New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4542690	0 (0.000)	17 (0.400)	15/466	1.1	100%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	0 (0.000)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit

AAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAA  >  NC_000913/4542747‑4543228                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                   aaaCGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGGCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaatt                                                                                                                                                                                                                                         >  2:98300‑M2/1‑240 (MQ=255)           aaGCATATAACTATTTGATCTGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTGCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtgccccaattgtcttgtattt                                                                                                                                                                                                                               <  1:350971‑M2/251‑22 (MQ=255)                          tGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgttttttta                                                                                                                                                                                                                 <  1:288723‑M2/250‑36 (MQ=255)                                                                 cACCTCCGCTATATGTAAAGCTAACGTGTCTGTGGCTCGACTCAGCTTCCTCATTCTTCTCTCCAAAAACCATCTCATGCAATATAAACAACTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAACCTGAAAAATTTTTTCCGCGATGCTTTCTTCTATTAGTCAAAAtggcctcaattgtcttgtatttatttgtttttttaactttattaccaataagctaaagcaatcctcttctctttt                                                                                                                                                                         >  2:84163‑M2/1‑176 (MQ=255)                                                                           atatGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATCAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcg                                                                                                                                                               >  1:331101‑M2/1‑166 (MQ=255)                                                                                     cTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatt                                                                                                                                                         <  1:206131‑M2/247‑92 (MQ=255)                                                                                             tctgtgactcgcccgttattcctcatacttctctccaaCAACCACCTCATGCAATATAAACATCTATAAATAAAGATCACAATCGAATATTAAGACAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCATCTCTGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctt                                                                                                                                             <  2:190201‑M2/233‑104 (MQ=255)                                                                                                                               ccAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattact                                                                                                             >  2:340354‑M2/1‑114 (MQ=255)                                                                                                                                              tGCAATATAAACATATATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataaagcac                                                                                              <  1:89497‑M2/249‑151 (MQ=255)                                                                                                                                                                  ataacGATCACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGATTGTCAGCGATGCTTTCCTATATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtttaacgcccagaatggcgaatatttcgatgc                                                                        <  2:45667‑M2/251‑173 (MQ=255)                                                                                                                                                                    aaaGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgccc                                                                      >  1:74255‑M2/1‑77 (MQ=255)                                                                                                                                                                                     atTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgcccgagataatccggaatta                                                     >  1:347114‑M2/1‑60 (MQ=255)                                                                                                                                                                                                   tAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttctttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgcccgcgataatcctgaattaaacgcgtatctgc                                        <  1:274958‑M2/250‑205 (MQ=255)                                                                                                                                                                                                   tAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgcccgagataatcctgaattaaacgagtatctgc                                        <  1:68591‑M2/250‑205 (MQ=255)                                                                                                                                                                                                                     ccGCGATGCTTTCCTCTATGAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcaaagaatggcgaatatttcgatgcccgagataatcctgaattaaaagagtatctgcaccacgctccgccaattc                      <  1:113858‑M2/250‑223 (MQ=255)                                                                                                                                                                                                                         gATGCTTTCCTCTATGCGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctctttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcccagtatggcgaatatttcgatgcccgagataatcctgaattaaacgagtatctgccccactctccgccaattcataac                 <  1:332477‑M2/251‑228 (MQ=255)                                                                                                                                                                                                                                        gAGTCAAAAtggccccaattgtcttgtatttatttgtttttttaactttattatcaataagttaaatcaaacctcttctcgttttaatttttcgtttatgagattatttctttcccataatccggcaaaacgagcagcattactggcggtataacgcacagtatggcgaatatttcgatgcccgagataatcctgaattaaacgagtatctgcaccacgctccgccaattcataaccgcaagcatgcctta  >  1:208359‑M2/1‑9 (MQ=255)                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                   AAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAA  >  NC_000913/4542747‑4543228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ 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.