New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 2443835	NA (NA)	11 (0.080)	7/164	NT	NA	noncoding (47/80 nt)	REP171 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP171 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913	= 2443868	NA (NA)					noncoding (80/80 nt)	REP171 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP171 (repetitive extragenic palindromic) element; contains 2 REP sequences

ATTGTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGgcctgat‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2443737‑2443835 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCCG  <  NC_000913/2443868‑2443763                                                                                                                                                                                                               ATTGTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGG                                                                                                           <  2:2837917/100‑1  TTGTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGC                                                                                                          <  1:1255082/100‑1  TTGTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGC                                                                                                          >  2:3854332/1‑100   TGTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCC                                                                                                         <  1:1487021/100‑1   TGTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCC                                                                                                         <  2:103580/100‑1   TGTTGAAGGGTAAAGCGGTTAAGGCGCGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGCGACGTCTAGGC                                                                                                          >  2:3521969/1‑99    GTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCT                                                                                                        >  1:575612/1‑100    GTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCT                                                                                                        >  1:3069986/1‑100    GTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCT                                                                                                        <  1:230848/100‑1    GTTGAACGGTAAAGCGGTTAAGGCGGGGTAATCTTCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCT                                                                                                        <  2:303430/100‑1     TTGAAGGGTAAAGCGGTTAAGGCGGGTTAATCTGCTCTCGCAGTTTTTGGCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTG                                                                                                       <  2:3305845/100‑1      TGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGA                                                                                                      >  2:2309563/1‑100      TGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGA                                                                                                      <  1:3301221/100‑1       GAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGct                                                                                                     >  1:2149630/1‑98       GAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGAT                                                                                                     <  2:291030/100‑1       GAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGAT                                                                                                     <  2:2030964/100‑1       GAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGAT                                                                                                     >  1:130970/1‑100       GAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGAT                                                                                                     >  1:352481/1‑100       GAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGAT                                                                                                     >  1:2904686/1‑100        AAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATn                                                                                                    <  2:649471/100‑2                              GGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCA                                                                              <  2:1510820/100‑1                              GGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCA                                                                              <  1:1682463/100‑1                                TAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGG                                                                            <  1:3792254/100‑1                                TAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGG                                                                            <  1:4017619/100‑1                                TAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGG                                                                            <  1:647109/100‑1                                 AATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGGC                                                                           <  2:391785/100‑1                                   TCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGGC                                                                           <  2:3176704/98‑1                                       CTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACAC                                                                     <  1:2378518/100‑1                                        TCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACG                                                                    <  1:1477666/100‑1                                                              GGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTATGCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGC                                              <  1:508794/100‑1                                                                       GCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCC                                     <  2:3882798/100‑1                                                                                                    GCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATT        <  1:3182233/100‑1                                                                                                    GCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATT        <  1:3465650/100‑1                                                                                                    GCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATT        >  2:1702974/1‑100                                                                                                     CCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTA       <  1:2495610/100‑1                                                                                                     CCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTA       >  2:732728/1‑100                                                                                                      nTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAAACACTGCCAAAGCTGGTTAC      >  2:1999017/2‑100                                                                                                       TGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACC     >  1:874697/1‑100                                                                                                       TGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAAACACTGCGAGAGCAGATTACC     >  1:3559894/1‑100                                                                                                          TGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCCG  <  1:3584090/100‑1                                                                                                          TGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCCG  >  1:2249437/1‑100                                                                                                          TGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCCG  >  2:777258/1‑100                                                                                                                                                                                                               ATTGTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGgcctgat‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2443737‑2443835 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCCG  <  NC_000913/2443868‑2443763

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.