New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 3285741	3 (0.230)	3 (0.240)	3/244	1.4	35.4%	coding (264/792 nt)	agaD	N‑acetylgalactosamine‑specific enzyme IID component of PTS
	?	NC_000913_3_pae_tpiA	= 3285798	8 (0.630)					coding (321/792 nt)	agaD	N‑acetylgalactosamine‑specific enzyme IID component of PTS

AAAAAGATTTATAAGGACGACAAACCGGGCTTAAGCGCGGCGATGAAAGATAACCTCGAATTTATTAATACCCACCCGAATCTGGTCGGATTCCTGATGGGGTTATTAATTTCGATGGAAGAAAAAGGAGAAAACCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/3285604‑3285741 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcATCGCCAATCCCGGCGATTGGGCCAAACAGTGCCACTTTGAGGCCTTTAATGGTGTCGCGGTTTTCTCCTTTTTCTTCCATCGAAATTAATAACCCCATCAGGAATCCGACCAGATTCGGGTGGGT  <  NC_000913_3_pae_tpiA/3285798‑3285673                                                                                                                                                                                                                                                                          AAAAAGATTTATAAGGACGACAAACCGGGCTTAAGCGCGGCGATGAAAGATAACCTCGAATTTATTAATACCCACCCGAATCTGGTCGGATTCCTGATGGGGTTATTAATTTCGATGGAAGAAAAAGGAGAAAACC                                                                                                                                  <  2:134115/136‑1                                                                                                      GTTATTAATTTCGATGGAAGAAAAAGGAGAAAACCGCATCGCCAATCCCGGC                                                                                                                 >  1:125379/1‑52                                                                                                      GTTATTAATTTCGATGGAAGAAAAAGGAGAAAACCGCATCGCCAATCCCGGC                                                                                                                 <  2:125379/52‑1                                                                                                                                 AGAAAACCGCATCGGCAATCCCGGCGATTGGGCCAAACAGTGCCACTTTGAGGCCTTTAATGGTGTCGCGGTTTTCTCCTTTTTCTTCCATCGAAATTAATAACCCCATCAGGAAGCCGACCAGATTCGGGTGGGT  <  2:134280/136‑1                                                                                                                                                                                                                                                                          AAAAAGATTTATAAGGACGACAAACCGGGCTTAAGCGCGGCGATGAAAGATAACCTCGAATTTATTAATACCCACCCGAATCTGGTCGGATTCCTGATGGGGTTATTAATTTCGATGGAAGAAAAAGGAGAAAACCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/3285604‑3285741 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcATCGCCAATCCCGGCGATTGGGCCAAACAGTGCCACTTTGAGGCCTTTAATGGTGTCGCGGTTTTCTCCTTTTTCTTCCATCGAAATTAATAACCCCATCAGGAATCCGACCAGATTCGGGTGGGT  <  NC_000913_3_pae_tpiA/3285798‑3285673

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