New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 2232735	NA (NA)	3 (0.190)	3/240	1.9	NA	intergenic (+7/‑143)	cdd/sanA	cytidine/deoxycytidine deaminase/DUF218 superfamily vancomycin high temperature exclusion protein
	?	NC_000913_3_pae_pgi	= 2232765	NA (NA)					noncoding (30/34 nt)	REP155 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP155 (repetitive extragenic palindromic) element; contains 1 REP sequences

TCAAGGGTTATGATTACCCGGATATCCAGCGCGCGGTTCTGGCAGAAAAAGCCGATGCGCCGTTGATTCAGTGGGATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGCCGTTTCTTGCGCAAAACCAGCGGGTAAAGTAGCCTGATGGAAATTTTCCTTAGATCGAGTCTCCTGCATG  >  NC_000913_3_pae_pgi/2232589‑2232880                                                                                                                                                   |                                                                                                                                                  tcAAGGGTTATGATTACCCGGATATCCAGCGCGCGGTTCTGGCAGAAAAAGCCGATGCGCCGTTGATTCAGTGGGATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTgcc                                                                                                                                                >  4:122352‑M1/1‑147 (MQ=255)        ttATGATTACCCGGATATCCAGCGCGCGGTTCTGGCAGAAAAAGCCGATGCGCCGTTGATTCAGTGGGATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATgcg                                                                                                                                         >  1:103550/1‑150 (MQ=255)           tGATTACCCGGATATCCAGCGCGCGGTTCTGGCAGAAAAAGCCGATGCGCCGTTGATTCAGTGGGATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATgcggcg                                                                                                                                      >  2:198707/1‑150 (MQ=255)                     gATATCCAGCGCGCGGTTCTGGCAGAAAAAGCCGATGCGCCGTTGATTCAGTGGGATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCtt                                                                                                                            <  4:78053/150‑1 (MQ=255)                             gcgcgcGGTTCTGGCAGAAAAAGCCGATGCGCCGTTGATTCAGTGGTATTGCATCTTCTCTACGCTTAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCt                                                                                                                    <  3:74153/150‑1 (MQ=255)                                                            ccGTTGATTCAGTGGGATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCaccaggcttaagcgagaagcactcggtcgata                                                                                     >  2:103550‑M2/1‑118 (MQ=255)                                                              gTTGATTCAGTGGGATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGc                                                                                   >  4:71548/1‑150 (MQ=255)                                                                      aGTGGGATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTg                                                                                                                  <  4:13054/111‑1 (MQ=255)                                                                      aGTGGGATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTg                                                                                                                  >  3:13054/1‑111 (MQ=255)                                                                          ggATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGcc                                                                       <  2:115235/150‑1 (MQ=255)                                                                              gCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGCCGttt                                                                   >  2:133550/1‑150 (MQ=255)                                                                               ccACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGCCGTTTc                                                                  <  1:198707/150‑1 (MQ=255)                                                                                   cTCCGCAACGCTGAACGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGCCGTTTCTTgc                                                              >  4:102743/1‑150 (MQ=255)                                                                                   cTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAAc                                                                                                                                 >  1:150546/1‑83 (MQ=255)                                                                                   cTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAAc                                                                                                                                 <  2:150546/83‑1 (MQ=255)                                                                                    tCCGCAACGCTGAAAGCTCTCGGCTGTCACAGGAACCGCCGAGTGCTTCTCGCCTAACCCTGGTCCCGGATACGGCGCGAACCCCTTGTCCCGCTTGCCACCCCTCTCCCGGTGTCCAAATGCCCGGCGAACAGCTTGCCTTTTCTCgcc                                                             >  4:19420/1‑149 (MQ=255)                                                                                       gCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGCCGTTTCt                                                                 <  2:21358/143‑1 (MQ=255)                                                                                       gCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGCCGTTTCt                                                                 >  1:21358/1‑143 (MQ=255)                                                                                         aaCGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGCCGTTTCTTGCGCaaaa                                                        >  3:104836/1‑150 (MQ=255)                                                                                                          gCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTg                                                                                                    <  1:200412/89‑1 (MQ=255)                                                                                                          gCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTg                                                                                                    >  2:200412/1‑89 (MQ=255)                                                                                                               cacaGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGCCGTTTCTTGCGCAAAACCAGCGGGTAAAGTAGCCTGAt                                  <  3:102743/150‑1 (MQ=255)                                                                                                                    tATCGACCGAGTGCTTCTCGCTTAAGCCTGGTgccggacaaggcgttcacgccgcatccggcaccaggcttaagcgagaagcactcggtcgatactgtgacagccgagagctttcagcgttgcggaggtggcatcccactgaatcaacgg                             >  2:103550‑M1/1‑32 (MQ=255)                                                                                                                         aCCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTcc                                                                                                      >  3:57536/1‑72 (MQ=255)                                                                                                                         aCCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTcc                                                                                                      <  4:57536/72‑1 (MQ=255)                                                                                                                             aGTGCTTCTCGCTTAAGCCTGGTgccggacaaggcgttcacgccgcatccggcaccaggctta                                                                                                           <  1:28542‑M1/63‑41 (MQ=255)                                                                                                                             aGTGCTTCTCGCTTAAGCCTGGTgccggacaaggcgttcacgccgcatccggcaccaggctta                                                                                                           >  2:28542‑M1/1‑23 (MQ=255)                                                                                                                                 cTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCtctc                                                                                                       >  1:59866/1‑63 (MQ=255)                                                                                                                                 cTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCtctc                                                                                                       <  2:59866/63‑1 (MQ=255)                                                                                                                                          tAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCaccaggcttaagcgagaagcact                                                                                              <  1:28542‑M2/63‑24 (MQ=255)                                                                                                                                          tAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCaccaggcttaagcgagaagcact                                                                                              >  2:28542‑M2/1‑40 (MQ=255)                                                                                                                                               cTGGTGCCGGATGCGGCGTGGACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGCCGTTTCTTGCGCAAAACCAGCGGGTAAAGTAGCCTGATGGAAATTTTCCTTAGATCGAGTCTTCTGCATg  <  4:104836/150‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                  TCAAGGGTTATGATTACCCGGATATCCAGCGCGCGGTTCTGGCAGAAAAAGCCGATGCGCCGTTGATTCAGTGGGATGCCACCTCCGCAACGCTGAAAGCTCTCGGCTGTCACAGTATCGACCGAGTGCTTCTCGCTTAAGCCTGGTGCCGGATGCGGCGTGAACGCCTTGTCCGGCTTGCCAGCCCTCTCCTGGTGTCGAAATTCCCGGCAAACAGTTTGCCGTTTCTTGCGCAAAACCAGCGGGTAAAGTAGCCTGATGGAAATTTTCCTTAGATCGAGTCTCCTGCATG  >  NC_000913_3_pae_pgi/2232589‑2232880

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.