New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	2549534 =	45 (1.420)	4 (0.130)	4/274	4.1	8.5%	noncoding (69/98 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_vch_tpiA	2549564 =	43 (1.430)					noncoding (2549564/4641682 nt)	repeat_region	repeat region
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCATCAACTTGTCCAGCGACGGTGCGAAATAATAGCCGCCGGTTACCGGTTTGGTGA  >  NC_000913_3_vch_tpiA/2549419‑2549710                                                                                                                                                   |                                                                                                                                                   tcagtAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCgtgt                                                                                                                                                 >  1:304817/1‑149 (MQ=255)              tggctggTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCACACAATATATTGAATTAGCACGATTTCG‑TCGGCCGCATACCGCGTTACCGCCGCATCCGCCGTGTACACCGCGCaact                                                                                                                                    >  2:399503/1‑146 (MQ=21)                 ctggTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACACTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGt                                                                                                                                 >  1:422343/1‑149 (MQ=255)                  tggTCTGAGAGTGCTGACAAACGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTc                                                                                                                                >  1:525689/1‑149 (MQ=255)                     tCTGAGAGTGCTGACAAACGCAAAACTGCTTTATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGTCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTcaac                                                                                                                             <  1:474019/149‑1 (MQ=255)                       tGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCCCATCCGGCATGTACAACGCGCACCTGGTcaacaa                                                                                                                           >  2:347060/1‑149 (MQ=255)                        gagaGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAAt                                                                                                                          >  2:424739/1‑149 (MQ=255)                         agagTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATc                                                                                                                         <  1:537161/149‑1 (MQ=255)                            gTGCGGACAAACGCAAAACTGCCTTATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGa                                                                                                                      <  2:150456/149‑1 (MQ=255)                                tGACCAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGAAACCCACAATATAATGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTCGTCAACAATCTGAGGcc                                                                                                                  >  1:415986/1‑149 (MQ=18)                                tGACAAACGCAAAACTACCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAATGCGTTCAAGCCGCATCCGGCCTGTCAAACGACCCCTTCGTCAACACTCTGAGGcc                                                                                                                  >  2:238621/1‑149 (MQ=18)                                    aaaCGCAAAACTGCCTGATGCGCTACGCGTATCAGGCCTACGTAGAGCCAACAATATATTGAATTAAAAC‑ACTCCGTTATTTCTGATAAGGCGTTCCCGCCGACTCGGGGTTGTCCAACGCGCACTTTGTAAACAATCTGAGGCgagtg                                                                                                              >  2:137275/1‑148 (MQ=12)                                      aCGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCA‑TAGACCGGATAAGGCGTTCACAAAGAAACGGAAGTGTACAACGCGCACTTGGACAACAATCTGAGGCcagtcag                                                                                                            >  1:349765/1‑149 (MQ=21)                                          aaaaCTGCTTGATGCTCTACGCTTATTAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAAt                                                                                                        <  1:136332/149‑1 (MQ=255)                                             aCTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGGGCACTTGGGCAACACTCTGAGGCCAGTCGGTCATGtt                                                                                                     >  2:36730/1‑149 (MQ=21)                                                 ccTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTACACGCCGGATGCGGCGTGAAc                                                                                                                                               >  2:538330/1‑103 (MQ=21)                                                 ccTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTACACGCCGGATGCGGCGTGAAc                                                                                                                                               <  1:538330/103‑1 (MQ=21)                                                     aTGCGCTACGCTTATCCGGCGTACGTGGAGCCCATAATGTATTGAATTAGCTCCATTGCG‑TAGGCCGGATAAGGCGTTCACGCCTTATCCTGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTg                                                                                             <  2:253329/149‑1 (MQ=37)                                                         gcTACGCTTATCAGGCCTACGTGGAGCCGACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAATAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCt                                                                                         <  2:92406/149‑1 (MQ=255)                                                           tACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCAGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCAAGTCAGTAATGTTACTGCCTGGACtat                                                                                       >  1:68239/1‑147 (MQ=255)                                                             ggCTTCTCAGGTCTCACTGGAGACCACAATATCTTGATTTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATTCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCATTCAGTAATGTTACTGCCTGGCCTTTaa                                                                                     <  2:28017/148‑1 (MQ=25)                                                              gCTTATCAGGCCTACGTGGAGCCTACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAAt                                                                                    <  1:495847/149‑1 (MQ=255)                                                              gCTTATCAGGCCTACGTGGAGCCCCCACTATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAAt                                                                                    >  1:92014/1‑149 (MQ=255)                                                              gCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAAGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAAt                                                                                    >  1:315698/1‑149 (MQ=255)                                                                  aTCAGGCCTACGTGGATCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAAt                                                                                <  2:304817/149‑1 (MQ=255)                                                                  aTCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAAt                                                                                <  2:525689/149‑1 (MQ=255)                                                                    cAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGa                                                                              <  2:230971/149‑1 (MQ=255)                                                                      cgCCTACGTAGAGCCCACAATTTAGTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAAt                                                                            <  1:36730/148‑1 (MQ=255)                                                                         gtACTTGGAGCCCACTATATATTGCAGTACGACGATTTCG‑TAGGTCGGATAAGGTCTTCACGCCGCATCCGGCGTACACAACGCTCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCTTTTAATCAATGAATCAg                                                                         <  2:253445/148‑1 (MQ=255)                                                                          tACGTGGATCCTACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGACTGGCCTTTACTCAATGAATCAGa                                                                        >  2:50844/1‑149 (MQ=255)                                                                             gTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAAc                                                                     <  1:424739/149‑1 (MQ=255)                                                                                     cacaATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAg                                                             <  2:203509/149‑1 (MQ=255)                                                                                             atTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCATCa                                                     >  1:536304/1‑149 (MQ=255)                                                                                              ttGAATTAGCACGAGTGCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCATCaa                                                    <  2:339968/149‑1 (MQ=255)                                                                                                       cACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCAt                                                       >  1:295468/1‑137 (MQ=255)                                                                                                       cACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCAt                                                       <  2:295468/137‑1 (MQ=255)                                                                                                        aCGATTTCG‑TAGGCCGGATAAGGCGTTCACGTTGCATCTGGTGTGTAAAAAGAGAATTTGGTAAAAAATTTGAGGAAAGTAAGTAATGTTAATGAATGGCATTTAATCAATGAATAAGAAACGCTTAAAGCGCAATCAACTTGTACAGc                                          >  1:200269/1‑149 (MQ=255)                                                                                                                g‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCATCAACTTGTCCAGCGCCGGTGc                                  >  1:424314/1‑149 (MQ=255)                                                                                                                  tAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAAGCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAACGCCATCAACTTGTCCAGCGACAGTGCg                                 >  2:17413/1‑149 (MQ=255)                                                                                                                    ggCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTAAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCATCAACTTGTCCAGCGACGGTGCGaa                               >  1:274271/1‑149 (MQ=255)                                                                                                                          aTAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCACCAACTTGTCCAGCGACGGTGCGCAataata                         >  2:143660/1‑149 (MQ=255)                                                                                                                               gCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGACAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACACTTACAGCGCCATCAACTTGTCCAGCGACGGTGCGAAATAATAgccgc                    >  1:261865/1‑149 (MQ=255)                                                                                                                                       gccgcATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCAGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCATCAACTTGTCCAGCGACGGTGCGAAATAATAACCGCCCGTTAcc            >  2:60019/1‑149 (MQ=255)                                                                                                                                             tCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCATCAACTTGTCCAGCGACGGTGCGAAATAATAGCCGCCGGTTACCGGTTTg      <  1:529668/149‑1 (MQ=255)                                                                                                                                              ccGGCGTGGACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGATTCGTTTTTAACTCCATCAACTTGTCCAGCGACGGTGCGAAATAATAGCCGCCGGTTACCGGTTTgg     <  1:354709/149‑1 (MQ=255)                                                                                                                                                 gCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCCATGCATCAGAAACGCTTACAGCACCATCAACTTGACCAGCGGCGGTGCGAAATAATAGCCTCCGGTTACCCGTCTGGTgc  >  2:242029/1‑148 (MQ=255)                                                                                                                                                   |                                                                                                                                                   TCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCG‑TAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTGGCCTTTAATCAATGAATCAGAAACGCTTACAGCGCCATCAACTTGTCCAGCGACGGTGCGAAATAATAGCCGCCGGTTACCGGTTTGGTGA  >  NC_000913_3_vch_tpiA/2549419‑2549710

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.