New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	93 (0.870)	6 (0.060)	6/174	NT	6.5%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542995 =	82 (0.770)					intergenic (+362/‑120)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit

CATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4542778‑4542682 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAA  >  NC_000913/4542995‑4543091                                                                                                                                                                                                    CATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAAA                                                                                                 <  1:1391929/99‑1        AACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAAATGTTTCA                                                                                          >  1:2045642/1‑99                  TGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAAATGTTTCATCTTTTGGGG                                                                                >  1:409465/1‑99                                                       AAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACA                                           >  1:1516369/1‑99                                                        AAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAA                                          >  1:759410/1‑99                                                          AATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAA                                        >  1:1478232/1‑99                                                                      ATTTATGATATGGACAGTTTGGCCCCAAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAG                            <  1:551849/99‑1                                                                                                AAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAA  <  1:2252600/99‑1                                                                                                                                                                                                    CATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4542778‑4542682 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAA  >  NC_000913/4542995‑4543091

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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.