New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	3933799 =	55 (0.950)	3 (0.050)	3/326	NT	5.8%	coding (1614/1911 nt)	PP_3467	Sigma‑54 dependent transcriptional regulator
	?	AE015451	3933920 =	45 (0.820)					coding (1493/1911 nt)	PP_3467	Sigma‑54 dependent transcriptional regulator

CACCCTTGGGGGCGGGTGACGAGCAGGACATCGACGTGGCGCTGATCTGCGCCACCCACCGCGACCTCAAGCGCCTGGTGCAGGAGCAGCACTTCCGTGAAGACCTGTTCTACCGGGTCAACGGTGTGTCGCTGCGCCTGCCGGCCCTGCGTGAACGCGACGACCTGGCGGCGATCATCCAGGGCCTGCTGGACAAGGCCGATGCGCGTGGCGTAACCCTCGACCCGGCGTTGACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AE015451/3934034‑3933799 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgttgaccCGGTAGAACAGGTCTTCACGGAAGTGCTGCTCCTGCACCAGGCGCTTGAGGTCGCGGTGGGTGGCGCAGATCAGCGCCACGTCGATGTCCTGCTCGTCACCCGCCCCCAAGGGTGCTACGCGGCGCTCCTGCAGTACCCGCAACAGGCGTGCTTGCAGGGCGAGCGGCATGTCGCCGATTTCGTCGAGGAACAGCGTGCCACCATGGGCCTGCATCAGCCGCCCGACCATGC  >  AE015451/3933920‑3934151                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CACCCTTGGGGGCGGGTGACGAGCAGGACATCGACGTGGCGCTGATCTGCGCCACCCACCGCGACCTCAAGCGCCTGGTGCAGGAGCAGCACTTCCGTGAAGACCTGTTCTACCGGGTCAACGGTGTGTCGCTGCGCCTGCCGGCCCTGCGTGAACGCGACGACCTGGCGGCGATCATCCAGGGCCTGCTGGACAAGGCCGATGCGCGTGGCGTAACCCTCGACCCGGCGTTGACC                                                                                                                                                                                                                                          <  1:903427/236‑1                                                                         GCCTGGTGCAGGAGCAGCACTTCCGTGAAGACCTGTTCTACCGGGTCAACGGTGTGTCGCTGCGCCTGCCGGCCCTGCGTGAACGCGACGACCTGGCGGCGATCATCCAGGGCCTGCTGGACCAGGCCGATGCGCGTGGCGTAACCCCCGACCCGGCGTTG                                                                                                                                                                                                                                             >  2:93641/1‑161                                                                                                                                GTCGCTGCGCCTGCCGGCCCTGCGTGATCGCGACGACCTGGCGGCGATCATCCAGGGCCTGCTGGACAAGGCCGATGCGCGTGGCGTAACCCTCGACCCGGCGTTGACCCGGTAGACCAGGTCTTCACGGAAGTGCTGCTCCTGC                                                                                                                                                                                                      <  2:579088/145‑1                                                                                                                                                                                               GGACAAGGCCGATGCGCGTGGCGTAACCCTCGACCCGGCGTTGACCCGGTAGAACAGGTCTTCACGGAAGTG                                                                                                                                                                                                                <  1:230349/72‑1                                                                                                                                                                                               GGACAAGGCCGATGCGCGTGGCGTAACCCTCGACCCGGCGTTGACCCGGTAGAACAGGTCTTCACGGAAGTG                                                                                                                                                                                                                >  2:230346/1‑72                                                                                                                                                                                                                                          ACCCGGTAGAACAGGTCTTCACGGAAGTGCTGCTCCTGCACCAGGCGCTTGAGGTCGCGGTGGGTGGCGCAGATCAGCGCCACGTCGATGTCCTGCTCGTCACCCGCCCCCAAGGGTGCTACGCGGCGCTCCTGCAGTACCCGCAACAGGCGTGCTTGCAGGGCGAGCGGCATGTCGCCGATTTCGTCGAGGAACAGCGTGCCACCATGGGCCTGCATCAGCCGCCCGACCATGC  >  1:149597/1‑235                                                                                                                                                                                                                                          ACCCGGTAGAACAGGTCTTCACGGAAGTGCTGCTCCTGCACCAGGCGCTTGAGGTCGCGGTGGGTGGCGCAGATCAGCGCCACGTCGATGTCCTGCTCGTCACCCGCCCCCAAGGGTGCTACGCGGCGCTCCTGCAGTACCCGCAACAGGCGTGCTTGCAGGGCGAGCGGCATGTCGCCGATTTCGTCGAGGAACAGCGTGCCACCATGGGCCTGCATCAGCCGC            >  1:986186/1‑225                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CACCCTTGGGGGCGGGTGACGAGCAGGACATCGACGTGGCGCTGATCTGCGCCACCCACCGCGACCTCAAGCGCCTGGTGCAGGAGCAGCACTTCCGTGAAGACCTGTTCTACCGGGTCAACGGTGTGTCGCTGCGCCTGCCGGCCCTGCGTGAACGCGACGACCTGGCGGCGATCATCCAGGGCCTGCTGGACAAGGCCGATGCGCGTGGCGTAACCCTCGACCCGGCGTTGACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AE015451/3934034‑3933799 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgttgaccCGGTAGAACAGGTCTTCACGGAAGTGCTGCTCCTGCACCAGGCGCTTGAGGTCGCGGTGGGTGGCGCAGATCAGCGCCACGTCGATGTCCTGCTCGTCACCCGCCCCCAAGGGTGCTACGCGGCGCTCCTGCAGTACCCGCAACAGGCGTGCTTGCAGGGCGAGCGGCATGTCGCCGATTTCGTCGAGGAACAGCGTGCCACCATGGGCCTGCATCAGCCGCCCGACCATGC  >  AE015451/3933920‑3934151

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 38 ≤ 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.