New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4008401 =	NA (NA)	9 (0.070)	8/164	NT	NA	noncoding (5/34 nt)	REP289 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP289 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	4008431 =	NA (NA)					intergenic (+54/+8)	rhtC/rhtB	threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump

TGAATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATCCGAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4008506‑4008401 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atccgacATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCC  >  NC_000913/4008431‑4008528                                                                                                                                                                                                              TGAATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTA                                                                                                          >  2:1313361/1‑100  GAATAAGATTTTCGGCTCGTTGTTTATGCTTGTGGGAGCGCTGTTAGCATCGGCGGGGCCTGAGTGAAAAATAATGTCGGATGTGGCGTAATCGCCTTAT                                                                                                         >  1:1335851/1‑100  GAATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTAT                                                                                                         >  2:1676635/1‑100  GAATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTAT                                                                                                         <  1:987051/100‑1  GAATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTAT                                                                                                         >  1:420176/1‑100   AATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATC                                                                                                        <  2:901472/100‑1   AATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATC                                                                                                        <  1:2334018/100‑1   AATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATC                                                                                                        <  1:891708/100‑1    ATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGCGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATCC                                                                                                       >  1:3250833/1‑100    ATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGACAAATAATGTCGGATGCGGCGTAAACGCCTTATCC                                                                                                       >  1:3647269/1‑100    ATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATCC                                                                                                       >  1:2082009/1‑100    ATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATCC                                                                                                       <  2:895716/100‑1    ATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATCC                                                                                                       >  1:3581489/1‑100    ATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATCC                                                                                                       <  1:2958520/100‑1       AGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATCCGAC                                                                                                    >  2:3542518/1‑100          TTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATAAGGCGTTTACGCCGCATCCGACAT                                                                                                  <  1:3620493/99‑1               GGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATAAGGCGTTTACGCCGCATCCGACATTATTTT                                                                                            <  2:2881933/100‑1                                                                CGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAAC                                           >  2:2973636/1‑100                                                                 GTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACG                                          >  2:930869/1‑100                                                                  TGAAAAATAATGTCGGATGCCGCGTAAACGCCTTATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGA                                         >  2:3510043/1‑100                                                                    AAAAATAATGTCGGATGCGGCGTAAACGCCTTATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGC                                       >  1:2677222/1‑100                                                                         TAATGTCGGATGCGGCGTAAACGCCTTATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAA                                  >  1:989963/1‑100                                                                          AATGTCGGATGCGGCGTAAACGCCTTATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAA                                 >  2:3616499/1‑100                                                                           ATGTCGGATGCGGCGTAAACGCCTTATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAATGAGCCGAAAAT                                >  1:304016/1‑100                                                                           ATGTCGGATGCGGCGTAAACGCCTTATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAAT                                >  2:3518816/1‑100                                                                                                    ATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTT       <  2:2179301/100‑1                                                                                                    ATCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTT       <  2:2178871/100‑1                                                                                                     TCCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACCACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTG      <  2:2609846/100‑1                                                                                                      CCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGG     <  2:2398289/100‑1                                                                                                      CCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGG     >  2:2665992/1‑100                                                                                                      CCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGG     >  1:1303635/1‑100                                                                                                      CCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGG     <  2:3393111/100‑1                                                                                                      CCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGG     <  2:2069384/100‑1                                                                                                      CCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGG     <  2:710468/100‑1                                                                                                      CCGACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGG     <  1:1392018/100‑1                                                                                                        GACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTC   >  2:1716352/1‑100                                                                                                        GACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTC   >  1:3484245/1‑100                                                                                                         ACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCC  <  1:327031/100‑1                                                                                                         ACATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCC  >  1:2494467/1‑100                                                                                                                                                                                                              TGAATAAGATTTTCGGCTCGTTGTTTATGCTGGTGGGAGCGCTGTTAGCATCGGCGAGGCATGCGTGAAAAATAATGTCGGATGCGGCGTAAACGCCTTATCCGAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4008506‑4008401 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atccgacATTATTTTTCACGCATGCCTCGCCGATGCTAACAGCGCTCCCACCAGCATAAACAACGAGCCGAAAATCTTATTCAGCGCCTTCATCTGCTTTGGTCC  >  NC_000913/4008431‑4008528

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.