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.

GTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGC  >  NC_000913_3_vch_tpiA/1552139‑1552425                                                                                                                                                 |                                                                                                                                               gtAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCCGATGCGGCGTGAACGCCTTATCCGGAATGAACAcc                                                                                                                                            >  1:263797/1‑149 (MQ=255)   aGGCCTAATAAGGTTAGCGAATCAGGTAATGTTGTGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCt                                                                                                                                          <  2:159153/149‑1 (MQ=18)    ggacTGAGAGGCGGAGGGAATCAGGCAATGTTGTGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCtt                                                                                                                                         <  2:96968/146‑1 (MQ=17)     gcatGATAAGCGTAGCGCATCAGGCAATGTTGCTTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTc                                                                                                                                        <  1:256406/146‑1 (MQ=255)     gCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTc                                                                                                                                        >  1:102175/1‑149 (MQ=255)      ccTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATCTTGTAGACAAAGTCGGCTTTTTACATGCCCGTAGCGGCCTAAAAGCATTATACGGCATGAAAACACttga                                                                                                                                       >  1:168746/1‑147 (MQ=21)        tGATAAGCGTAGCGCATCAGACAATGTTGCGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAAAGTAGGCTTTGTTCATGCCGGATGCGGCGTGAAAGCCTTATCCGGCATGAATACCTTTCaaa                                                                                                                                     >  2:265208/1‑149 (MQ=21)        ataTAAGCGGAGGGCATAAGGCAATGTTGTGTTTGTCATCATTTTCAAATGGCGCTGTAAAAGGCTTTATTTTCATATTGTAGACAACGTAGCTGTGGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCaaa                                                                                                                                     <  1:304846/147‑1 (MQ=17)         taTAAGTGTAGTGCATCAAGCAATGGTGTGTTGGTTATCTCATGCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAAt                                                                                                                                    <  1:80976/148‑1 (MQ=14)          aTAAGCGTAGCGCATCAGGCAATGTTGTGTTTGTGTTTAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATc                                                                                                                                   <  1:185045/149‑1 (MQ=255)          aTAAGCGTAGCGCATCAGGCAATGTTGGGTTTGTTATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATc                                                                                                                                   <  1:268428/149‑1 (MQ=255)          aTAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATc                                                                                                                                   <  2:102175/149‑1 (MQ=255)          aTAAGCGGAGCGCATCAGGCAATGTTGTGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATAGTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATc                                                                                                                                   <  2:353529/149‑1 (MQ=255)                gTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGACGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATCCAATAg                                                                                                                             >  1:153382/1‑149 (MQ=255)                   gcgcATCAGGCAATGTTGCGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCCTTTTCTTATTGTATTCAACGTAGGCTTTGTTCATGCAGGATGCGGCGTGGACGACTTATTCGCCTTGAAAACCCTTCACATCCgattgatt                                                                                                                          >  2:324677/1‑149 (MQ=18)                          aGGCAATGTTGCGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATCCAATAGATTGCAGTGa                                                                                                                   >  2:237027/1‑149 (MQ=255)                            tcAATGTTGCTTTTATCATAAGTTTAAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTTTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATCCAATAGATTGCAGTGAAc                                                                                                                 <  1:193955/148‑1 (MQ=14)                                         tGTCATCAGTTGCCAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAAGCTTTGTTGATGCCGGATGAGGCGGGACCGCCTTATCCGGCATAAACACCCTCAAAATCAAATAGCTTGATGTGAACCGGTAGGCGTGAt                                                                                                    >  2:249439/1‑149 (MQ=11)                                                 gTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGCTGCGGCGTGAACGCCTTATCCGGCATGAAAAACCTTCAAATCCAATAGATTGCAGTGAAGGTGTAGGCATGCTAAGCGtta                                                                                            >  2:236969/1‑147 (MQ=11)                                                      aaaTGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCAGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCATTCAAATCCAATAGATTGTAGTGACACTGTAGTCCTGATAAGAGTAGAGCaa                                                                                       >  1:209162/1‑148 (MQ=11)                                                        aTGGCGCTGTAAAATGCGTCATTTTCATATTGTAGAAAATGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGACTTATCCGGCATGAAAACCCTTCAAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCa                                                                                     <  1:173558/149‑1 (MQ=255)                                                                                         aGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATgg                                                    <  2:153382/149‑1 (MQ=35)                                                                                                              tGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAAc                                                                                                                                             <  2:110647‑M2/38‑1 (MQ=255)                                                                                                              tGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAAc                                                                                                                                             >  1:110647‑M2/2‑39 (MQ=255)                                                                                                              tGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAAACCTTCAAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGTATCAGGCAATGTTGAGTTTGTCATAAGTTCTAAATGGTGCTTTATAAAGTGCCAtttt                               >  1:89665‑M2/2‑149 (MQ=255)                                                                                                                 CGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCACTTTATAAAGCgccatttagaa                            <  2:174999‑M2/149‑5 (MQ=255)                                                                                                                           gTGAACGCCTTATCCGGCATGAAAACCCTTCAAATCCAATAGATTGCAGTTAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAAc                  <  1:152614/149‑1 (MQ=255)                                                                                                                                   cTTATCCGGCATGAAAACCCTTCAAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACTGc          >  1:255908/1‑149 (MQ=255)                                                                                                                                           gCATGAAAACCCTTCAAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCTCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATcgc  <  2:209162/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                               GTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTTCAAATGGCGCTGTAAAAGGCGTCATTTTCATATTGTAGACAACGTAGGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCATGAAAACCCTTCAAATCCAATAGATTGCAGTGAACGTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATGTTGCGTTTGTCATCAGTTCTAAATGGCGCTTTATAAAGTGCCATTTTTTTATTGCGTAACCAGACGGCGTAATCGC  >  NC_000913_3_vch_tpiA/1552139‑1552425

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.