New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2714300 =	NA (NA)	4 (0.050)	4/162	NT	NA	noncoding (18/98 nt)	RIP188 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP188 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913	4441401 =	NA (NA)					noncoding (9/98 nt)	RIP335 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP335 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site

TGTCGACAAAGTGCGCTTTATTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGGCCTGATA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2714405‑2714300 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcctgataCGCTATGCCGATCAGGCCTAC  >  NC_000913/4441401‑4441421                                                                                                                                 TGTCGACAAAGTGCGCTTTATTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGG                              >  2:819173/1‑99  GTCGACAAAGTGCGCTTTATTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGGCC                            <  2:1358897/100‑1  GTCGACAAAGTGCGCTTTATTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGGCC                            <  2:553597/100‑1    CGACAAAGTGCGCTTTATTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGGCCTG                          >  1:1738696/1‑100      ACAAAGTGCGCTTTATTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGGCCTGAT                        >  2:72118/1‑100                     TTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGGCCTGATGCGCTAcgcttatca         <  1:220542/100‑10                       CATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGGCCTGATGCGCTACGCTTATCAGG       <  2:1239818/100‑1                        ATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCTACGTAGGCCTGATGCGCTACGCTTATCAGGC      <  2:885339/100‑1                         TGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGGCCTGATGCGCTACGCTTATCAGGCC     <  2:332911/100‑1                            CGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGGCCTGATGCGCTACGCTTATCAGGCCTAC  <  1:1229879/100‑1                                                                                                                                 TGTCGACAAAGTGCGCTTTATTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGATCGTGCAAATTCAATATATTGCATGAGCCACGTAGGCCTGATA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2714405‑2714300 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcctgataCGCTATGCCGATCAGGCCTAC  >  NC_000913/4441401‑4441421

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ 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.