New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	409056 =	NA (NA)	11 (0.090)	7/164	NT	NA	noncoding (5/37 nt)	REP34 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP34 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	409089 =	NA (NA)					intergenic (+139/+19)	ykiA/rdgC	pseudogene/nucleoid‑associated ssDNA and dsDNA binding protein; competitive inhibitor of RecA function

CAGCGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/409160‑409056 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atccggcATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTCATCAGGATGAAAT  >  NC_000913/409089‑409187                                                                                                                                                                                                              CAGCGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTAT                                                                                                          <  1:1708592/100‑1  AGCGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATC                                                                                                         >  1:3166521/1‑100   GCGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCC                                                                                                        <  2:3391424/100‑1   GCGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCC                                                                                                        <  2:3139658/100‑1   GCGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCC                                                                                                        >  1:2266026/1‑100   GCGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATC                                                                                                         >  2:1956358/1‑99    CGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCG                                                                                                       <  1:2987564/100‑1    CGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCG                                                                                                       >  1:773805/1‑100    CGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCG                                                                                                       >  1:581130/1‑100     GTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCGG                                                                                                      <  1:211143/100‑1     GTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCGG                                                                                                      >  1:1784510/1‑100     GTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCGG                                                                                                      >  1:407231/1‑100      TTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTCAATGCCGGATGCGACGCCTGCCGCGTCTTATCCGGC                                                                                                     <  1:2695654/100‑1                                             CAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCAC                                                              >  1:2164474/1‑100                                                                  CTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTT                                         >  1:58169/1‑100                                                                   TTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTG                                        >  1:278146/1‑100                                                                   TTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTT                                         >  2:2290265/1‑99                                                                      AATGCCGGATGCGACGCCTGCCGCGTCTTATCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAAT                                     >  2:1571318/1‑100                                                                       atggcgcacGCGACGCCTGCAGCGTCTTATCCGGCATTAAAGGAAATTCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATT                                    <  2:2893405/91‑1                                                                       ATGCCGGATGCGACGCCTGCCGCGTCTTATCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATT                                    >  1:1275657/1‑100                                                                         GCCGGATGCGACGCCTGCCGCGTCTTATCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAA                                  >  1:2213135/1‑100                                                                         GCCGGATGCGACGCCTGCCGCGTCTTATCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAA                                  >  1:729759/1‑100                                                                         GCCGGATGCGACGCCTGCCGCGTCTTATCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAA                                  >  1:3381842/1‑100                                                                          CCGGATGCGACGCCTGCCGCGTCTTATCCGGCATT‑AAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACG                                >  2:3359102/1‑100                                                                                                    TCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGACTTAACGCTGCCAGTTCACCAGTCATCAGGAT       >  2:2401877/1‑100                                                                                                    TCCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTCATCAGGA        <  2:2872661/99‑1                                                                                                     CCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTCATCAGGATG      <  1:2883536/100‑1                                                                                                     CCGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTCATCAGGATG      >  2:1238539/1‑100                                                                                                     CCGGCATGAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGATTTGAATTAACGCTCCCAGTTCACCAGTCATCAGGATG      >  2:2508138/1‑100                                                                                                      CGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTCATCAGGATGA     >  1:1861674/1‑100                                                                                                      CGGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTCATCAGGATGA     >  1:3696592/1‑100                                                                                                       GGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTCATCAGGATGAA    <  2:2832916/100‑1                                                                                                       GGCATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCGGCCAGTTCACCAGTCATCAGGATG      <  2:2576186/98‑1                                                                                                         CATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCTCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTAATCAGCATGAAAT  >  2:2050622/1‑100                                                                                                         CATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTTACGCTGCCAGTTCACCAGTCATCAGGATGAAAT  >  2:1513790/1‑100                                                                                                         CATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTCATCAGGATGAAAT  >  1:2965907/1‑100                                                                                                         CATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTCATCAGGATGAAAT  >  1:2837895/1‑100                                                                                                                                                                                                              CAGCGTTAATTCAAAACCTGATTGAAGGATTAGGTGGCGAAGCACAACGTTAATTGCTGATTTTCCTTTAATGCCGGATGCGACGCCTGCCGCGTCTTATCCGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/409160‑409056 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atccggcATTAAAGGAAAATCAGCAATTAACGTTGTGCTTCGCCACCTAATCCTTCAATCAGGTTTTGAATTAACGCTGCCAGTTCACCAGTCATCAGGATGAAAT  >  NC_000913/409089‑409187

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