New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	3409687 =	23 (0.580)	3 (0.080)	3/308	NT	12.2%	intergenic (‑253/‑283)	PP_3022/PP_3024	Transcriptional regulator, AraC family/conserved protein of unknown function
	?	AE015451	3409701 =	22 (0.600)					intergenic (‑267/‑269)	PP_3022/PP_3024	Transcriptional regulator, AraC family/conserved protein of unknown function

CGTGAACCCGTACAGTTTTTATCGCTGGCTGTTACTTGACCGCAGGGCCCGGAACCCACCGAAATAGAGGGCTGTTGTCAGAGGAAACGAGAATGGACCTTTCAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGTGGTGGGCGCGGCCTACCTGTTCTACATCGCCTGGCAACTGTGGCGCGCACCCGTGAGCGAGACCGTGGTGGCAAGCGATCACCCAGGCGG  >  AE015451/3409473‑3409884                                                                                                                                                                                                                                     |                                                                                                                                                                                        cGTGAACCCGTACAGTTTTTATCGCTGGCTGTTACTTGACCGCAGGGCCCGGAACCCACCGAAATAGAGGGCTGTTGTCAGAGGAAACGAGAATGGACCTTTCAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCtt                                                                                                                                                                                  <  1:443617/236‑1 (MQ=255)              aGTTTTTATCGCTGGCTGTTACTTGACCGCAGGGCCCGGAACCCACCGAAATAGAGGGCTGTTGTCAGAGGAAACGAGAATGGACCTTTCAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTAAcc                                                                                                                                                                                    >  1:286212/1‑221 (MQ=255)                           ggctgTTACTTGACCGCAGGGCCCGGAACCCACCGAAATAGAGGGCTGTTGTCAGAGGAAACGAGAATGGACCTTTCAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTgg                                                                                                                                                         >  1:504250/1‑235 (MQ=255)                             ctgTTACTTGACCGCAGGGCCCGGAACCCACCGAAATAGAGGGCTGTTGTCAGAGGAAACGAGAATGGACCTTTCAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGcc                                                                                                                                                       >  1:708354/1‑234 (MQ=255)                                           cAGGGCCCGGAACCCACCGAAATAGAGGGCTGTTGTCAGAGGAAACGAGAATGGACCTTTCAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCa                                                                                                                                        >  1:439902/1‑236 (MQ=255)                                                                  agagGGCTGTTGTCAGAGGAAACGAGAATGGACCTTTCAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGAt                                                                                                                                                  <  2:439119/203‑1 (MQ=255)                                                                                            aaTGGACCTTTCAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCt                                                                                                                                                           <  2:503050/168‑1 (MQ=255)                                                                                            aaTGGACCTTTCAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGgtggtg                                                                                        <  1:278635/235‑1 (MQ=255)                                                                                                       cAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGtggtgg                                                                                       <  1:273733/225‑1 (MQ=255)                                                                                                        aaGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCcgcgg                                                                                                                                                   >  2:70311/1‑163 (MQ=255)                                                                                                             gccgcgccccccaccttgatggccaggaataggtattcgctggtatgcaacaccactgccaggcccatcgctgccagggcgatcatgccgcagaaggcaaggatacGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGc                                                                                                                                                     >  2:589950‑M1/107‑157 (MQ=255)                                                                                                                          cccTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCGAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATg                                                                                                                                                 <  1:15869/148‑1 (MQ=255)                                                                                                                                            gAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCa                                                                                                                                                       >  2:462533/1‑124 (MQ=255)                                                                                                                                                ttcgctggtatgcaacaccactgccaggcccatcgctgccagggcgatcatgccgcagaaggcaaggatacggccggcgccggccGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAgtg                                                                                                                                     <  2:691530‑M2/53‑1 (MQ=255)                                                                                                                                                aTGGCGCCAGGGCCTAACACCCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGTGGTGGGCGCGGCCTACCTGTTCTACATCGCCTGGCAACTGTGGCGCGCACCCGt                                      <  2:265509/233‑1 (MQ=255)                                                                                                                                                   gcgcCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGTGGTGGGCGCGGcc                                                                               <  1:312284/189‑1 (MQ=255)                                                                                                                                                          ggCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGtggtgg                                                                                       >  1:428462/1‑174 (MQ=255)                                                                                                                                                          ggCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGtggtgg                                                                                       <  2:428461/174‑1 (MQ=255)                                                                                                                                                           gcaacaccactgccaggcccatcgctgccagggcgatcatgccgcagaaggcaacgctacGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATggg                                                                                                                                               <  1:554967‑M1/57‑1 (MQ=255)                                                                                                                                                                  cactgccaggcccatcgctgccagggcgatcatgccgcagaaggcaaggatacGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGaa                                                                                                                   <  2:691530‑M1/85‑1 (MQ=255)                                                                                                                                                                   cccTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGTGGTGGGCGCGGcc                                                                               <  1:625973/172‑1 (MQ=255)                                                                                                                                                                        ttgtCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCAt                                                                                                                                                                    <  1:45316/83‑1 (MQ=255)                                                                                                                                                                            cccatcgctgccagggcgatcatgccgcagaaggcaaggatacggccggcgccggccGTAGCGTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGc                                                                                                                              <  1:554967‑M2/60‑1 (MQ=255)                                                                                                                                                                                  gctgccagggcgatcatgccgcagaaggcaaggatacggccggcgccggccGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGTGGGGGGCGCGGc                                                                                >  2:589950‑M2/52‑157 (MQ=255)                                                                                                                                                                                     ccgcccgccGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAg                                                                                                                                                      <  2:173536/83‑1 (MQ=255)                                                                                                                                                                                     aCGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGTGGTGGGCGCGGCCTACCTGTTCTACATCGCCTGGCAACTGTGGCGCGCACCCGTGAGCGAGACCGTGGTGGCAAGCGATCACCCAggcgg  >  2:608212/1‑232 (MQ=255)                                                                                                                                                                                      cGCCAGCCGTTACGGCCTGCGCCCCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAg                                                                                                                       <  1:198888/114‑1 (MQ=255)                                                                                                                                                                                                            aCCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGTGGTGGGCGCGGCCTACCTGTTCTACATCGCCTGGCAACTGTGGCGCGCACCCGTGAGCGAGACCg                           >  2:265161/1‑184 (MQ=255)                                                                                                                                                                                                                  tGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGTGGTGGGCGCGGCCTACCTGTTCTACCTCTCCTGGCAACTGGGgcgcggcccc                                        >  2:203509/1‑160 (MQ=255)                                                                                                                                                                                                                  tGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGTGGTGGGCGCGGCCTACCTGTTCTACATCGCCTGGCAACTGTGGCGCGCACCCGTGAGc                                  >  1:579823/1‑171 (MQ=255)                                                                                                                                                                                                                           GGCGCCGGCCGTCTCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATTCCAGCGAATACCTATTCCTGGCCATCAAGGTGGTGGGCGCGGcc                                                                               >  2:194680‑M1/1‑117 (MQ=255)                                                                                                                                                                                                                               ccggccGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTgg                                                                                                                                          >  2:298479‑M2/7‑54 (MQ=255)                                                                                                                                                                                                                               CCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTgg                                                                                                                                          >  1:298480‑M1/1‑54 (MQ=255)                                                                                                                                                                                                                                     |                                                                                                                                                                                        CGTGAACCCGTACAGTTTTTATCGCTGGCTGTTACTTGACCGCAGGGCCCGGAACCCACCGAAATAGAGGGCTGTTGTCAGAGGAAACGAGAATGGACCTTTCAAGCCTGCTGCTTTTCATCCCTGCCTGCTTCGCCTTGAACATGGCGCCAGGGCCTAACAACCTGTTGTCACTGCACAACGCCAGCCGTTACGGCCTGCGCACCGCCTGCGTGGCCGGCGCCGGCCGTATCCTTGCCTTCTGCGGCATGATCGCCCTGGCAGCGATGGGCCTGGCAGTGGTGTTGCATACCAGCGAATACCTATTCCTGGCCATCAAGGTGGTGGGCGCGGCCTACCTGTTCTACATCGCCTGGCAACTGTGGCGCGCACCCGTGAGCGAGACCGTGGTGGCAAGCGATCACCCAGGCGG  >  AE015451/3409473‑3409884

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ 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.