New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 2291296	54 (1.020)	3 (0.060)	3/260	NT	5.9%	noncoding (144/199 nt)	RIP160 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site	RIP160 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site
	?	NC_000913_3_pae_pgi	3231380 =	43 (0.840)					noncoding (129/283 nt)	REP231 (repetitive extragenic palindromic) element; contains 6 REP sequences	REP231 (repetitive extragenic palindromic) element; contains 6 REP sequences

CAATAATTTGCAACTGCTGGCGGATGCGGCGTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGC  >  NC_000913_3_pae_pgi/3231234‑3231522                                                                                                                                                   |                                                                                                                                               cAATAATTTGCAACTGCTGGCGGATGCGGCGTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCGTATcccccc                                                                                                                                              >  2:184626/1‑149 (MQ=255)  aataatTTGCAACTGCTGGCGGATGCGGCGTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCt                                                                                                                                             >  1:673045/1‑149 (MQ=255)        ttGCAACTGCTGGCGGATGCGGCGTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACAtgt                                                                                                                                       <  2:717426/149‑1 (MQ=255)        atggatttatcatcgggctgagatttatgacaaacgcaaaactgcctgatgcgctacgcttttcagtcctacgttgatcgatcaatttattgaatttacacaattttgtaggccggataaggcgttcacgccgcatccgGCCtacacta                                                                                                                                       >  2:426701‑M2/140‑146 (MQ=255)          gCAACTGCTTGCGGAGTATGCGTAAACGCATTAACCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACAtgtgt                                                                                                                                     <  1:358892/149‑1 (MQ=17)           cAACTGCTGGCGGATGCGGCGTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACAtgtgtg                                                                                                                                    <  1:916418/149‑1 (MQ=255)                  tttcGGCTGCGGCGTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGCTAAAACGCGGCAAGCGTTGCCTCCCGCAACTACACCGTGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCGACCTCTGTGTGcccta                                                                                                                             >  2:517848/4‑147 (MQ=17)                  tgGCGGATGGGGCGTAAACGCCTTATCTGCCTTACATGTGCAATCCTCCTGGCGGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGt                                                                                                                             <  2:153759/149‑1 (MQ=255)                  tgGCGGATGCGGCGTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTccctt                                                                                                                             >  2:306533/1‑147 (MQ=255)                   ggCGGATGCGGCGTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGTCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTa                                                                                                                            <  1:455404/149‑1 (MQ=255)                     cGGATGCGGCGTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCCACTGCACCGCGCCACTGGCGGATGCGGCGCGCACGCCTTCTCCGCCCTCCCTGTGTGTTCCCGTAgg                                                                                                                          >  2:898738/1‑149 (MQ=18)                          gcggcgTAAACGCATTAGCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGTCCTACATGTGTGTTCCCGTAGCTCGGa                                                                                                                     <  1:977358/149‑1 (MQ=255)                            ggcgTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGACCGCCTTATCCGCCCTACCTGTGTTTTCCCGTAGGTCGGATa                                                                                                                   >  2:686230/1‑149 (MQ=255)                            ggcgTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATa                                                                                                                   >  1:942958/1‑149 (MQ=255)                            ggcgTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAACCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCCTGAACGCCTAATCCGCCGTACATGTGTGTTCCCTTAGGTCGGATa                                                                                                                   >  1:526881/1‑149 (MQ=18)                             gcgTAAAGGCTTTATCCGCCCTACATGGGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCAACCTGCAACGGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATaa                                                                                                                  <  2:362800/149‑1 (MQ=18)                              cgTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAg                                                                                                                 >  2:813800/1‑149 (MQ=255)                                  ctcGCCTTATCCGGCCTACATGTTCATGCCTGCTGGCTGGATAAAACGCGGCAAGCGTTGCATCCGGGAATTGCTCCGCGACACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATTTTTGTTCCCGTAGGTCTGATAAGAcgc                                                                                                             <  2:53643/147‑1 (MQ=17)                                    cGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGa                                                                                                           <  2:907195/149‑1 (MQ=255)                                    cGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGa                                                                                                           <  1:142132/149‑1 (MQ=255)                                              gCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAGACGTCGc                                                                                                 >  2:54649/1‑149 (MQ=255)                                                      tgtgCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCg                                                                                                     <  2:210407/137‑1 (MQ=255)                                                      tgtgCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCg                                                                                                     >  1:210407/1‑137 (MQ=255)                                                           aaTCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGACGCATCCGGCATCTGc                                                                                    >  1:328193/1‑149 (MQ=255)                                                              cctcctCGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGAGGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCAcc                                                                                 <  2:997715/149‑1 (MQ=255)                                                               ctcctGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACcg                                                                                >  2:984727/1‑149 (MQ=255)                                                                ccctGGTCGGATAAAACGCGGCAGGTGTTTGATCCGGCAAGTGCCCCGCGCCACTGGTGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCTGATAAGACGCGTCAAGCGTCGCATCCGGCAGCTGCACcgc                                                                               <  2:564690/148‑1 (MQ=18)                                                                          aTAAAACGCGCCAAGCGTTGCATCCGGCAACTGGACAGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCg                                                                     <  2:742194/149‑1 (MQ=255)                                                                              aaggcgGCAAGCGTTGCATCCGGCATCTGCACAGAGCCACTGGCGGATGCGGCGTGAACGCCTTATCCCGCGTCCATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCATCGCTTCCGGCCTCTGCAGCGGACTCCTGGCggttc                                                                 >  2:400934/4‑146 (MQ=17)                                                                               aCGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATgc                                                                >  1:947605/1‑149 (MQ=255)                                                                                    gCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGt                                                           >  1:658066/1‑149 (MQ=255)                                                                                       aGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGt                                                           <  2:838160/146‑1 (MQ=255)                                                                                       aGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGt                                                           >  1:838160/1‑146 (MQ=255)                                                                                                    gCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGcc                                           <  1:625479/149‑1 (MQ=255)                                                                                                             ccGCGCCACTGGCGGATGCGGCGTGAACGCTTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACAtgtg                                  <  2:478780/149‑1 (MQ=255)                                                                                                             ccGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCACTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACAtgtg                                  <  2:979198/149‑1 (MQ=255)                                                                                                                 gcCACTGGCGGATGCGCCGTAAACGTCTTATCCGCCCTACATGTGTGTTCCCTTAGGTCGGATAAGACGCTACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAAt                              <  1:927665/149‑1 (MQ=17)                                                                                                                   cACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGAATTATCCGCCCTACATGTGCAATTc                            >  1:684306/1‑149 (MQ=255)                                                                                                                      tGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGt                         >  1:522862/1‑149 (MQ=255)                                                                                                                       ggCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTa                        <  1:110996/149‑1 (MQ=255)                                                                                                                         cggataaggcgttcacgccgcatccgCCCTACATGTGTGTTCCCGTAGGTc                                                                                                                        >  2:352699‑M2/27‑51 (MQ=255)                                                                                                                         cggataaggcgttcacgccgcatccgCCCTACATGTGTGTTCCCGTAGGTc                                                                                                                        <  1:352699‑M2/25‑1 (MQ=255)                                                                                                                          ggATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAAcc                     >  1:889539/1‑149 (MQ=255)                                                                                                                             tGCGGAGTGCGCGCCTTATGCGCTCTACATGTGTGTACCCGTAGGTCGGATAAGACGCCACAAGCGTCGCATCAAGCATCTGCTTCGCGTTACTTGCGGATGCGTCGTGGACGCCTTATCCGCCCTACATGTGCAATTCAGTAACCTgg                  <  2:162816/149‑1 (MQ=18)                                                                                                                                   gTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTTCACCGCTCCACTGGCGGATGCGGCATGGACTCCTTATCCGCCCTACATGTTCAATTCCGTAACCTGGATaaaa            >  1:19235/1‑149 (MQ=18)                                                                                                                                   gTGAACGCCTTACCCGCCCTACATGGGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCACCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATaaaa            <  1:284671/149‑1 (MQ=255)                                                                                                                                    tGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAAc           <  1:984727/149‑1 (MQ=255)                                                                                                                                      aaCGCCTTATCCGCCCTACATGTGTGGTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAAcgc         <  1:610158/149‑1 (MQ=255)                                                                                                                                           cTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGt                                                                                                    >  2:350173/1‑53 (MQ=255)                                                                                                                                           cTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGt                                                                                                    <  1:350173/53‑1 (MQ=255)                                                                                                                                            ttATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCAACAAg   >  1:91693/1‑149 (MQ=255)                                                                                                                                             tATCCGCCCTACATGTGTGTTCCTGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGc  <  1:423956/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                               CAATAATTTGCAACTGCTGGCGGATGCGGCGTAAACGCCTTATCCGCCCTACATGTGCAATCCTCCTGGCCGGATAAAACGCGGCAAGCGTTGCATCCGGCAACTGCACCGCGCCACTGGCGGATGCGGCGTGAACGCCTTATCCGCCCTACATGTGTGTTCCCGTAGGTCGGATAAGACGCGACAAGCGTCGCATCCGGCATCTGCACCGCGCCACTGGCGGATGCGGCGTGGACGCCTTATCCGCCCTACATGTGCAATTCCGTAACCTGGATAAAACGCGACAAGC  >  NC_000913_3_pae_pgi/3231234‑3231522

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.