New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 4583053	28 (0.970)	5 (0.180)	5/274	3.2	16.4%	intergenic (‑89/+112)	hsdM/hsdR	DNA methyltransferase M/endonuclease R Type I restriction enzyme
	?	NC_000913_3_pae_tpiA	= 4583140	24 (0.870)					intergenic (‑176/+25)	hsdM/hsdR	DNA methyltransferase M/endonuclease R Type I restriction enzyme
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATCGCGCAGGTTGTCGCACAGCTTCCACAGCTTCGCGACCAGATCGTTATTGTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCAGAGGCAGCCTGAAGGATGAAGTGTATACGTGTCAGGCCAGCTCGTCCCAGATATAATCGCTGA  >  NC_000913_3_pae_tpiA/4582908‑4583196                                                                                                                                                   |                                                                                                                                                 aTCGCGCAGGTTGTCGCACAGCTTCCACAGCTTCGCGACCAGATCGTTATTGTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACCAAATC‑ATTTAGGTTg                                                                                                                                               >  1:193018/1‑149 (MQ=255)          gTTGTCGCACAGCTTCCACAGCTTCGCGACCAGATCGTTATTGTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAggc                                                                                                                                      <  2:140934/149‑1 (MQ=255)                gCACAGCTTCCACAGCTTCGCGACCAGATCGTTATTGTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAag                                                                                                                                >  2:49803/1‑149 (MQ=255)                 cacagcttccatagctgcGCGACCAGTGCTTTATTGTTGATTTGTAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAagt                                                                                                                               <  2:181043/149‑1 (MQ=38)                  acagcttccacagcttcGCGACCAGATCGTTATTGTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAagtg                                                                                                                              >  1:366400/1‑149 (MQ=255)                     gcttccacagcttcGCGACCAGATCGTTATTGTTCCTTGTGAGTTCGGTAAACTAAGCAGCGGCCCAAATTCATCGGGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAagtgagt                                                                                                                           <  2:460662/149‑1 (MQ=255)                           acagcttgGCGACCAGATCGTGATTGTTCACTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATcc                                                                                                                     <  2:194081/149‑1 (MQ=255)                                      accaagtCGTTATTGTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTa                                                                                                          <  2:78204/143‑1 (MQ=255)                                       ccAGATCGTTATTGTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTAc                                                                                                         >  1:78578/1‑149 (MQ=255)                                           aTCGTTATTGTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ACTCAGGTTGCATCATGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGaa                                                                                                     >  1:418368/1‑149 (MQ=255)                                               ttATTGTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCACATTCATCAACCCCAAGCAGTAGACCTTGCTCAGGGTATTGT‑CTTAATTCCTTTTTTGATTTCATCAATACGGCAATTGATTGAATCCCCGGGAGCGTACAGAAGTAc                                                                                                 >  2:497789/1‑149 (MQ=255)                                                    gTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGAc                                                                                            >  2:354538/1‑149 (MQ=255)                                                         ttGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCgggg                                                                                       >  2:44408/1‑149 (MQ=255)                                                          tgtgAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGt                                                                                      <  2:145923/149‑1 (MQ=255)                                                            tgAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATACCCGGGAGCGTACAGAAGTACGTGACCGGGGGGa                                                                                    >  1:185522/1‑149 (MQ=255)                                                                    gTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGGGGCAAGTGAGTGAATCCCCGGTAGCGTACAGAAGTACGTGACCGGGGTGAACGAacgc                                                                            >  2:55248/1‑149 (MQ=255)                                                                               agcGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCag                                                                >  1:165125/1‑149 (MQ=255)                                                                                    cccAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGAAGAGGCa                                                           >  2:265152/1‑149 (MQ=255)                                                                                                         aagaagaaATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCAGAGGCAGCCTGAAGGATGAAGTGtata                                      <  2:359404/149‑1 (MQ=255)                                                                                                           gaagaaATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACACACGTACGTGACCGGCGTGAACGAGCGCAT‑CCAAAGCAGAGGCAGCCTGAAGGATGAAGTGTATACg                                    >  1:71953/1‑149 (MQ=37)                                                                                                                aaTTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCAGAGGCAGCCTGAAGGATGAAGTGTATACGTGTCa                               >  1:440633/1‑149 (MQ=255)                                                                                                                 agtGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCAGAGGCAGCCTGAAGGATGAAGTGTATACGTGTCAg                              <  2:461379/147‑1 (MQ=255)                                                                                                                   tGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCAGAGGCAGCCTGAAGGATGAAGTGTATACGTGTCAGGc                            <  1:354538/149‑1 (MQ=255)                                                                                                                             aaTATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGACCGAGCGCAGCCCCACG‑GTAGCCAGCCTGAAGGATGAAGTGTATACGTGTCAGGCCAGCTCGTcc                  <  1:497789/149‑1 (MQ=38)                                                                                                                               tataCACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCAGAGGCAGCCTGAAGGATGAAGTGTATACGTGTCAGGCCAGCTCGTCCCa                <  1:44408/149‑1 (MQ=255)                                                                                                                                   cacaAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCAGAGGCAGCCTGAAGGATGAAGTGTATACGTGTCAGGCCAGCTCGTCCCAGata            <  2:165125/149‑1 (MQ=255)                                                                                                                                          tC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCAGAGGCAGCCTGAAGGATGAAGTGTATACGTGTCAGGCCAGCTCGTCCCAGATATAATCGc     >  2:421032/1‑149 (MQ=255)                                                                                                                                              ttCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCAGAGGCAGCCTGAAGGATGAAGTGTATACGTGTCAGGCCAGCTCGTCCCAGATATAATCGCTGa  >  1:310466/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                 ATCGCGCAGGTTGTCGCACAGCTTCCACAGCTTCGCGACCAGATCGTTATTGTTCATTGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATTCATCGAGCCGCAGAAGAAGAAATTGCCGAGGGTAATATACACAAAATC‑ATTCAGGTTGCATCAAGGCGGCAAGTGAGTGAATCCCCGGGAGCGTACAGAAGTACGTGACCGGGGTGAACGAGCGCAG‑CCAACGCAGAGGCAGCCTGAAGGATGAAGTGTATACGTGTCAGGCCAGCTCGTCCCAGATATAATCGCTGA  >  NC_000913_3_pae_tpiA/4582908‑4583196

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.