New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1552149	NA (NA)	5 (0.140)	5/272	4.3	NA	noncoding (79/97 nt)	RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913_3_pae_tpiA	2549473 =	NA (NA)					noncoding (8/98 nt)	RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
Rejected: Coverage evenness skew score above cutoff.

TGTTCGAAAGCGGTCAGTTGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTG  >  NC_000913_3_pae_tpiA/2549327‑2549619                                                                                                                                                   |                                                                                                                                                   tGTTCGAAAGCGGTCAGTTGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGCAGTAATAAAAAGGCCAGTCAGTAATGTTACTGCCTGGTCTGAGAGTGCTGACACACGCAAAACTGCCTTGTgcg                                                                                                                                                  >  2:148370/1‑149 (MQ=255)   ttCGAAAGCGGTCAGTTGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAACCTGCCTGGTGCGCt                                                                                                                                                >  2:151224/1‑149 (MQ=255)        aaGCGGTCAGTTGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCCGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCt                                                                                                                                           >  1:295423/1‑149 (MQ=255)        aaGCGGTCAGTTGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCt                                                                                                                                           >  2:532846/1‑149 (MQ=255)              tCAGTTGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAg                                                                                                                                     <  1:300453/149‑1 (MQ=255)                cgTTGCCGATTGCAACTTATGGTTGTGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGc                                                                                                                                   <  2:367885/148‑1 (MQ=255)                    gCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCTGGCCTAc                                                                                                                               >  1:530987/1‑149 (MQ=255)                     ccGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCCGGCCTACg                                                                                                                              >  1:74391/1‑149 (MQ=255)                       gATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACggg                                                                                                                            >  1:290874/1‑147 (MQ=255)                       gATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTg                                                                                                                            <  1:600713/149‑1 (MQ=255)                         ttGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGa                                                                                                                          >  2:451954/1‑149 (MQ=255)                          tGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAg                                                                                                                         <  1:474221/149‑1 (MQ=255)                            cAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGCCAGAGCCGACACTGACTCATCTTCTTCTTGCGCTACGCTTATCAAGCCTACGTGGAGcc                                                                                                                       >  2:551270/1‑149 (MQ=255)                             aaCTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTTGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGccc                                                                                                                      >  1:455392/1‑149 (MQ=255)                             aaCTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGccc                                                                                                                      >  1:607293/1‑149 (MQ=255)                                     gTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCGGTAATGTTACTGGCTGGTCTGAGAGTGCTAACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAatata                                                                                                              >  1:268727/1‑149 (MQ=255)                                     gTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAatata                                                                                                              >  1:196015/1‑149 (MQ=255)                                              ttGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAg                                                                                                     >  1:122027/1‑149 (MQ=255)                                              gtcgtCAGGTTGATGCGGCGTTAAAGCAGAAGTCAGAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAATGCAAAACTGCCTGATGCGCTACGCTTATCAGGCTTACGTGGAGCCCACAATATATTGAATTAg                                                                                                     <  1:153786/145‑1 (MQ=37)                                                      gtgtATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGAttt                                                                                             >  1:267742/1‑149 (MQ=255)                                                         tATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAAAGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGGGCCCACAATATATTGAATTTGCAGGATTTCGt                                                                                          >  1:65237/1‑149 (MQ=255)                                                         tATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTAACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGt                                                                                          <  2:268727/149‑1 (MQ=255)                                                           tGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGATCCCACAATATATTGAATTAGCACGATTTCGTAg                                                                                        <  1:578962/149‑1 (MQ=255)                                                            gcggcgTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAgg                                                                                       >  2:395630/1‑149 (MQ=255)                                                             cggcgTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGc                                                                                      >  2:383752/1‑149 (MQ=255)                                                                 gTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGAACGATTTCGTAGGCCgta                                                                                  >  1:304160/1‑147 (MQ=255)                                                                    aaaGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATaa                                                                               <  2:122027/149‑1 (MQ=255)                                                                    aaaGCAGAAGTAATAAAAAGGCCAGTCAGTAAAGTTACTGGCAGGGCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATac                                                                               >  1:510511/1‑148 (MQ=255)                                                                       gCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGTTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGc                                                                            <  1:383752/149‑1 (MQ=255)                                                                       gCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGc                                                                            >  1:594199/1‑149 (MQ=255)                                                                       gCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGc                                                                            <  1:395630/149‑1 (MQ=255)                                                                       gCAGAAGTAATAAAAAGGCCAGTCAATAAAGTTACTGGCTAATCAGAGAGAGCTGTAAAATGCTAAACTGCCTGATGCGCTACGCCTGTCAGGCCTACGGGTAGCCCCCAATTAAGGTAATGATCACGATGTGATAGGCAGGAGAAGGc                                                                            >  2:153121/1‑149 (MQ=255)                                                                             gTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCAc                                                                      >  1:17650/1‑149 (MQ=255)                                                                               aataaGAAGGACAGTCTGTAATGTTACTGGCTGGTCTGAGTGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCAcgc                                                                    <  2:1713/149‑1 (MQ=255)                                                                                        gCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGcc                                                                                     >  1:335210/1‑123 (MQ=255)                                                                                        gCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGcc                                                                                     <  2:335210/123‑1 (MQ=255)                                                                                            gtcagtAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCgtg                                                       >  2:211110/1‑149 (MQ=255)                                                                                            gtcagtAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCATATCAGGCCTACGTGGAGCCCACCATATAGTGAATTAGCACGATTTCGTAGACCGGCTAAGGCTTTCACGCCCCATCCGGCgtg                                                       >  2:609866/1‑149 (MQ=25)                                                                                             gctggaaTGTTAATGGCTGGCTTGAGAGTACGGATAAACGCAAAACTGCCTGGTGCGCTACGCTGATCAGGACTAGGGGGAGCCCACAATATATGGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCgtgt                                                      <  1:148370/144‑1 (MQ=18)                                                                                               agtAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACAATTCCATAGGCCGGATAAAGCGTTCACACCGCATCCGCCGTGTAc                                                    >  2:325795/1‑149 (MQ=21)                                                                                                 tAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTATGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACaa                                                  >  1:602672/1‑149 (MQ=255)                                                                                                 tAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACaa                                                  >  1:244695/1‑149 (MQ=255)                                                                                                 tAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACaa                                                  <  2:602672/149‑1 (MQ=255)                                                                                                     gTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGGTTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGCCGTGTACAAcgcg                                              >  1:72729/1‑149 (MQ=255)                                                                                                          tggctggTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACtt                                         >  2:102036/1‑149 (MQ=255)                                                                                                           tgcggggcTGAGGGGGCTGACAAACGAAAAACTGCCTGAGGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTg                                        <  2:65237/142‑1 (MQ=21)                                                                                                           ggctggTCTGAAATTGCTAACAAATGCAAATCTGCCTGATGTGTTACGTTTACCAGGCTTACGTGGAGCACACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTg                                        <  1:151224/149‑1 (MQ=21)                                                                                                                     tgagGGCTGACAAACGCAGAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCGCGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATc                              <  2:642345/148‑1 (MQ=255)                                                                                                                           aagACAAACGCAAAACTGCCTGATGCTCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGc                        <  2:455392/147‑1 (MQ=255)                                                                                                                                 aaCGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCcagtca                  <  2:402628/149‑1 (MQ=255)                                                                                                                                     cAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTAACGCCGCATCCGGCGTGTACAACGCGCACATGGTCAACAATCTGAGGCCAGTCCGTaa              >  1:75584/1‑149 (MQ=255)                                                                                                                                      aaaaCTGTCTGATCCGCTGCGGTTATTAGGTCGACGTGGTTCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAAt             <  2:608752/149‑1 (MQ=21)                                                                                                                                       aaaCTGCCGGATGCGCTATGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATg            <  1:319488/149‑1 (MQ=255)                                                                                                                                           ggCCTGCGGCGCTACTCTTATCAGGACTATGTGAACCCCACAATAGATGGTATTAGCACGATTTCGTAGGCCGAATAAGGCGTTCACGCCGCATCCGGCGTTTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTAc        <  1:153121/148‑1 (MQ=25)                                                                                                                                            gCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACt       <  2:310835/149‑1 (MQ=255)                                                                                                                                                gATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATCTTACTGCCt   >  2:497063/1‑149 (MQ=255)                                                                                                                                                 aTGCGCTACGCACATCAGGCCTACGTGGAGCCCACGATATCTCGCATTAGCACGATTTCGTAGGCTGGATAAGGCGTTCACGACGCATCCGGCATGTATAACGCGCACTTGGTCTACAATCTGAGGCCGGACAGTCATGCTACTGCCTg  <  2:510511/149‑1 (MQ=25)                                                                                                                                                   |                                                                                                                                                   TGTTCGAAAGCGGTCAGTTGCCGATTGCAACTTATGGTTGGGTAGTTGATCAGGTGTATGCGGCGTTAAAGCAGAAGTAATAAAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCGTGTACAACGCGCACTTGGTCAACAATCTGAGGCCAGTCAGTAATGTTACTGCCTG  >  NC_000913_3_pae_tpiA/2549327‑2549619

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ 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.