New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 4284640	NA (NA)	5 (0.210) +CTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGC	3/170	3.8	14.2%	intergenic (‑167/+33)	yjcH/acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
	?	NC_000913_3_pae_pgi	= 4459704	50 (1.260)					noncoding (30/84 nt)	REP338 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP338 (repetitive extragenic palindromic) element; contains 2 REP sequences
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TTTACGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/4284579‑4284640 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTGATAAGACGCGACAGCGTCGCATCAGGCAT  <  NC_000913_3_pae_pgi/4459704‑4459673                                                               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||                                 cttgtGCCGCATCCGGCAATCAAGGCCTGATGCGACGCTGTCGCGTCTTATCAGGCAAACGACTAGTTCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATAAGACGCGACAGCGTCGCATCAGGCA   <  1:335606/144‑1      GCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTG                                                                            <  1:50330/71‑1      GCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTG                                                                            >  2:50330/1‑71                GCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCC                                 >  1:289715/1‑104                GCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCC                                 <  2:289715/104‑1                GCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAA                                         >  1:115678/1‑96                GCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAA                                         <  2:115678/96‑1                 CAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATAAGACGCGACAGCGTCGCATCAGGCAT  <  1:57721/134‑1                 CAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATAAGACGCGACAGCGTCGCATCAGGCAT  >  2:57721/1‑134                                                               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||                                 TTTACGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/4284579‑4284640 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTGATAAGACGCGACAGCGTCGCATCAGGCAT  <  NC_000913_3_pae_pgi/4459704‑4459673

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