New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	= 72172	NA (NA)	8 (0.390) +GCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAG	4/204	2.6	44.4%	noncoding (37/85 nt)	REP7 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP7 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913_3_vch_tpiA	= 4296197	14 (0.490)					noncoding (333/600 nt)	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites

CATCGGCGTGGTGGCGCTGGTGGTGTTAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTGGTCATACCCTGCCAGGCGATGCGCCC  >  NC_000913_3_vch_tpiA/72028‑72312                                                                                                                                                 |                                                                                                                                             cagcggcggGGTGGCGCTGGTGGTGTTAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACaaaa                                                                                                                                          <  2:451266/146‑1 (MQ=255) cATCGGCGTGGTGGCGCTGGTGGTGTTAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACaaaa                                                                                                                                          <  2:73747/149‑1 (MQ=255) cATCGGCGTGGTGGCGCTGGTGGTGTTAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGAGAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACaaaa                                                                                                                                          <  1:55188/149‑1 (MQ=255)  aTCGGCGTGGTGGCGCTGGTGGTGTTAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAAc                                                                                                                                         <  2:292160/149‑1 (MQ=255)           gtggCGCTGGTGGTGTTAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTAccc                                                                                                                                >  1:47101/1‑149 (MQ=255)              gcccTGGTGGTGTTAAGTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGATAGAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTa                                                                                                                             <  2:226891/146‑1 (MQ=255)                    gtggtgTTAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGtcggtcgg                                                                                                                       >  2:194174/1‑149 (MQ=255)                         gtTAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAg                                                                                                                  >  2:417371/1‑149 (MQ=255)                          ttAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAgg                                                                                                                 <  2:443218/149‑1 (MQ=255)                                         ttGATGCCTGTGTATATCGAGATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATc                                                                                                  <  1:259947/149‑1 (MQ=255)                                             tGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAc                                                                                              >  1:276752/1‑149 (MQ=255)                                                cGGTGTATATCGATATTTTGTGTATAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCCGGCCTACAAATCGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGt                                                                                           <  2:83960/149‑1 (MQ=255)                                                  gtgtATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGc                                                                                         <  1:497283/149‑1 (MQ=255)                                                  gtgtATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGCTCGGATAAAGCGTTCACGCCGCATCCGACAGTGc                                                                                         >  2:437738/1‑149 (MQ=255)                                                          cGATGTGTTGCGTAAAGTGGTTGGGGTTTAGGGGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAAc                                                                                 <  2:174175/149‑1 (MQ=255)                                                          cGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAAc                                                                                 <  1:49323/149‑1 (MQ=255)                                                          cGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAAc                                                                                 <  2:283532/149‑1 (MQ=255)                                                           gATATTTTGCGTAAAGTGGGTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTAACGCCGCCTCCGACAGTGCATCCTCAcc                                                                                >  2:71240/1‑149 (MQ=38)                                                           gATATTTCGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAAcc                                                                                <  1:17927/149‑1 (MQ=255)                                                                    cGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATccc                                                                       <  1:417371/149‑1 (MQ=255)                                                                        aaGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAATACGCACTACCCGTAGGTCGGATAACGCGTTCACGCCGCATCCGACAGTGCATACTCACCCGTCATCCCCact                                                                   >  2:430185/1‑147 (MQ=255)                                                                        aaGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAAt                                                                   >  2:393280/1‑149 (MQ=255)                                                                           tGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTg                                                                                          >  1:392158/1‑123 (MQ=255)                                                                           tGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTg                                                                                          <  2:392158/123‑1 (MQ=255)                                                                                ggggTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGa                                                           >  1:177138/1‑149 (MQ=255)                                                                                 gggTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGaa                                                          <  2:277274/149‑1 (MQ=255)                                                                                 gggTTAAGGAGAAAGTCTTGGGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTAATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGaa                                                          <  2:426007/149‑1 (MQ=255)                                                                                   gTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATCCTAACCCGTAATCCCCAATAGTGCGGAAGc                                                        >  1:167887/1‑149 (MQ=255)                                                                                   gTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGAGGCGAAGc                                                        >  1:341832/1‑149 (MQ=255)                                                                                                      gCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTcaac                                     >  1:338701/1‑149 (MQ=255)                                                                                                               cagATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTg                            <  1:320339/147‑1 (MQ=255)                                                                                                                tGATGCGACGCTTGCCGCGTCTTATCAGGCCTACgccagacagcgcaatagcctgatttagcgtgattttgtaggtcggatgcggcataaacgccttatccga                                                                         <  2:196167‑M1/103‑70 (MQ=255)                                                                                                                tGATGCGACGCTTGCCGCGTCTTATCAGGCCTACgccagacagcgcaatagcctgatttagcgtgattttgtaggtcggatgcggcataaacgccttatccga                                                                         >  1:196167‑M1/1‑34 (MQ=255)                                                                                                                 gATGCGACGCTTGCCGCGTCTTATCAGGCCTACgccagacagcgcaatagcctgatttagcgtgattttgtaggtcgga                                                                                                >  2:321211‑M1/1‑33 (MQ=255)                                                                                                                 gATGCGACGCTTGCCGCGTCTTATCAGGCCTACgccagacagcgcaatagcctgatttagcgtgattttgtaggtcgga                                                                                                <  1:321211‑M1/79‑47 (MQ=255)                                                                                                                 gATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCACCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTGGt                          <  1:278923/149‑1 (MQ=255)                                                                                                                  aTGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCGGCATCCGACAGTCCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTCCCGCCCAACACCTCACTGGTc                         >  2:410089/1‑149 (MQ=38)                                                                                                                    gCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTGGTCAt                       >  2:442465/1‑149 (MQ=255)                                                                                                                             gCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTGGTCATACCCTGCCa              <  1:442465/149‑1 (MQ=255)                                                                                                                               cgcgTCTTATCAGGCCTACgccagacagcgcaatagcctgatttagcgtgattttgtaggtcggatgcggcataaacgccttatccgacctacaaaatcacgctaaatcagg                                                 <  2:317964‑M1/112‑94 (MQ=255)                                                                                                                               cgcgTCTTATCAGGCCTACgccagacagcgcaatagcctgatttagcgtgattttgtaggtcggatgcggcataaacgccttatccgacctacaaaatcacgctaaatcagg                                                 >  1:317964‑M1/1‑19 (MQ=255)                                                                                                                               cgcgTCTTATCAGGCCTACgccagacagcgcaatagcctgatttagcgtgattttgtaggtcggatgcggcataaacgccttatccgacctacaaaatcacgctaaatcagg                                                 <  2:317866‑M1/112‑94 (MQ=255)                                                                                                                               cgcgTCTTATCAGGCCTACgccagacagcgcaatagcctgatttagcgtgattttgtaggtcggatgcggcataaacgccttatccgacctacaaaatcacgctaaatcagg                                                 >  1:317866‑M1/1‑19 (MQ=255)                                                                                                                                     ttATCAGGCCTACAAAACGCACTACCCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTGGTCATACCCTGCCCGCCGATgc      >  1:54717/1‑149 (MQ=255)                                                                                                                                         cacgtcTACACAACGAGCTACCGGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAGTAGTGCTGAAGCACTCGCCTTACCGCTCAACAACTCATTGTTCATACCCTGCGAGGCGATGCGccc  <  2:206510/144‑1 (MQ=38)                                                                                                                                               tACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTGGTCATACCCTGCCAgg            <  2:450897/133‑1 (MQ=255)                                                                                                                                               tACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTGGTCATACCCTGCCAgg            >  1:450897/1‑133 (MQ=255)                                                                                                                                                 |                                                                                                                                             CATCGGCGTGGTGGCGCTGGTGGTGTTAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTGGTCATACCCTGCCAGGCGATGCGCCC  >  NC_000913_3_vch_tpiA/72028‑72312

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.