New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 610184	NA (NA)	6 (0.390)	6/238	1.1	NA	noncoding (68/98 nt)	RIP54 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP54 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913_3_pae_pgi	1954429 =	NA (NA)					noncoding (1/98 nt)	RIP139 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP139 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site

GGGAGGTATGCGTAGTTTTCATATCGACCATATTCGAGACTGATGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGTTAGCATCAGAAGTGGGTGTTTACGCTCATATACCACGTACGTCCCGGCTCGTTATAGGTATACGCCCCGGCACCGGCGATATA  >  NC_000913_3_pae_pgi/610058‑610331                                                                                                                                |                                                                                                                                                    gggaggTATGCGTAGTTTTCATATCGACCATATTCGAGACTGATGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGgccggatgcggcgtgaacgcctt                                                                                                                              <  2:201513‑M1/150‑24 (MQ=255)      gTATGCGTAGTTTTCATATCGACCATATTCGAGACTGATGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCg                                                                                                                         >  1:36349/1‑150 (MQ=255)                           aCCATATTCGAGACTGATGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTg                                                                                                    <  1:177489/150‑1 (MQ=255)                            ccATATTCGAGACTGATGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGt                                                                                                   <  4:87430/150‑1 (MQ=255)                                      gaCTGATGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTg                                                                                         <  4:43202/150‑1 (MQ=255)                                      gaCTGATGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTg                                                                                         <  4:43205/150‑1 (MQ=255)                                          gatgaCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGt                                                                                     <  2:142370/150‑1 (MQ=255)                                             tgcaaACGTAAAGCTGCCTGATACGCTACGCATATCAGGACTACATAGTCCCTGCAATATATTGAATTAGCAAG‑GTTTTGTAGgccggatgcggcgtgaacgccttatccggcctacaaaaccttgctaattcaatatattgcagggact                                                                                  <  2:91302‑M1/148‑68 (MQ=255)                                                          cTGCCTGATGCGCTATGCTTATCAGGCCTACATAGTCCCTGCAATATATTGAATTAGCAAG‑GTTTTGTAGgccggatgcggcgtgaacgccttatccggcctacaaaaccttgctaattcaatatattgcagggactatgtaggcctgat                                                                     <  2:66675‑M1/150‑81 (MQ=255)                                                                                     cTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGTTAGCATCAGAAGt                                                                        >  3:5863/1‑120 (MQ=255)                                                                                     cTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGTTAGCATCAGAAGt                                                                        <  4:5863/120‑1 (MQ=255)                                                                                                          ttGAATTGGCAAGATTTTTGTAGgccggatgcggcgtgaacgccttatccggc                                                                                                                       >  1:190306‑M1/1‑23 (MQ=255)                                                                                                          ttGAATTGGCAAGATTTTTGTAGgccggatgcggcgtgaacgccttatccggc                                                                                                                       <  2:190306‑M1/53‑31 (MQ=255)                                                                                                             aaTTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGTTAGCATCAGAAGTgg                                                                      >  2:11836/1‑99 (MQ=255)                                                                                                             aaTTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGTTAGCATCAGAAGTgg                                                                      <  1:11836/99‑1 (MQ=255)                                                                                                                  gCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGTTAGCATCAGAAGTGGGTGTTTACGCTCATATACCACGTACGTCCCGGCTCGTTATAGGTATACGCCCCGGc              >  1:183351/1‑150 (MQ=255)                                                                                                                    aaGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGTTAGCATCAGAAGTGGGTGTTTACGCTCATATACCACGTACGTCCCGGCTCGTTATAGGTATACGCCCCGGCAc            >  2:96785/1‑150 (MQ=255)                                                                                                                    aaGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGTTAGCATCAGAAGTGGGTGTTTACGCTCATATACCACGTACGTCCCGGCTCGTTATAGGTATACGCCCCGGCAc            >  3:7518/1‑150 (MQ=255)                                                                                                                        gttttgTAGgccggataaggcgttcacgccgcatccggcctacaaaaccttgctaattcaatatattgcagggactatgtaggcctgataagcatagcgcatcaggcagctttacgtttgcataacctcagcgcccgtttccgggcgcta        <  1:66675‑M1/149‑142 (MQ=255)                                                                                                                              tAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGTTAGCATCAGAAGTGGGTGTTTACGCTCATATACCACGTACGTCCCGGCTCGTTATAGGTATACGCCCCGGCACCGGCGAtata  <  1:104832/150‑1 (MQ=255)                                                                                                                                |                                                                                                                                                    GGGAGGTATGCGTAGTTTTCATATCGACCATATTCGAGACTGATGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACATGGT‑CCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACGACGCGCACTTTGTCAACAATCTGACGTTAGCATCAGAAGTGGGTGTTTACGCTCATATACCACGTACGTCCCGGCTCGTTATAGGTATACGCCCCGGCACCGGCGATATA  >  NC_000913_3_pae_pgi/610058‑610331

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.