New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 2443835	NA (NA)	16 (0.190)	8/164	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

TGTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGgcctgat‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2443739‑2443835 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCCG  <  NC_000913/2443868‑2443763                                                                                                                                                                                                             TGTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCC                                                                                                         <  2:1461062/100‑1  GTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAGCGCCTTATCCGACCTACGTGTGACGTGTAGGCCT                                                                                                        <  1:1523791/100‑1  GTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCT                                                                                                        >  2:516551/1‑100  GTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCT                                                                                                        >  2:2466668/1‑100   TTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTG                                                                                                       <  2:971726/100‑1   TTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTG                                                                                                       >  1:1040276/1‑100   TTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTG                                                                                                       >  2:1417231/1‑100   TTGAAGGGTAAAGCGGTTAAGGCGGGGCAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTG                                                                                                       >  1:1280503/1‑100    TGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGA                                                                                                      >  1:550961/1‑100    TGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGA                                                                                                      <  1:1286501/100‑1    TGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGA                                                                                                      >  2:453700/1‑100       AGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGAT                                                                                                     <  1:1440036/98‑1                            GGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGTCGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCA                                                                              <  1:1015182/100‑1                            GGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTAGCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCA                                                                              <  1:825383/100‑1                             GTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAG                                                                             <  2:1520291/100‑1                              TAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGG                                                                            <  2:150153/100‑1                              TAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGG                                                                            <  2:1211893/100‑1                              TAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGG                                                                            <  1:725149/100‑1                              TAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGG                                                                            <  1:311955/100‑1                              TAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGG                                                                            <  1:2441441/100‑1                              TAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGG                                                                            <  1:2350127/100‑1                               AATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGGC                                                                           <  2:826880/100‑1                                ATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGGCC                                                                          <  1:466853/100‑1                                ATCTGCTCGCGCAGTGTTTGGCGGATGCGGCGTGAACGCCTTATCCGACCTACGGGTGACGTGTAGGCGTGATGCGACGCTTATCGCGTCTTATCAGG                                                                            <  1:2323507/98‑1                                 TCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGGCCT                                                                         <  2:2341655/100‑1                                 TCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATGCGACGCTTATCGCGTCTTATCAGGCCT                                                                         <  2:2026779/100‑1                                   TGCTCTCGCAGTGTTTGCCGGATGCGGCGTGATCGCCTTTGCCGACCTACGCGTTACGTGTAGGCCTGATGCGACGCTTATCGCTTCTTATCAGGCCTAC                                                                       <  1:129579/100‑1                                        TCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGCATGCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTC                                                                  <  2:2179275/100‑1                                                                                                  GCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATT        <  2:212059/100‑1                                                                                                  GCCTAATGCGACGCATATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGA          <  2:1134179/98‑1                                                                                                   CCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTA       >  1:1581981/1‑100                                                                                                    CTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTAC      <  1:1474809/100‑1                                                                                                     TGATGCGANGCTTATCGCGTCTTATCNGGCCNACNCGTCACACGNAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCGNATTcc      >  2:2247212/1‑97                                                                                                     TGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACC     >  2:495556/1‑100                                                                                                     TGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACC     <  2:1558311/100‑1                                                                                                      GATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCC    >  1:1447821/1‑100                                                                                                       ATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCC   <  1:1017354/100‑1                                                                                                       ATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCAGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCC   >  1:1040287/1‑100                                                                                                       ATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGCTCAGATACGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCC   >  1:1039493/1‑100                                                                                                        TGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCCG  >  1:518102/1‑100                                                                                                        TGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCC   >  1:985069/1‑99                                                                                                                                                                                                             TGTTGAAGGGTAAAGCGGTTAAGGCGGGGTAATCTGCTCTCGCAGTGTTTGCCGGATGCGGCGTGAACGCCTTATCCGACCTACGTGTGACGTGTAGgcctgat‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2443739‑2443835 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCCTGATGCGACGCTTATCGCGTCTTATCAGGCCTACACGTCACACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAACACTGCGAGAGCAGATTACCCCG  <  NC_000913/2443868‑2443763

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.