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

ACGCCGCATCCGACATCCAACGTCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATA  >  NC_000913_3_pae_tpiA/2304776‑2305069                                                                                                                                                    |                                                                                                                                                   gccacatccggcatggtatgccggatgtggcgtatgctgataagacgcgccagcgtcgcatcaggcaaccggctcgggcgttagatgttggatgcggcgtaaccgccttatccaacctacggggtggagcacttcacagcggtgtagGc                                                                                                                                                   >  2:343601‑M1/148‑149 (MQ=255)  ccacatccggcatggtatgccggatgtggcgtatgctgataagacgcgccagcgtcgcatcaggcaaccggctcgggcgttagatgttggatgcggcgtacccgccttatccgacctaaagggtggagcacttcaccgcggtgtagGcc                                                                                                                                                  <  1:455902‑M1/3‑1 (MQ=255)  ccacatccggcatggtatgccggatgtggcgtatgctgataagacgcgccagcgtcgcatcaggcaaccggctcgggcgttagatgttggatgcggcgtaaccgccttatccaacctacggggtggagcacttcacagcggtgtagGcc                                                                                                                                                  <  1:479908‑M1/3‑1 (MQ=255)          ggcatggtatgccggatgtggcgtatgctgataagacgcgccagcgtcgcatcaggcaaccggctcgggcgttagatgttggatgcggcgtaaccgccttatccaacctacggggtggagcacttcacagcggtgtagGCCTGATGCGa                                                                                                                                          <  2:493841‑M1/11‑1 (MQ=255)                tCCAACGTCCGAGCAGTTTGCCTGATGCGTCGCTGGCGCGTCTTATCAGTCCTACACCGCTGCGAAGTGCTCCACCCCGTAGCTCAGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCATCCCGGTTGCCTGAAGCGACGCTgg                                                                                                                                    >  2:466450/1‑149 (MQ=11)                  cAACGTCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGgcg                                                                                                                                  >  1:370835/1‑149 (MQ=32)                  cAACGTCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGgcg                                                                                                                                  >  1:417940/1‑149 (MQ=32)                              gcgtatgctgataagacgcgccagcgtcgcatcaggcaaccggctcgggcgttagatgttggatgcggcgtaaccgccttatccaacctacggggtggagcacttcacagcggtgtagGCCTGATGCGACGCTGGCGCGTCTTATCAgg                                                                                                                      >  1:493841‑M1/119‑149 (MQ=255)                                       gataagacgcgccagcgtcgcatcaggcaaccggctcgggcgttagatgttggatgcggcgtaaccgccttatccaacctacggggtggagcacttcacagcggtgtagGc                                                                                                                                                   <  1:262939‑M1/2‑1 (MQ=255)                                       gataagacgcgccagcgtcgcatcaggcaaccggctcgggcgttagatgtcggatgcggcgtaaccgccttatccaacctacggggtggagcacttcacagcggtgtagGc                                                                                                                                                   >  2:262939‑M1/110‑111 (MQ=255)                                                                 gcaaccggctcgggcgttagatgttggatgcggcgtaaccgccttatccaacctacggggtggagcacttcacagcggtgtagGCCTGATGCGACGCTGGCGCGTCTTATCAGGc                                                                                                                     <  2:362573‑M1/32‑1 (MQ=255)                                                                 gcaaccggctcgggcgttagatgttggatgcggcgtaaccgccttatccaacctacggggtggagcacttcacagcggtgtagGCCTGATGCGACGCTGGCGCGTCTTATCAGGc                                                                                                                     >  1:362573‑M1/84‑115 (MQ=255)                                                                                          ccccGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCa                                                          >  1:382508/1‑149 (MQ=11)                                                                                              gTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACAt                                                      <  1:112918/149‑1 (MQ=32)                                                                                                  gTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTaa                                                  <  1:58246/149‑1 (MQ=35)                                                                                                  gTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTaa                                                  <  1:266508/149‑1 (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)                                                                                                                  aacctacggggtggagcacttcacagcggtgtagGCCTGATGCGACGCTGGCGCGTCTTATCAg                                                                                                                       <  2:310750‑M1/30‑1 (MQ=255)                                                                                                                  aacctacggggtggagcacttcacagcggtgtagGCCTGATGCGACGCTGGCGCGTCTTATCAg                                                                                                                       >  1:310750‑M1/35‑64 (MQ=255)                                                                                                                     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)                                                                                                                                                    |                                                                                                                                                   ACGCCGCATCCGACATCCAACGTCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGATAAGGCGGTTACGCCGCATCCAACATCTAACGCCCGAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGCATA  >  NC_000913_3_pae_tpiA/2304776‑2305069

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.