New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 265251	72 (0.930)	7 (0.100)	5/248	NT	8.5%	intergenic (‑45/+53)	yafX/ykfF	CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein
	?	NC_000913	2775896 =	84 (1.160)					intergenic (+80/‑23)	ypjI/yfjX	pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related/CP4‑57 prophage; putative antirestriction protein

AAAACGCCAGCGGCGATGGCTGGCGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/265226‑265251 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gctggcgtTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCCGCTAACGGATCCGAATTTGAGTTGAGCGTAACGCAGGTACCCGATGAACAGCATATCCGCTTCTGGCCGCAGCACTTTGGCACCATCCCGC  >  NC_000913/2775896‑2776042                                                                                                                                                                               AAAACGCCAGCGGCGATGGCTGGCGTTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCCGCTAACGGATCCGAATTTGAGTTGAGCGTAACGCAGGTACCCGATGAACAGCATATCCGCTTCTGGC                          >  1:262015/1‑149 AAAACGCCAGCGGCGATGGCTGGCGTTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCCGCTAACGGATCCGAATTTGAGTTGAGCGTAACGCAGGTACCCGATGAACAGCATATCCGCTTCTGGC                          >  1:51045/1‑149 AAAACGCCAGCGGCGATGGCTGGCGTTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCCGCTAACGGATCCGAATTTGAGTTGAGCGTAACGCAGATACCCGATGAACAGCATATCCGCTTCTGac                          >  3:555314/1‑147  AAACGCCAGCGGCGATGGCTGGCGTTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCC                                                                                             <  3:154894/81‑1  AAACGCCAGCGGCGATGGCTGGCGTTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCC                                                                                             >  4:154894/1‑81    ACGCCAGCGGCGATGGCTGGCGTTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCCGCTAAC                                                                                       <  1:445223/85‑1    ACGCCAGCGGCGATGGCTGGCGCTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCCGCTAcc                                                                                       >  2:445223/1‑83                     TGGCGTTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCCGCTAACGGATCCGAATTTGAGTTGAGCGTAACGCAGGTACCCGATGAACAGCATATCCGCTTCTGGCCGCAGCACTTTGGCACCATC      >  3:71980/1‑149                         GTTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCCGCTAACGGATCCGAATTTGAGTTGAGCGTAACGCAGGTACCCGATGAACAGCATATCCGCTTCTGGCCGCAGCATTTTGGCACCATCCCGC  >  3:582053/1‑149                         GTTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCCGCTAACGGATCCGAATTTGAGTTGAGCGTAACGCAGGTACCCGATGAACAGCATATCCGCTTCTGGCCGCAGCACTTTGGCACCATCCCGC  >  2:380615/1‑149                                                                                                                                                                               AAAACGCCAGCGGCGATGGCTGGCGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/265226‑265251 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gctggcgtTTTTTATTCACGGAGACATACCCATGACAACACAGACACAGTACGACCTCGTACCCGCTAACGGATCCGAATTTGAGTTGAGCGTAACGCAGGTACCCGATGAACAGCATATCCGCTTCTGGCCGCAGCACTTTGGCACCATCCCGC  >  NC_000913/2775896‑2776042

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ 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.