New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	3269740 =	NA (NA)	4 (0.260)	4/238	1.6	NA	noncoding (19/98 nt)	RIP237 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP237 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913_3_pae_pgi	= 4137879	NA (NA)					noncoding (91/98 nt)	RIP307 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP307 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site

GCAATATAGACTTAATAACTTCTTACAAAGTCTATTATTAATACCGTAGATATTTATTCATCTTACCCTGTGCACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTA  >  NC_000913_3_pae_pgi/3269594‑3269881                                                                                                                                                   |                                                                                                                                              aagcggataaaaaattcctgaacaacgtgggagtttcagattactggcacagagtgccggatgcggagtgaacgccttatccggcctacaaaagcacgcaaattcaatatattgcagagattgcgtaggcctgataagcgtagcgcAt                                                                                                                                              >  1:110282‑M1/147‑148 (MQ=255) aagcggataaaaaattcctgaacaacgtgggagtttcagattactggcacagagtgccggatgcggagtgaacgccttatccggcctacaaaagcacgcaaattcaatatattgcagagattgcgtaggcctgataagcgtagcgcAt                                                                                                                                              <  2:110282‑M1/2‑1 (MQ=255)                   cttcttACAAAGTCTATTATTAATACCGTAGATATTTATTCATCTTACCCTGTGCACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGc                                                                                                                          >  4:84197/1‑150 (MQ=255)                   cttcttACAAAGTCTATTATTAATACCGTAGATATTTATTCATCTTACCCTGTGCACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGc                                                                                                                          >  4:60674/1‑150 (MQ=255)                                           aCCGTAGATATTTATTCATCTTACCCTGTGCACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCtttt                                                                                                  >  4:13260/1‑150 (MQ=255)                                             cGTAGATATTTATTCATCTTACCCTGTGCACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGt                                                                                                <  3:60674/150‑1 (MQ=255)                                               tAGATATTTATTCATCTTACCCTGTGCACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAg                                                                                              <  3:22282/150‑1 (MQ=255)                                                             tCTTACCCTGTGCACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGt                                                                                >  2:95638/1‑150 (MQ=255)                                                              cTTACCCTGTGCACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGtt                                                                               >  1:139935/1‑150 (MQ=255)                                                                  cccTGTGCACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCAcg                                                                           >  2:190822/1‑150 (MQ=255)                                                                         cACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATc                                                                    >  4:49961/1‑150 (MQ=255)                                                                            cAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCgg                                                                 >  2:104898/1‑150 (MQ=255)                                                                             aaaaGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGc                                                                >  4:59324/1‑150 (MQ=255)                                                                                    aaaaCTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATa                                                         <  1:190822/150‑1 (MQ=255)                                                                                      aaCTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAata                                                                                                                      >  3:113556/1‑87 (MQ=255)                                                                                      aaCTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAata                                                                                                                      <  4:113556/87‑1 (MQ=255)                                                                                                      tttGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCt                                       <  3:13260/150‑1 (MQ=255)                                                                                                          aatatattgcagagatggcgtaggcctgataagcgtagcgcATCAGGCCTACGCCATCTCTGCAATATAtt                                                                                                                  <  3:105860‑M1/30‑1 (MQ=255)                                                                                                          aatatattgcagagatggcgtaggcctgataagcgtagcgcATCAGGCCTACGCCATCTCTGCAATATAtt                                                                                                                  >  4:105860‑M1/42‑71 (MQ=255)                                                                                                                aTGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCTGAAACccgcc                             <  2:3475/150‑1 (MQ=255)                                                                                                                         gCAAAAAGGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTGTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGtt                    >  2:200076/1‑150 (MQ=255)                                                                                                                         gCAAAAAAGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCTGAAACCCGCCCGAACGGtt                    >  2:200086/1‑150 (MQ=255)                                                                                                                              aaTGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTttatta               <  3:49961/150‑1 (MQ=255)                                                                                                                                 gcctgataagcgtagcgcATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCa                                                                                           <  4:122655‑M1/53‑1 (MQ=255)                                                                                                                                 gcctgataagcgtagcgcATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCa                                                                                           >  3:122655‑M1/19‑71 (MQ=255)                                                                                                                                          gcTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCTGaaa                                   <  4:101852/118‑1 (MQ=255)                                                                                                                                          gcTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCTGaaa                                   >  3:101852/1‑118 (MQ=255)                                                                                                                                          gcTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGt   >  2:13952/1‑150 (MQ=255)                                                                                                                                           cTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTa  >  1:21700/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                              GCAATATAGACTTAATAACTTCTTACAAAGTCTATTATTAATACCGTAGATATTTATTCATCTTACCCTGTGCACCAAAAGCAAAAACTCACTGACGCGGGTTTGAAACTGATGGCAACCGCAAAAATGCCTGATGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATGAATAAAGCGCACTCAACAATCTGAAACCCGCCGGAACGGTTTATTACGTACATCAGGTA  >  NC_000913_3_pae_pgi/3269594‑3269881

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.