New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4441393 =	NA (NA)	11 (0.080)	6/164	NT	NA	noncoding (1/98 nt)	RIP335 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP335 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913	4441418 =	NA (NA)					noncoding (26/98 nt)	RIP335 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP335 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site

TTGTCTATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTATCAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4441498‑4441393 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcaggcCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAACAA  >  NC_000913/4441418‑4441516                                                                                                                                                                                                               TTGTCTATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTA                                                                                                           >  2:719470/1‑100  TGTCTATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTAT                                                                                                          >  2:921852/1‑100  TGTCTATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTAT                                                                                                          <  1:1205317/100‑1  TGTCTATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTAT                                                                                                          >  2:3512636/1‑100   GTCTATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTATC                                                                                                         >  1:4258960/1‑100   GTCTATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTATC                                                                                                         <  1:2241298/100‑1     CTATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTATCAG                                                                                                       >  1:474145/1‑100     CTATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTATCA                                                                                                        <  1:999964/99‑1      TATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTATCAG                                                                                                       <  1:2477791/99‑1       ATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTATCAGGC                                                                                                     <  1:297350/100‑1                                                                     AAGGACTGCGTAGGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACG                                       >  1:3035735/1‑100                                                                          CTGCGTAGGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCA                                  >  2:1022200/1‑100                                                                            GCGTAGGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATC                                >  1:2160267/1‑100                                                                              GTAGGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAG                              >  2:1388032/1‑100                                                                               TAGGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCACTATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGG                             >  1:676305/1‑100                                                                               TAGGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGG                             >  2:2391243/1‑100                                                                               TAGGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGG                             >  2:1300902/1‑100                                                                                 GGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCA                           >  1:1971042/1‑100                                                                                 GGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCA                           >  2:2715888/1‑100                                                                                 GGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCA                           >  1:200328/1‑100                                                                                 GGCCTGATCGGCATAGCGTATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCA                           >  1:1595375/1‑100                                                                                           tcttccgatcTCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGA                 <  1:24131/90‑1                                                                                                    ATCAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTAT        <  1:1388027/100‑1                                                                                                      CAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCA      <  2:4386764/100‑1                                                                                                      CAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCA      <  2:4065778/100‑1                                                                                                      CAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCA      <  1:3656612/100‑1                                                                                                      CAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCA      <  2:1378316/100‑1                                                                                                      CAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCA      <  2:3736264/100‑1                                                                                                      CAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCA      <  2:2108151/100‑1                                                                                                      CAGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCA      <  2:3347929/100‑1                                                                                                       AGGCCTACGCAGTCCTTGCAATATATTTAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAA     <  1:2946012/100‑1                                                                                                       AGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAA     <  1:4012529/100‑1                                                                                                       AGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAA     <  2:634651/100‑1                                                                                                       AGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAA     <  1:312194/100‑1                                                                                                       AGGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAA     <  2:1599787/100‑1                                                                                                        GGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAAC    >  1:1160601/1‑100                                                                                                        GGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAAC    >  1:1537028/1‑100                                                                                                        GGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAAC    <  2:2245917/100‑1                                                                                                        GGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAAC    >  2:1904547/1‑100                                                                                                        GGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAAC    >  1:2798130/1‑100                                                                                                        GGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAA     >  1:1139662/1‑99                                                                                                        GGCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATAAA     >  2:710843/1‑99                                                                                                         GCCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAACA   >  1:3562393/1‑100                                                                                                          CCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAACAA  >  2:1783986/1‑100                                                                                                          CCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAACAA  <  1:425797/100‑1                                                                                                          CCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGACTAGAAAAAGAGCACTTTATCAACAA  >  1:3685784/1‑100                                                                                                                                                                                                               TTGTCTATGCCTGATGCGGCGTAAACGACTTACCAGGCCTACAAAATCGTCCAAATTCAATATATTGCAAGGACTGCGTAGGCCTGATCGGCATAGCGTATCAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4441498‑4441393 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcaggcCTACGCAGTCCTTGCAATATATTGAATTTGGACGATTTTGTAGGCCTGGTAAGTCGTTTACGCCGCATCAGGCATAGACAAAGAGCACTTTATCAACAA  >  NC_000913/4441418‑4441516

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ 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.