New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3625629 =	NA (NA)	25 (0.210)	12/166	NT	17.9%	noncoding (41/82 nt)	RIP260 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP260 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913	3625675 =	115 (0.960)					intergenic (+161/+4)	yhhI/yhhJ	putative transposase/putative ABC transporter permease

ATTTTTCACCATTGCGCTGCTGCGATTCAGGAAGACGATTGGGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3625733‑3625629 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcaattGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGGCCAGA  >  NC_000913/3625675‑3625773                                                                                                                                                                                                              ATTTTTCACCATTGCGCTGCTGCGATTCAGGAAGACGATTGGGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTG                                                                                                          <  2:2373366/100‑1   TTTTCACCATTGCGCTGCTGCGATTCAGGAAGACGATTGGGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGC                                                                                                         >  2:3208665/1‑99    TTTCACCATTGCGCTGCTGCGATTCAGGAAGACGATTGGGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAA                                                                                                       >  2:318115/1‑100    TTTCACCATTGCGCTGCTGCGATTCAGGAAGACGATTGGGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAA                                                                                                       >  2:3561885/1‑100     TTCACCATTGCGCTGCTGCGATTCAGGAAGACGATTGGGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAAT                                                                                                      >  1:2341964/1‑100     TTCACCATTGCGCTGCTGCGATTCAGGAAGACGATTGGGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAAT                                                                                                      >  1:2342692/1‑100      TCACCATTGCGCTGCTGCGATTCAGGAAGACGATTGGGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATT                                                                                                     <  1:3265799/100‑1                                         GGGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAAT                                                                  >  1:2006698/1‑100                                          GGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGCGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATC                                                                 >  2:153751/1‑100                                                 GGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAG                                                          >  2:721879/1‑100                                                       AATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAAT                                                    >  1:2914550/1‑100                                                        ATACAATTGCCCGATGTGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCGTAGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATG                                                   >  2:617628/1‑100                                                        ATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATG                                                   >  1:1428279/1‑100                                                             ATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAA                                              >  2:2463223/1‑100                                                             ATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAA                                              >  2:2462846/1‑100                                                             ATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAA                                              >  1:1497469/1‑100                                                              TTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAA                                             >  2:3202810/1‑100                                                              TTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAA                                             >  2:2267734/1‑100                                                               TGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAA                                            >  2:328134/1‑100                                                               TGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAA                                            >  1:3198594/1‑100                                                               TGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAA                                            >  1:156239/1‑100                                                                GCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAA                                           >  2:553154/1‑100                                                                GCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAA                                           >  2:3020791/1‑100                                                                GCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAA                                           >  2:1506244/1‑100                                                                GCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAA                                           >  1:2917589/1‑100                                                                GCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAA                                           >  1:295562/1‑100                                                                GCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAA                                           >  1:739656/1‑100                                                                GCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTAGTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAA                                           >  2:858025/1‑100                                                                    GATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCG                                       >  1:3375495/1‑100                                                                    GATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCG                                       >  2:2713649/1‑100                                                                        CGTAAGCTTATAGGGACTACGCATCGG‑GCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGC                                      >  2:3095008/1‑96                                                                             GCTTATAGGGACTACGCATCGG‑GCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTG                             <  1:3095031/100‑1                                                                                                   atctATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCG        <  1:1340131/96‑1                                                                                                    GCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGG       >  2:2730394/1‑100                                                                                                    GCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGG       <  1:2540851/100‑1                                                                                                    GCAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGG       <  1:1587988/100‑1                                                                                                     CAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGGC      <  1:776526/100‑1                                                                                                     CAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGGC      <  2:1674877/100‑1                                                                                                     CAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGGC      >  1:2996435/1‑100                                                                                                     CAATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAAGGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGGC      <  1:2565909/100‑1                                                                                                      AATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGGCC     <  2:630057/100‑1                                                                                                      AATTGTATTTACGCCACTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGGC      <  2:2038312/99‑1                                                                                                       ATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGagat    >  2:1340123/1‑96                                                                                                       ATTGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGGACA    >  1:681973/1‑100                                                                                                         TGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGGCCAGA  <  2:1708377/100‑1                                                                                                                                                                                                              ATTTTTCACCATTGCGCTGCTGCGATTCAGGAAGACGATTGGGACAATGGCGTAAATACAATTGCCCGATGCGTAAGCTTATAGGGACTACGCATCGGTGCAATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3625733‑3625629 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcaattGTATTTACGCCATTGTCCCAATCGTCTTCCTGAATCGCAGCAGCGCAATGGTGAAAAATGCGCCGCCAATTGCCATCAGCGTCAGAAACTGCGGCCAGA  >  NC_000913/3625675‑3625773

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