCCCTTCGGAAGGTGAGATCAGTGCCAGTAACGCCG  >  NC_000913_3_vch_tpiA/3676090‑3676369                                                                                                                                      |                                                                                                                                                   gcgACATCAGTCGTTGTAATAAGAGTGAAAAGCCTGATGCGCTACGCTTATCAGGCCTGAATTTCCATACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGcc                                                                                                                                     >  1:89143/1‑149 (MQ=255)                   ataaGAGTTAAAAGCCTGATGCGCTACGCCTATCAGGCCTGAATTTTCATACAATATATTTCATTAGCAAGGAATTGCAGGTCCGAGAAGTCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGttt                                                                                                                   <  2:331135/149‑1 (MQ=25)                       gagTGAAAAGCCTGATGCGCTACGCTTATCAGGCCTGAATTTCCATACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACaaa                                                                                                                                                 >  2:300245/1‑115 (MQ=255)                       gagTGAAAAGCCTGATGCGCTACGCTTATCAGGCCTGAATTTCCATACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACaaa                                                                                                                                                 <  1:300245/115‑1 (MQ=255)                          tGAAAAGCCTGATGCGCTACGCTTATCAGGCCTGAATTTCCATACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGcc                                                                                                            >  1:241689/1‑149 (MQ=255)                           gAAAAGCTTTATGTGCTACGTTTATCAGGCCTGAATTTCCATACAATATATTGAAGTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTACATCTGTTTAATTGCCg                                                                                                           <  1:43914/149‑1 (MQ=25)                             aaaGCCTGATGCGCTACGCTTATCAGGCCTGAATTTCCATACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGa                                                                                                         <  2:293572/149‑1 (MQ=255)                                  cTGATCCGCTACTCTTATCAGGTCTGAATTTCCATACAATATATTGAATTCGCAATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATTCGGCATGAACAAAGCCCACTTTGCTAACAATCGAAATCTGTTTAATTGCCGGATGTCa                                                                                                    <  2:247145/149‑1 (MQ=25)                                         gcTACGCTTATCAGGCCTGAATTTCCATACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCACCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATcc                                                                                             <  1:91796/149‑1 (MQ=255)                                           tACGCTTATCAGGCCTGAATTTCCATACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCgg                                                                                           >  1:87877/1‑149 (MQ=255)                                                   tCAGCCATGAATTTCCATACAATATATTGAATTAGAAAGGATTTGTACGCCGGATAAGTCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTatc                                                                                   <  1:9863/149‑1 (MQ=37)                                                         cTGAATTTCCATACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCAct                                                                             >  2:211994/1‑149 (MQ=255)                                                                    tACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTaaa                                                                                                                          <  2:75900/93‑1 (MQ=255)                                                                    tACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTaaa                                                                                                                          >  1:75900/1‑93 (MQ=255)                                                                                  ttCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCAGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTccc                                                    >  1:11179/1‑148 (MQ=255)                                                                                     gCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTACATCTGCGACAAAATAGTCCGaca                                                 >  1:395902/1‑149 (MQ=255)                                                                                     gCAAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCAGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGaca                                                 <  1:183095/149‑1 (MQ=255)                                                                                     gCAAGAATTTGGAGGCCGAATAAGGCGTTCACGCCGCATCCGGGATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGaca                                                 <  1:69219/149‑1 (MQ=255)                                                                                       aaGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGACACt                                               >  2:289575/1‑149 (MQ=255)                                                                                         ggATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGACACTGa                                             >  1:298382/1‑149 (MQ=255)                                                                                                                gggaCGCCGCATCCGGCATGAACAAAGCACACTGTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGACACTGATTAGCCTCCCCTTCGGAAGGTga                      <  2:89143/146‑1 (MQ=255)                                                                                                                     gccgcATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGACACTGATTAGCCTCCCCTTCGGAAGGTGAGATCa                 <  2:298382/149‑1 (MQ=255)                                                                                                                       cgcATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTTCGACAAAATCGTCCGACACTGATTAGCCTCCCCTTCGGAAGATGAAATCAGt               >  1:300649/1‑149 (MQ=255)                                                                                                                                   gAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGACACTGATTAGCCTCCCCTTCGGAAGGTGAGATCAGTGCCAGTAAcgcc   <  2:241689/149‑1 (MQ=255)                                                                                                                                    aaCAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGACACTGATTAGCCTCCCCTTCGGAAGGTGAGATCAGTGCCAGTAAcgccg  >  1:248220/1‑149 (MQ=255)                                                                                                                                    aaCAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGACACTGATTAGCCTCCCCTTCGGAAGGTGAGATCAGTGCCAGTAAcgccg  >  1:247690/1‑149 (MQ=255)                                                                                                                                      |                                                                                                                                                   GCGACATCAGTCGTTGTAATAAGAGTGAAAAGCCTGATGCGCTACGCTTATCAGGCCTGAATTTCCATACAATATATTGAATTCGCAAGGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCAGACATCCGGCAATTATCATCACTTCTTCATCTGCGACAAAATCGTCCGACACTGATTAGCCTCCCCTTCGGAAGGTGAGATCAGTGCCAGTAACGCCG  >  NC_000913_3_vch_tpiA/3676090‑3676369

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.