New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 284691	16 (0.990)	3 (0.190)	3/244	1.9	20.3%	coding (1491/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein
	?	NC_000913_3_pae_pgi	= 284723	8 (0.510)					coding (1523/1968 nt)	yagF	CP4‑6 prophage; dehydratase family protein

GGGCGAAGATGGCGTATACCACCACACCGGCCGGGTGCGGGTGTTTGTCTCGGAAGCGCAGGCGATCAAGGCGATCAAGCGGGAAGAGATTGTGCAGGGCGATATCATGGTGGTGATCGGCGGCGGGCCGTCCGGCACCGGCATGGAAGAGACCTACCAGCTCACCTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTC  >  NC_000913_3_pae_pgi/284583‑284846                                                                                                                                             |                                                                                                                            gggCGAAGATGGCGTATACCACCACACCGGCCGGGTGCGGGTGTTTGTCTCGGAAGCGCAGGCGATCAAGGCGATCAAGCGGGAAGAGATTGTGCAGGGCGATATCATGGTTGTGATCGGCGGCGGGCCGTCCGGCACCGGCATGGAaga                                                                                                                    <  1:63631/150‑1 (MQ=255)       aGATGGCGTATACCACCACACCGGCCGGGTGCGGGTGTTTGTCTCGGAAGCGCAGGCGATCAAGGCGATCAAGCGGGAAGAGATTGTGCAGGGCGATATCATGGTGGTGATCGGCGGCGGGCCGTCCGGCACCGGCATGGAAGAGACCTa                                                                                                              <  2:101489/150‑1 (MQ=255)                                                                                                   gCGATATCATGGTGGTGATCGGCGGCGGGCCGTCCGGCACCGGCATGGAAGAGACCGACCAGCGCACCTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCt                  >  4:3766/1‑150 (MQ=255)                                                                                                           aTGGTGGTGATCGGCGGCGGGCCGTCCGGCACCGGcatgatatcgccctgcacaatctcttcccgcttgatcgccttgatcgcctgcgcttccgagacaaacacccgcacccggccggtgtg                                      >  3:54884‑M2/1‑35 (MQ=255)                                                                                                           aTGGTGGTGATCGGCGGCGGGCCGTCCGGCACCGGcatgatatcgccctgcacaatctcttcccgcttgatcgccttgatcgcctgcgcttccgagacaaacacccgcacccggccggtgtg                                      <  4:54884‑M2/122‑88 (MQ=255)                                                                                                             ggtggtGATCGGCGGCGGGCCGTCCGGCACCGGcatgatatcgccctgcacaatctcttcccgcttgatcgccttgatcgcctgcgcttccgagacaaacacccgcacccggccggtgtggtggtatacgccatcttcgcccaccaccga        <  2:90671‑M2/150‑118 (MQ=255)                                                                                                              gtggtgATCGGCGGCGGGCCGTCCGGCACCGGCATGGAAGAGACCTACCAGCTCACCTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGc                                                            <  1:197856/97‑1 (MQ=255)                                                                                                              gtggtgATCGGCGGCGGGCCGTCCGGCACCGGCATGGAAGAGACCTACCAGCTCACCTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGc                                                            >  2:197856/1‑97 (MQ=255)                                                                                                                   gATCGGCGGCGGGCCGTCCGGCACCGGCATGGAAGAGACCTACCAGCTCACCTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTc  >  4:100693/1‑150 (MQ=255)                                                                                                                                             gcaTGGAAGAGACCTACCAGCTCACCTCCGCGCTAAAg                                                                                        >  1:109043/1‑38 (MQ=255)                                                                                                                                             gcaTGGAAGAGACCTACCAGCTCACCTCCGCGCTAAAg                                                                                        <  2:109043/38‑1 (MQ=255)                                                                                                                                             |                                                                                                                            GGGCGAAGATGGCGTATACCACCACACCGGCCGGGTGCGGGTGTTTGTCTCGGAAGCGCAGGCGATCAAGGCGATCAAGCGGGAAGAGATTGTGCAGGGCGATATCATGGTGGTGATCGGCGGCGGGCCGTCCGGCACCGGCATGGAAGAGACCTACCAGCTCACCTCCGCGCTAAAGCATATCTCGTGGGGCAAGACGGTGTCGCTCATCACCGATGCGCGCTTCTCGGGCGTGTCGACGGGCGCCTGCTTCGGCCACGTGTC  >  NC_000913_3_pae_pgi/284583‑284846

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.