New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	411213 =	49 (0.380)	10 (0.080)	7/212	NT	16.9%	noncoding (136/191 nt)	REP35 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP35 (repetitive extragenic palindromic) element; contains 4 REP sequences
	?	NC_000913	4295835 =	NA (NA)					noncoding (1/600 nt)	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites

ACGCTTGCCGCGTCTTATCAGGCCTACAAAAGGTGCCAGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGAGTATCCGCCGCTTGCTGGCGCTTATAGCGACCA  >  NC_000913/411088‑411357                                                                                                                              |                                                                                                                                                 aCGCTTGCCGCGTCTTATCAGGCCTACAAAAGGTGCCAGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGt                                                                                                                           >  2:603881/1‑149 (MQ=255)         cgcgTCTTATCAGGCCTACAAAAGGTGCCAGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGa                                                                                                                   <  1:603881/149‑1 (MQ=255)             tCTTATCAGGCCTACAAAAGGTGCCAGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAAtgt                                                                                                                                        >  4:283163/1‑124 (MQ=255)             tCTTATCAGGCCTACAAAAGGTGCCAGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAAtgt                                                                                                                                        <  3:283163/124‑1 (MQ=255)                  tCAGGCCTACAAAAGGTGCCAGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGt                                                                                                                           >  4:427000/1‑132 (MQ=255)                  tCAGGCCTACAAAAGGTGCCAGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGt                                                                                                                           <  3:427000/132‑1 (MQ=255)                                    ccAGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAg                                                                                                                                   >  4:963891/1‑106 (MQ=255)                                    ccAGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAg                                                                                                                                   <  3:963891/106‑1 (MQ=255)                                       gAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGt                                                                                                           <  3:1193537/127‑1 (MQ=255)                                       gAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGt                                                                                                           >  4:1193537/1‑127 (MQ=255)                                           cGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGaa                                                                                                                                 <  3:1282573/101‑1 (MQ=255)                                           cGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGaa                                                                                                                                 >  4:1282573/1‑101 (MQ=255)                                               ggCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGc                                                                             >  2:1134383/1‑149 (MQ=255)                                                 ccGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGc                                                                                                                      >  2:802026/1‑106 (MQ=255)                                                 ccGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGc                                                                                                                      <  1:802026/106‑1 (MQ=255)                                                    gATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACcgc                                                                                                                             >  1:65068/1‑96 (MQ=255)                                                    gATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACcgc                                                                                                                             <  2:65068/96‑1 (MQ=255)                                                          gCGTTCACGCCGCATCGGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCa                                                                            >  3:523239/1‑139 (MQ=255)                                                          gCGTTCACGCCGCATCGGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCa                                                                            <  4:523239/139‑1 (MQ=255)                                                            gTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCACAATGTGCCAGAACCGCGTAGGGCGGATAAGGc                                                                                                             <  4:1252560/104‑1 (MQ=255)                                                            gTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGc                                                                                                             <  3:593513/104‑1 (MQ=255)                                                            gTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGc                                                                                                             >  3:1252560/1‑104 (MQ=255)                                                            gTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGc                                                                                                             >  4:593513/1‑104 (MQ=255)                                                            gTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATg                                                                                <  3:279143/133‑1 (MQ=255)                                                            gTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATg                                                                                >  4:279143/1‑133 (MQ=255)                                                             ttCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAAc                                                               <  1:1134383/149‑1 (MQ=255)                                                                aCGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAgg                                                                                                                        <  1:1352642/89‑1 (MQ=255)                                                                aCGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAgg                                                                                                                        >  2:1352642/1‑89 (MQ=255)                                                                      cATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTaa                                                                                  >  4:1181753/1‑121 (MQ=255)                                                                      cATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTaa                                                                                  <  3:1181753/121‑1 (MQ=255)                                                                              aaTAAGTTCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAAtgt                                                                                                                                        >  2:788663/1‑59 (MQ=255)                                                                              aaTAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAAtgt                                                                                                                                        <  1:788663/59‑1 (MQ=255)                                                                               aTAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAAtgtg                                                                                                                                       <  4:630928/59‑1 (MQ=255)                                                                               aTAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAAtgtg                                                                                                                                       >  3:630928/1‑59 (MQ=255)                                                                               aTAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCAc                                                                           >  4:1088721/1‑119 (MQ=255)                                                                               aTAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCAc                                                                           <  3:1088721/119‑1 (MQ=255)                                                                                  aGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAg                                          >  1:247463/1‑149 (MQ=255)                                                                                       tCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAAtgtg                                                                                                                                       <  2:1054432/51‑1 (MQ=255)                                                                                       tCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAAtgtg                                                                                                                                       >  1:1054432/1‑51 (MQ=255)                                                                                            ggcctgataagacgcggcaagcgtcgcatcaggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTc                                               <  2:294901‑M1/100‑1 (MQ=255)                                                                                            ggcctgataagacgcggcaagcgtcgcatcaggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTc                                               >  1:294901‑M1/35‑134 (MQ=255)                                                                                            ggcctgataagacgcggcaagcgtcgcatcaggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGa                                   <  4:388862‑M1/112‑1 (MQ=255)                                                                                            ggcctgataagacgcggcaagcgtcgcatcaggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGa                                   >  3:388862‑M1/35‑146 (MQ=255)                                                                                             gcctgataagacgcggcaagcgtcgcatcaggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGt                                                  <  3:1133549‑M1/97‑1 (MQ=255)                                                                                             gcctgataagacgcggcaagcgtcgcatcaggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGt                                                  >  4:1133549‑M1/34‑130 (MQ=255)                                                                                             gcctgataagacgcggcaagcgtcgcatcaggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGc                                             >  4:331872‑M1/34‑135 (MQ=255)                                                                                             gcctgataagacgcggcaagcgtcgcatcaggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGc                                             <  3:331872‑M1/102‑1 (MQ=255)                                                                                               cTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGAGTATcc                             >  2:335023/1‑149 (MQ=255)                                                                                                tGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTg                                                    >  1:693546/1‑125 (MQ=255)                                                                                                tGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTg                                                    <  2:693546/125‑1 (MQ=255)                                                                                                  ataagacgcggcaagcgtcgcatcaggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGa                                   >  4:995690‑M1/29‑140 (MQ=255)                                                                                                  ataagacgcggcaagcgtcgcatcaggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGa                                   <  3:995690‑M1/112‑1 (MQ=255)                                                                                                      gACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGa                                   >  3:939884/1‑136 (MQ=255)                                                                                                      gACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGa                                   <  4:939884/136‑1 (MQ=255)                                                                                                       aCGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCgaga                                                                      <  2:243860/100‑1 (MQ=255)                                                                                                       aCGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCgaga                                                                      >  1:243860/1‑100 (MQ=255)                                                                                                           ttGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGAGTATCCGCCGCTTGc                    <  2:163043/146‑1 (MQ=255)                                                                                                           ttGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGAGTATCCGCCGCTTGc                    >  1:163043/1‑146 (MQ=255)                                                                                                            tGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGAGTATCCGCCGCTTGCTGgc                <  1:335023/149‑1 (MQ=255)                                                                                                                   tCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTAccc                                                         <  4:678536/101‑1 (MQ=255)                                                                                                                   tCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTAccc                                                         >  3:678536/1‑101 (MQ=255)                                                                                                                          aggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGGTAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGAGTATCCGCCGCTTGCTGGCGCTTATAGCGACCa  <  2:1087709‑M1/145‑1 (MQ=255)                                                                                                                          aggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGAGTATCCGCCGCTTGCTGgcgc              <  4:865829‑M1/133‑1 (MQ=255)                                                                                                                          aggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGAGCATCCGCCGCTTGCTGgcgc              >  3:865829‑M1/5‑137 (MQ=255)                                                                                                                           ggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGa                                                                               >  4:684903‑M1/4‑71 (MQ=255)                                                                                                                           ggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGa                                                                               <  3:684903‑M1/68‑1 (MQ=255)                                                                                                                           ggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGc                                             >  1:1339896‑M1/4‑105 (MQ=255)                                                                                                                           ggcCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGc                                             <  2:1339896‑M1/102‑1 (MQ=255)                                                                                                                              |                                                                                                                                                 ACGCTTGCCGCGTCTTATCAGGCCTACAAAAGGTGCCAGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTGCTCCGATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCAAAATGTGCCAGAACCGCGTAGGGCGGATAAGGCGTTCACGCCGCATCCGGCAATAAGTAATGAGCACCGAGACTATAACCTACCCCAGTGGTTTCGCCAGCACCGGAGTATCCGCCGCTTGCTGGCGCTTATAGCGACCA  >  NC_000913/411088‑411357

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ 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.