New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	2304923 =	16 (0.550)	6 (0.220)	6/268	2.8	27.8%	noncoding (507/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
	?	NC_000913_3_pae_tpiA	2304955 =	16 (0.580)					noncoding (539/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences

CCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATACGCCACATCCGGCATACCATGCCGGATGTGGC  >  NC_000913_3_pae_tpiA/2304865‑2305101                                                                                           |                                                                                                                                                   ccccGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCa                                                                                          >  1:382508/1‑149 (MQ=11)     gTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACAt                                                                                      <  1:112918/149‑1 (MQ=32)         gTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTaa                                                                                  <  1:266508/149‑1 (MQ=35)         gTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTaa                                                                                  <  1:58246/149‑1 (MQ=35)          tCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCGCGCGAGTGGCTTGACGGGATGCATGCGCGTCTTATCCGCCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGCTTAGGCGGCTACGCCGCATCCCACATCTaaa                                                                                 >  1:74315/1‑148 (MQ=11)          tCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAAc                                                                                 >  1:354395/1‑149 (MQ=34)                aaGGTGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGa                                                                           <  1:484562/149‑1 (MQ=38)                  ggCGGTTACGCCGCATCCGACATCTAACGCCCGAGCCGGTGGCCTGGTGCGACGCTGGCGCGTCTTATCAGGCATAAACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCGAGc                                                                         <  2:76680/149‑1 (MQ=11)                         tcgccgcATCCGACATCCATCGCTCAAGCCGGTTGCCTGATGCGACGCCGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGCGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGc                                                                  <  1:223608/148‑1 (MQ=11)                            ccgcATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTTACGCCCGAGGCGGTTGCCTg                                                               >  2:164542/1‑149 (MQ=255)                                                   agcggtttGCCTGATGCGCCGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATc                                        <  2:277630/143‑1 (MQ=255)                                                    ggcGGTTGCGTGACGCGACGGTGGCACGGTTTAGCAAGCCTACACCGCCGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCa                                       <  2:215504/147‑1 (MQ=11)                                                    gCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCa                                       <  1:511929/149‑1 (MQ=39)                                                         tcGCCTGAGGCGACCCTGGCCCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATa                                  >  2:290289‑M1/3‑149 (MQ=255)                                                           gcctgataagacgcgccagcgtcgcatcaggcCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGc                                                                  >  1:362573‑M2/33‑115 (MQ=255)                                                           gcctgataagacgcgccagcgtcgcatcaggcCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGc                                                                  <  2:362573‑M2/83‑1 (MQ=255)                                                            cctgataagacgcgccagcgtcgcatcaggcCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATACGc                               >  1:493841‑M2/32‑149 (MQ=255)                                                             ctgataagacgcgccagcgtcgcatcaggcCTACACCGCTGTGAAGTGCTCCACCCCGTAGGtt                                                                                                                   >  1:310750‑M2/31‑64 (MQ=255)                                                             ctgataagacgcgccagcgtcgcatcaggcCTACACCGCTGTGAAGTGCTCCACCCCGTAGGtt                                                                                                                   <  2:310750‑M2/34‑1 (MQ=255)                                                              TGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCg                                                                       >  1:206731‑M1/1‑107 (MQ=255)                                                              TGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCg                                                                       <  2:206731‑M1/107‑1 (MQ=255)                                                               GATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCg                                                                                                         <  1:118329‑M1/72‑1 (MQ=255)                                                               GATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCg                                                                                                         >  2:118329‑M1/1‑72 (MQ=255)                                                                ATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCAACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGGCGCTGGCGCGTCTTATCCGCCTACGCcaca                           <  2:214499‑M1/149‑1 (MQ=255)                                                                   cGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATACGCCACATcc                        <  1:191571/149‑1 (MQ=255)                                                                       gCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATACGCCACATCCGGCa                    <  1:194732/149‑1 (MQ=255)                                                                           gcgcCTCTTATCAGGCCTACACCGCTGTGCAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCAACACCCAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATACGCCACATCCGGCATAcc                <  2:73509/149‑1 (MQ=17)                                                                                tcgcatcaggcCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATACGCCACATCCGGCATACCATGcc           <  2:493841‑M2/138‑1 (MQ=255)                                                                                        ggcCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATACGCCACATCCGGCATACCATGCCGGATGTgg   <  1:479908‑M2/146‑1 (MQ=255)                                                                                        ggcCTACACCGCGGTGAAGTGCTCCACCCTTTAGGTCGGATAAGGCGGGTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATACGCCACATCCGGCATACCATGCCGGATGTgg   <  1:455902‑M2/146‑1 (MQ=255)                                                                                         gcCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATc                                        >  2:262939‑M2/3‑111 (MQ=255)                                                                                         gcCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATc                                        <  1:262939‑M2/109‑1 (MQ=255)                                                                                         gcCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATACGCCACATCCGGCATACCATGCCGGATGTGGc  >  2:343601‑M2/3‑149 (MQ=255)                                                                                           |                                                                                                                                                   CCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATACGCCACATCCGGCATACCATGCCGGATGTGGC  >  NC_000913_3_pae_tpiA/2304865‑2305101

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.