New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 3231408	28 (0.900)	4 (0.130)	4/274	3.9	13.1%	noncoding (157/283 nt)	REP231 (repetitive extragenic palindromic) element; contains 6 REP sequences	REP231 (repetitive extragenic palindromic) element; contains 6 REP sequences
	?	NC_000913_3_pae_tpiA	= 3231427	26 (0.860)					noncoding (176/283 nt)	REP231 (repetitive extragenic palindromic) element; contains 6 REP sequences	REP231 (repetitive extragenic palindromic) element; contains 6 REP sequences
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCC  >  NC_000913_3_pae_tpiA/3231294‑3231564                                                                                                                                      |                                                                                                                                          tcctccAAGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCAc                                                                                                                            <  1:287259/149‑1 (MQ=255)      ctGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCgggc                                                                                                                       >  1:178519/1‑149 (MQ=255)         gCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGGTAAGACGCGCCAAACGTCGCCTCCGGCATCTTCACcgccgccc                                                                                                                    >  1:45431/1‑144 (MQ=18)                        gCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGt                                                                                                     >  1:217120/1‑149 (MQ=255)                         cAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTg                                                                                                    >  1:306059/1‑149 (MQ=255)                          aaGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCCCTGCCGGATGCGGCCTgg                                                                                                   >  2:235494/1‑149 (MQ=255)                              gTTGCCTCCGGCAACTGCACCCCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGc                                                                                               <  1:413024/149‑1 (MQ=255)                                             tGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACa                                                                                >  1:197884/1‑149 (MQ=255)                                                 ccGCGCCACTGGGTGATGGGGCGGGAACGCCTCATGCGCTTTACATGTGGGTTCGCGTAGGTTGGATAAGTCGCGTCCAGGGTCGCATCCTTCATCTCCACCGCGCCACGGGCGGATGCGGCGTCGACGCCTTATCCGCCCTACAtttg                                                                            <  2:139691/149‑1 (MQ=12)                                                 ccGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACAtgtg                                                                            <  1:177529/149‑1 (MQ=255)                                                 ccGCGCCACTGGCGCATGCGCCATGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACAtgtg                                                                            <  1:462039/149‑1 (MQ=255)                                                  cgcgCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGc                                                                           >  2:532098/1‑149 (MQ=255)                                                   gcgcCACTGGCGGATGCGGCGTGAACGCCTTATCAGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCATTATCCGCCCTACATTTGCa                                                                          >  2:434291/1‑149 (MQ=255)                                                               gATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCATTTCCGTAACCt                                                              >  1:456158/1‑149 (MQ=255)                                                                        tGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAAc                                                     >  1:144093/1‑149 (MQ=255)                                                                         gAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAAcg                                                    <  1:532098/149‑1 (MQ=255)                                                                          aaCGCCTTATCCGCCCTACAGGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCACATCCTGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAAcgc                                                   <  1:267007/149‑1 (MQ=255)                                                                                    ccGCCCTACCTGTGTGTTTCCGTAGGTCGGATAAAACGCCACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTc                                         <  2:86852/149‑1 (MQ=255)                                                                                     cGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCCTCCGGCCTCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACCAGTCCAATTCCGTAACCTGGATAACACGCGCCAACCGTCg                                        >  2:380219/1‑149 (MQ=18)                                                                                         cTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCCGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATc                                    >  2:249471/1‑149 (MQ=255)                                                                                          tACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATcc                                   <  1:344626/149‑1 (MQ=255)                                                                                           aCATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCg                                  >  2:299994/1‑149 (MQ=255)                                                                                                          tAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACGTGTCCACTTGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGc                   <  2:196667/149‑1 (MQ=21)                                                                                                                           gACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATcc  <  1:28949/149‑1 (MQ=255)                                                                                                                           gACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATcc  >  2:188446/1‑149 (MQ=255)                                                                                                                           gACAACCGGTGCATCCGGCATCTGCACCGCGCTCCTTGCGGATGCGGCGTGGACGCCTTATCCGCCTTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATcc  <  2:124774/149‑1 (MQ=25)                                                                                                                                      |                                                                                                                                          TCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCC  >  NC_000913_3_pae_tpiA/3231294‑3231564

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.