New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1040547 =	NA (NA)	13 (0.130)	9/158	NT	NA	noncoding (5/36 nt)	REP89 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP89 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	1040579 =	NA (NA)					intergenic (+42/‑38)	cbdX/appA	putative cytochrome bd‑II oxidase subunit/phosphoanhydride phosphorylase

AATCAGAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCATCAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1040655‑1040547 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcatcaggcAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATCTGCA  >  NC_000913/1040579‑1040676                                                                                                                                                                                                                 AATCAGAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATGTGACATTATTGATTGCCTGATGCGATGCTAATGCGCC                                                                                                             <  2:1658147/100‑1  ATCAGAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCG                                                                                                            <  1:2672284/100‑1  ATCAGAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCG                                                                                                            >  2:2268964/1‑100   TCAGAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTAATTGCCTGATGCGATGCTAATGCGCCG                                                                                                            >  2:2778940/1‑99    CAGAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCA                                                                                                          >  1:1884470/1‑100    CAGAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCA                                                                                                          <  2:765211/100‑1     AGAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCAT                                                                                                         >  2:1797985/1‑100      GAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGTTGCTAATGCGCCGCATC                                                                                                        >  2:1788492/1‑100      GAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCATC                                                                                                        <  2:2940164/100‑1      GAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCATC                                                                                                        >  1:2717341/1‑100      GAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCAGCAT                                                                                                         >  2:1000595/1‑99       AAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCATCA                                                                                                       >  2:192566/1‑100         GAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCATCAGG                                                                                                     <  2:1838477/100‑1          AGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCATCAGGC                                                                                                    <  1:1407820/100‑1          AGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCATCAGGC                                                                                                    >  2:1407810/1‑100                                                                      TATTGATTGCCTGATGCGATGCTAATACGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCAT                                        >  1:1895783/1‑100                                                                          GATTGCCTGATGCGATGCTAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTT                                    >  2:780961/1‑100                                                                            TTGCCTGATGCGATGCTAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTAT                                  >  1:1857228/1‑100                                                                              GCCTGATGCGATGCTAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCT                                >  1:1117116/1‑100                                                                              GCCTGATGCGATGCTAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCT                                >  2:2033295/1‑100                                                                              GCCTGATGCGATGCTAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCT                                >  1:1533367/1‑100                                                                              GCCTGATGCGATGCTAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCT                                >  1:1262340/1‑100                                                                               CCTGATGCGATGCTAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTC                               >  2:575309/1‑100                                                                               CCTGATGCGATGCTAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTC                               >  2:1069268/1‑100                                                                                CTGATGCGATGCTAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCT                              >  2:2056869/1‑100                                                                                  GATGCGATGCTAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTC                            >  1:2220769/1‑100                                                                                            TAATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTT                  >  2:2165963/1‑100                                                                                             AATGCGCCGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTA                 <  1:2056886/100‑1                                                                                                    CGCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGC          <  1:2463524/100‑1                                                                                                     GCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCA         >  1:1530310/1‑100                                                                                                     GCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCA         >  1:1181347/1‑100                                                                                                     GCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGC          >  1:2800149/1‑99                                                                                                     GCATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCGTAATCCCATTTTTAGCTCTTCTGATTCCGTTAACCCCGCA         >  1:1695760/1‑100                                                                                                      CATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAA        >  2:807863/1‑100                                                                                                      CATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAA        >  1:2674386/1‑100                                                                                                      CATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAA        >  1:2544809/1‑100                                                                                                       ATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAAT       >  2:1036705/1‑100                                                                                                       ATCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAAT       <  1:1064467/100‑1                                                                                                        TCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATC      >  2:1766278/1‑100                                                                                                        TCAGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATC      >  1:2212384/1‑100                                                                                                          AGGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATCTG    <  2:2212364/100‑1                                                                                                           GGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATCTGC   >  1:749160/1‑100                                                                                                           GGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATCTGC   <  2:460708/100‑1                                                                                                           GGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATCTGC   >  1:1987810/1‑100                                                                                                           GGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATCTGC   >  1:1387410/1‑100                                                                                                           GGCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTCAACCCCGCAATCTGC   >  1:3056929/1‑100                                                                                                            GCAATCAATAATGTCAGATATGAAAAGTGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATCTGCA  >  2:340231/1‑100                                                                                                            GCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATCTGCA  >  2:2341447/1‑100                                                                                                            GCAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATCTGCA  <  1:2161388/100‑1                                                                                                                                                                                                                 AATCAGAAGAGATAAAAATGGGATTAAGATCGCTTTCATCGATATGTTTCCGCTTTTCATATCTGACATTATTGATTGCCTGATGCGATGCTAATGCGCCGCATCAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1040655‑1040547 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcatcaggcAATCAATAATGTCAGATATGAAAAGCGGAAACATATCGATGAAAGCGATCTTAATCCCATTTTTATCTCTTCTGATTCCGTTAACCCCGCAATCTGCA  >  NC_000913/1040579‑1040676

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