New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 895186	38 (0.950)	7 (0.200)	4/272	NT	21.8%	noncoding (35/98 nt)	RIP82 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP82 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	CP009273	= 896203	17 (0.480)					intergenic (‑172/+119)	artJ/artM	arginine binding protein, periplasmic/arginine transporter subunit

GTGGCTGAAACGCCAAAATTGATTTTCTCTGCGGCAGAAGCACCGAAAGTAAAGGAAGCAAGTAAAGCGGCAAGAACTAACTTTTTCATGATGGAACTCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAATAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCGTCTTATCAGACCTACAAAACCCCCCGGCGAATGTACGCAGCCACATTAATTTCGCCGTTCGAATGCCAGCGCTTTGCGCTCGATCAGACGCATCATCAGCGTCAGCAGGCCGTTAACGACCAGGTAAATAATCCCTGCCGCACCGAACACCATTACATCGTAGGTGCGTCCGTACAACAACTGGCTGTATCCCATCACT  >  CP009273/895943‑896475                                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                                                 gttgCTTAAATGACAATATTGTTTTTATCTGCGGCAGAAGAACCGAAAGTAAAGGAAGAAAGTAAATAGGCAAGAACTAACTTTTTCATGATGGAACTCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAATAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATaa                                                                                                                                                                                                                                                                    <  1:47942/272‑1 (MQ=255) gtgaatgaaaaGCCAAAATTGATTTTCTCGGGGGCGTAAGCACCGAAAGTAAAGGAAGCAAGTAAAGCGGCAAGAAATAACTTTTTCATGATGGAAATCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAATAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTAtgtaggccggataa                                                                                                                                                                                                                                                                    >  2:712859‑M2/6‑261 (MQ=255)                    tGAGTTTCGCTGCCGCAGAAGCACCGAAAGTAAAGGAAGCAAGTGAAGCGGCAAGAACTTACTTTTTCATGTGTGAACTCCCGTCTGTCAATCTTATGATTTTTGGACGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAATAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATcc                                                                                                                                                                                                                                                  <  2:660266/274‑1 (MQ=255)                            tctGCGGCAGAAGTACCGAAAGTAAAGGAAGCAAGTAAAGAGGCAAGAACTAACTTTTTCATGATGGAACTCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAATAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTAtgtaggccggataaggcgtttacgccgcatccggcataaac                                                                                                                                                                                                                                         >  1:722068‑M2/1‑234 (MQ=255)                                                                                                                                                            tCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAATAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCGTCTTNTCAGACCTACAAAACCCCCCGGCGAATGTACGCAGCCACATTAATTTCCACGTTCGAATCCCAGCGCTTTGCGCTCGATCAAACGcaaca                                                                                                          >  1:555587/1‑274 (MQ=255)                                                                                                                                                                         aaataaacaaaCATGGTGAAATAATTAAATTGAAATAAAAAGTACGCACCATGGGTTTGGTTGTCCGGCTTAATGTGAAGAATTTATGCACGTTGGAGGCGGGAGAGGGCGTCCCCGCCGCATACGGCAAAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCGTCTTATCAGACCTACAAAACCCCCCGGCGAATGTACGCAGCCACATTAATTTCGCCGTTCGAATGGCAGCGCTTTGCGCTCGATCAGACGCATCAGCAGCGTCAGCAgg                                                                                            <  2:629960/267‑1 (MQ=255)                                                                                                                                                                                                 tttAAATGAAATAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCGTCTTATCAGACCTACAAAACCCCCCGGCGAATGTACGCAGCCACATTAATTTCGCCGTTCGAATGCCACCGCTTGCCGCTCGATCAGACGCATCAGCAGCGTCAGCCGGCCGTCAACGACCAGGTacaacatg                                                                    >  2:39319/1‑268 (MQ=255)                                                                                                                                                                                                           aTAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCGTCTTATCAGACCTACAAAACCCCCCGGCGAATGTACGCAGCCACATTAATTTCGCCGTTCGACTGCCAGCGCTTTGCGCTCGATCAGACGCATCATCAGCGTCAGCAGGCCGTTAACGACCAGGTAAATAAT‑CCTACCGCAc                                                          >  1:184027/1‑274 (MQ=255)                                                                                                                                                                                                                            cTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCAc                                                                                                                                                                                                                                       >  2:367174/1‑85 (MQ=255)                                                                                                                                                                                                                                gTGGGTTGTCCGTCTTCATTATAATAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTg                                                                                                                                                                                                                                   <  1:367181/85‑1 (MQ=255)                                                                                                                                                                                                                                 tGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGcaca                                                                                                                                                                                                                                            >  1:356340/1‑75 (MQ=255)                                                                                                                                                                                                                                  gggTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCGTCTTATCAGACCTACAAAACCACCCGGCGAATGTACGCAGCCACATTAATTTCGCCGTTCGAATGCCCGCGCTTTGCGCTCGATCAGACGCATCATCAGCGTCAGCCGTCCGTTAACGACCAGGCAAATAATCCCTGCCCCACCAAACAACAATAAATCGTAGGt                                    >  1:154131/1‑274 (MQ=255)                                                                                                                                                                                                                                    gTTGTCCGTCTTCATTATAAGAATTTATGCACTAtgtaggccggataaggcgtttacgccgcatccggcataaacaacgcgcactttg                                                                                                                                                                                                                            <  1:9344‑M2/88‑55 (MQ=255)                                                                                                                                                                                                                                     ttGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCa                                                                                                                                                                                                                                        <  2:356334/75‑1 (MQ=255)                                                                                                                                                                                                                                      tGTCCGTCTTCATTATAAGAATTTATGCACTAtgtaggccggataaggcgtttacgccgcatccggcataaacaacgcgcactttg                                                                                                                                                                                                                            <  1:74807‑M2/86‑55 (MQ=255)                                                                                                                                                                                                                                      tGTCCGTCTTCATTATAAGAATTTATGCACTAtgtaggccggataaggcgtttacgccgcatccggcataaacaacgcgcactttg                                                                                                                                                                                                                            <  2:116209‑M2/86‑55 (MQ=255)                                                                                                                                                                                                                                      tGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAgg                                                                                                                                                                                                                                          >  1:261120/1‑72 (MQ=255)                                                                                                                                                                                                                                      tGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACAGTGCTGATGTCTGATGc                                                                                                                                                                                                                     >  2:48978/1‑93 (MQ=255)                                                                                                                                                                                                                                      tGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGAAAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCCCGTCTTATCAGACCTACAAAAaccc                                                                                                                                                                                  >  1:581219/1‑128 (MQ=255)                                                                                                                                                                                                                                        tCCGTCTTCATTATAAGAATTTATGCACTAtgtaggccggataaggcgtttacgccgcatccggcataaacaacgcgcactttgtcag                                                                                                                                                                                                                        >  2:9344‑M2/1‑30 (MQ=255)                                                                                                                                                                                                                                          cGTCTTCATTATAAGAATTTATGCACTAtgtaggccggataaggcgtttacgccgcatccggcataaacaacgcgcactttgtcag                                                                                                                                                                                                                        >  2:74806‑M2/1‑28 (MQ=255)                                                                                                                                                                                                                                          cGTCTTCATTATAAGAATTTATGCACTAtgtaggccggataaggcgtttacgccgcatccggcataaacaacgcgcactttgtcag                                                                                                                                                                                                                        >  1:116210‑M2/1‑28 (MQ=255)                                                                                                                                                                                                                                          cGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCAcc                                                                                                                                                                                                                                      <  2:261117/72‑1 (MQ=255)                                                                                                                                                                                                                                          cGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACg                                                                                                                                                                                                                 <  1:48979/93‑1 (MQ=255)                                                                                                                                                                                                                                                    ttaAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGNGTCTTATCAGACCTACAAGACCCCCCGGCGAATGTACGCAGCCACATTAATTTCGCCGTTCGAATGCCAGCGCTTTGCGCTCGATCAGACGCATCATCAGCGTCAGCAGGCCGTTAACGACCAGGTAAATAATCCCTGCCGCACCGAACACCATTACATCGTAGGTGCGTCCGTACAACAACt                   <  1:531549/272‑1 (MQ=255)                                                                                                                                                                                                                                                             tATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCGTCTTATCAGACCTACAAAACCCCCCGGCGAATGTACGCAGCCACATTAATTTCGCCGTTCGAATGCCAGCGCTTTGCGCTCGATCAGACGCATCATCAGCGTCAGCAGGCCGt                                                                                        >  2:142544/1‑195 (MQ=255)                                                                                                                                                                                                                                                                 cACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCGTCTTATCAGACCTACAAAACCCCCCGGCGAATGTACGCAGCCACATTAATTTCGCCGTTCGAATGCCAGCGCTTTGCGCTCGATCAGACGCATCATCAGCGTCAGCAGGCCGTTAAc                                                                                    <  1:142545/195‑1 (MQ=255)                                                                                                                                                                                                                                                                   cTATGTAGGCTGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCGTCTTATCAGACCTACAAAACCCCCCGGCGAATGTACGCAGCCACATTAATTTCGCCGTTCGAATGCCAGCGCTTTGCGCTCGATCAGACGCATCATCAGCGTCAGCAGGCCGTTAACGAGCAGGTAAATAATCCCTGCCGCACCGAACACCATTACATCGTAAGTGCGTCCGTACAACAAACAGCTGTATCCCAACACt  >  1:724006/1‑275 (MQ=255)                                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                                                 GTGGCTGAAACGCCAAAATTGATTTTCTCTGCGGCAGAAGCACCGAAAGTAAAGGAAGCAAGTAAAGCGGCAAGAACTAACTTTTTCATGATGGAACTCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAATAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCGTCTTATCAGACCTACAAAACCCCCCGGCGAATGTACGCAGCCACATTAATTTCGCCGTTCGAATGCCAGCGCTTTGCGCTCGATCAGACGCATCATCAGCGTCAGCAGGCCGTTAACGACCAGGTAAATAATCCCTGCCGCACCGAACACCATTACATCGTAGGTGCGTCCGTACAACAACTGGCTGTATCCCATCACT  >  CP009273/895943‑896475

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ 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.