New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 540528	11 (0.680)	4 (0.260)	4/236	1.6	27.3%	intergenic (+20/‑37)	allB/ybbY	allantoinase/putative uracil/xanthine transporter
	?	NC_000913_3_pae_pgi	= 540537	11 (0.730)					intergenic (+29/‑28)	allB/ybbY	allantoinase/putative uracil/xanthine transporter

CCCGTATGTTGGCCGTACCATTGGCGCGCGTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTATTTTTTGCAACACGGTTGTGGTTCCTCCTACGCTACTTTCTGCTTTTCAG  >  NC_000913_3_pae_pgi/540379‑540675                                                                                                                                                      |                                                                                                                                                    cccGTATGTTGGCCGTACCATTGGCGCGCGTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCG                                                                                                                                                     >  4:48882‑M1/1‑150 (MQ=255)             ccGTACCATTGGCGCGCGTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGcgg                                                                                                                                         >  1:48437‑M2/1‑147 (MQ=255)                         cgcgcgTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGt                                                                                                                             <  3:48882/150‑1 (MQ=255)                                                  cGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTg                                                                                                    <  2:133663/150‑1 (MQ=255)                                                                 tACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGaaa                                                                                     <  1:96612/150‑1 (MQ=255)                                                                       aTTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGt                                                                               >  2:176523/1‑150 (MQ=255)                                                                            aCAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAAttt                                                                                                      <  4:81981/122‑1 (MQ=255)                                                                            aCAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAAttt                                                                                                      >  3:81981/1‑122 (MQ=255)                                                                                ggCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGAt                                                                      >  1:189431/1‑150 (MQ=255)                                                                                               ccGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGccgcaaggacgggc                                                                                                                                       >  3:13542‑M1/1‑56 (MQ=255)                                                                                               ccGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGccgcaaggacgggc                                                                                                                                       <  4:13542‑M1/70‑15 (MQ=255)                                                                                                    aGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTAtt                                                  <  1:176523/150‑1 (MQ=255)                                                                                                       tCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCttt                                                     <  3:73361/144‑1 (MQ=255)                                                                                                       tCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCttt                                                     >  4:73361/1‑144 (MQ=255)                                                                                                                  ttAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGccgcaaggacgggcattgcaggggccagattactgctgatgtttaa                                                                                                       <  3:104192‑M1/83‑47 (MQ=255)                                                                                                                  ttAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGccgcaaggacgggcattgcaggggccagattactgctgatgtttaa                                                                                                       >  4:104192‑M1/1‑37 (MQ=255)                                                                                                                  ttAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGcgggcattgcaggggccagattactgctgatgtttaa                                                                                                       <  3:104192‑M2/83‑38 (MQ=255)                                                                                                                  ttAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGcgggcattgcaggggccagattactgctgatgtttaa                                                                                                       >  4:104192‑M2/1‑46 (MQ=255)                                                                                                                                                aTGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTATTTTTTGCAACACGGTTGTGGTTCCTCCTACGCTACTTTCTGCttt      >  1:57601/1‑150 (MQ=255)                                                                                                                                                  gCCCGTCCTTGCGGcgggcattgcaggggccagattactgctgatgtttaaggataaattgacctttcgg                                                                                    >  3:13542‑M2/1‑14 (MQ=255)                                                                                                                                                  gCCCGTCCTTGCGGcgggcattgcaggggccagattactgctgatgtttaaggataaattgacctttcgg                                                                                    <  4:13542‑M2/70‑57 (MQ=255)                                                                                                                                                    ccgccgcaaggacgggcattgcaggggccagattactgctgatgtttaaggataaattgacctttcggcgcaacagggaagccctgttcaatgtcgtaaatcacatcaccacgtaagatggttttcgtgatacgcgcgccaatggtacgg  >  1:48437‑M1/1‑3 (MQ=255)                                                                                                                                                      |                                                                                                                                                    CCCGTATGTTGGCCGTACCATTGGCGCGCGTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTATTTTTTGCAACACGGTTGTGGTTCCTCCTACGCTACTTTCTGCTTTTCAG  >  NC_000913_3_pae_pgi/540379‑540675

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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.