New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	3409928 =	56 (1.280)	3 (0.070)	3/332	NT	5.3%	intergenic (‑494/‑42)	PP_3022/PP_3024	Transcriptional regulator, AraC family/conserved protein of unknown function
	?	AE015451	= 3450711	52 (1.230)					intergenic (‑125/+258)	PP_5558/PP_3069	putative transcriptional xre family of phage origin/Outer membrane autotransporter

TCACATGATATCCATTCAATGCGCAGGTGATTTGTAAGTACGACAAGCGTGGCAATTTGCCTCTGTTCGCCTGCTGAGTCAATGCATGGAGGGTTGATACCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AE015451/3410072‑3409928 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggttACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGGCTTTCTCGCTATACTGTTCAT  <  AE015451/3450711‑3450606                                                                                                                                                                                                                                                             TCACATGATATCCATTCAATGCGCAGGTGATTTGTAAGTACGACAAGCGTGGCAATTTGCCTCTGTTCGCCTGCTGAGTCAATGCATGGAGGGTTGATACCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTTACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGG                       <  1:610990/230‑1                                                                                                    CCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTTACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGGCT                     >  1:512423/1‑133                                                                                                    CCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTTACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGGCT                     <  2:512421/133‑1                                                                                                                                               GTTACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGGCTTTCTCGCTATACTGTTCAT  >  1:216633/1‑109                                                                                                                                               GTTACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGGCTTTCTCGCTATACTGTTCAT  <  2:216631/109‑1                                                                                                                                                                                                                                                             TCACATGATATCCATTCAATGCGCAGGTGATTTGTAAGTACGACAAGCGTGGCAATTTGCCTCTGTTCGCCTGCTGAGTCAATGCATGGAGGGTTGATACCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AE015451/3410072‑3409928 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggttACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGGCTTTCTCGCTATACTGTTCAT  <  AE015451/3450711‑3450606

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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.