New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	= 4932141	37 (0.910)	3 (0.080)	3/322	NT	6.9%	coding (77/741 nt)	fliA	RNA polymerase sigma 28 (sigma F) factor for class III flagellar operons
	?	AE015451	= 4932230	45 (1.150)					coding (818/834 nt)	PP_4342	flagellar synthesis regulator, putative ATPase

TTTGCGCACTTCGTCCAGCATGGCCCCGCGAATGCGGATGCCGGCGTAGGTCTCAAAGCTGGCGCCCTTGCTGGCGTCGTATTTGTTGGCCACTTCCAGCAGGCCGATCATGCCGGCCTGGATCAGGTCCTCGACCTGCACGTTGGCCGGCAAGCGCGCCAACAGGTGGTAGGCGATGCGCTTGACCAGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AE015451/4931951‑4932141 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑accagcgCGGGACCCGTACTATGAACGCCAGCGGCTTCAAGATGTACAGCCGGGCGGCGAAGGACGCCCAGTACGAGCTGATCGAACGCTACGCCCCGCTGGTCAAGCGCATCGCCTACCACCTGTTGGCGCGCTTGCCGGCCAACGTGCAGGTCGAGGACCTGATCCAGGCCGGCATGAT  <  AE015451/4932230‑4932057                                                                                                                                                                                                                                                                                                                                                                               TTTGCGCTCTTCGTCCAGCATGGCCGCGCGAATGCGGATGCCGGCGTAGGTCTCAAAGCTGGCGCCCTTGCTGGCGTCGTATTTGTTGGCCACTTCCAGCAGGCCGATCATGCCGGCCTGGATCAGGTCCTCGACCTGCACGTTGGCCGGCAAGCGCGCCAACAGGTGGTAGGCGATGCGCTTGACCAGCGCGGGACCCGTACTATGAACGCCAGCG                                                                                                                                                      <  1:221310/217‑1                                                                                                               TGCCGGCCTGGATCAGGTCCTCGACCTGCACGTTGGCCGGCAAGCGCGCCAACAGGTGGTAGGCGATGCGCTTGACCAGCGCGGGACCCGTACTATGAACGCCAGCGGCTTCAAGATGTACAGCCGGGCGGCGAA                                                                                                                          <  1:562098/135‑1                                                                                                               TGCCGGCCTGGATCAGGTCCTCGACCTGCACGTTGGCCGGCAAGCGCGCCAACAGGTGGTAGGCGATGCGCTTGACCAGCGCGGGACCCGTACTATGAACGCCAGCGGCTTCAAGATGTACAGCCGGGCGGCGAA                                                                                                                          >  2:562097/1‑135                                                                                                                                                                                        cgCCAGCGCGGGACCCGTACTAGGAACGCCAGCGGCTTCAAGATGTACAGCCGGGCGGCGAAGGACGCCCAGTACGAGCTGATCGAACGCTACGCCCCGCTGGTCAAGCGCATCGCCTACCACCTGTTGGCGCGCTTGCCGGCCAACGTGCAGGTCGAGGACCTGATCCAGGCCGGCATGAT  <  2:240795/180‑1                                                                                                                                                                                        GACGAGCGCGGGACCCGTACTATGAACGCCAGCGGCTTCAAGATGTACAGCCGGGCGGCGAAGGACGCCCAGTACGAGCTGATCGAACGCTACGCCCCGCTGGTCAAGCGCgcca                                                                     <  2:53903/115‑5                                                                                                                                                                                         ACCAGCGCGGGACCCGTACTATGAACGCCAGCGGCTTCAAGATGTACAGCCGGGCGGCGAAGGACGCCCAGTACGAGCTGATCGAACGCTACGCCCCGCTGGTCAAGCGCATCGCCTACCACCTGTTGGCGCGCTTGCCGGCCCACGTGCAGGTCGACGACCTGATCCAG             >  2:116709/1‑170                                                                                                                                                                                            AGCGCGGGACCCGTACTATGAACGCCAGCGGCTTCAAGATGTACAGCCGGGCGGCGAAGGACGCCCAGTACGAGCTGATCGAACGCTACGCCCCGCTGGTCAAGCGCATCGCCTACCACCTGTTGGCGCGCTTGCCGGCCAACGTGCAGGTCGAGGACCTGATCCAGGCCGG        >  2:22745/1‑172                                                                                                                                                                                                                                                                                                                                                                               TTTGCGCACTTCGTCCAGCATGGCCCCGCGAATGCGGATGCCGGCGTAGGTCTCAAAGCTGGCGCCCTTGCTGGCGTCGTATTTGTTGGCCACTTCCAGCAGGCCGATCATGCCGGCCTGGATCAGGTCCTCGACCTGCACGTTGGCCGGCAAGCGCGCCAACAGGTGGTAGGCGATGCGCTTGACCAGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AE015451/4931951‑4932141 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑accagcgCGGGACCCGTACTATGAACGCCAGCGGCTTCAAGATGTACAGCCGGGCGGCGAAGGACGCCCAGTACGAGCTGATCGAACGCTACGCCCCGCTGGTCAAGCGCATCGCCTACCACCTGTTGGCGCGCTTGCCGGCCAACGTGCAGGTCGAGGACCTGATCCAGGCCGGCATGAT  <  AE015451/4932230‑4932057

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ 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.