New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	3312700 =	17 (0.980)	4 (0.250)	3/254	2.1	21.7%	coding (78/945 nt)	truB	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase
	?	NC_000913_3_pae_pgi	3312734 =	13 (0.800)					coding (44/945 nt)	truB	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase
Rejected: Coverage evenness skew score above cutoff.

CTGGATAAACCTCAGGGTATGTCCAGCAAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/3312729‑3312700 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tccagcaacAAAACGCCGTTAATGTCGCGACCGCGACGACGAGGACGACTCATTAGTCCTCCTTGCTGTCGTCCGGGTTAACACGACGTTCTTCGTCATGTTTGACCACGCTGGTCACCAGGTTTGACATGCGCATCCCTTCAACCAGAGAGTTGT  >  NC_000913_3_pae_pgi/3312734‑3312880                                                                                                                                                                                   CTGGATAAACCTCAGGGTATGTCCAGCAACAAAACGCCGTTAATGTCGCGACCGCGACGACGAGGACGACTCATTAGTCCTCCTTGCTG                                                                                          >  1:128479/1‑89 CTGGATAAACCTCAGGGTATGTCCAGCAACAAAACGCCGTTAATGTCGCGACCGCGACGACGAGGACGACTCATTAGTCCTCCTTGCTG                                                                                          <  2:128479/89‑1 CTGGATAAACCTCAGGGTATGTCCAGCAACAAAACGCCGTTAATGTCGCGACCGCGACGACGAGGACGACTCATTAGTCCTCCTTGCT                                                                                           <  1:170118/88‑1 CTGGATAAACCTCAGGGTATGTCCAGCAACAAAACGCCGTTAATGTCGCGACCGCGACGACGAGGACGACTCATTAGTCCTCCTTGCT                                                                                           >  2:170118/1‑88                         AGCAACAAAACGCCGTTAATGTCGCGACCGCGACGACGAGGACGACTCATTAGTCCTCCTTGCTGTCGTCCGGGTTAACACGACGTTCTTCGTCATGTTTGACCACGCTGGTCACCAGGTTTGACATGCGCATCCCTTCAACCAGAGAGT     >  2:128606/1‑150                            AACAAAACGCCGTTAATGTCGCGACCGCGACGACGAGGACGACTCATTAGTCCTCCTTGCTGTCGTCCGGGTTAACACGACGTTCTTCGTCATGTTTGACCACGCTGGTCACCAGGTTTGACATGCGCATCCCTTCAACCAGAGAGTTGT  <  3:82257/150‑1                                                                                                                                                                                   CTGGATAAACCTCAGGGTATGTCCAGCAAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/3312729‑3312700 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tccagcaacAAAACGCCGTTAATGTCGCGACCGCGACGACGAGGACGACTCATTAGTCCTCCTTGCTGTCGTCCGGGTTAACACGACGTTCTTCGTCATGTTTGACCACGCTGGTCACCAGGTTTGACATGCGCATCCCTTCAACCAGAGAGTTGT  >  NC_000913_3_pae_pgi/3312734‑3312880

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.