New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4409175 =	NA (NA)	4 (0.040)	4/480	NT	6.3%	noncoding (22/98 nt)	RIP331 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site	RIP331 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site
	?	NC_000913	4409236 =	59 (0.660)					noncoding (83/98 nt)	RIP331 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site	RIP331 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site

ATGCACGGCACCGTCGCTTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGC‑GTGATTATGTAGGCCGGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4409476‑4409175 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atgtaggccggataaACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGTCAGTATCAGGA  >  NC_000913/4409236‑4409520                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ATGCACGGCACCGTCGCTTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGC‑GTGATTAT                                                                                                                                                                                                                                                                                                            >  1:574825/1‑289     ACGGCACCGTCGCTTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGC‑GTGATTATGTAG                                                                                                                                                                                                                                                                                                        <  2:63407/289‑1     ACGGCACCGTCGCGTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGTGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGCTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGC‑GTGATTATGTAG                                                                                                                                                                                                                                                                                                        <  2:599514/289‑1      CGGCACCGTCGCTTTTCTCGTCGCGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGTCTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGTCCTCCAGCAGGGCATGCACTGCGTGGATGCCGTACTTCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTTCCTGTTGCACTACCTTTATCCGTCCTACATGATCTCTGCCATATATTTATTTTGC‑GTGATTATGTAta                                                                                                                                                                                                                                                                                                       >  1:870313/1‑287       GGCACCGTCGCTTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGC‑GTGATTATGTAGGC                                                                                                                                                                                                                                                                                                      <  2:903280/289‑1                   TTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGC‑GTGATTATGTAGGCCGGATAAACGTA                                                                                                                                                                                                                                                                                          <  1:711995/289‑1                                                                                           tcACAGACGTTCGACTTCACGGCCTTGTAAAAGAAAGCTTTCCTGAACCCGTTCAAGGGCGCGCGCCAGCAGTGCCTTCACTCCGTGGATGCCGTAGATCATTTCTCTCATTACTGTACTCGTTGTTGACGTTTTGCCTGATGCGCTACCTTTATCCGGCCTACATGATCTCGGCAATATATGGAATTTGC‑GTGATTATGTAGGCCGGATAAACGTAGTGCATCAGGCAACACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGG                                                                                                                                                                                                                  <  1:434230/287‑1                                                                                                  CGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGC‑GTGATTATG                                                                                                                                                                                                                                                                                                           >  1:316253/1‑193                                                                                                  CGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGC‑GTGATTATG                                                                                                                                                                                                                                                                                                           <  2:316253/193‑1                                                                                                                                                                              CGTGGATGCCGTAAATATTGTCGCTCATTAATGTACTCGTTGTTTACGTTTTGTCTGATGCACTACGTTTATCCGGCCTACATAATCAC‑GCAAATTAAATATATTGCAGAGATCATGTAGGCTGGATAAACGTAGGGAATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTA                                                                                                                                                                        <  2:104954/248‑1                                                                                                                                                                                         TAAATCCTTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATAATCACGCAAATTCAATATATTGCA‑GAGATCATGTAGGCCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGC                                                                                                                          <  2:34318/283‑1                                                                                                                                                                                                   CGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATAATCACGCCAATTCAATATATTTCA‑GAGATCATGTAGGCCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACCCAGTGCAAGAACTGCTGGAGCGCGCCCCTGAACGCTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAACAGTCTGCTAGCGCTGATTCACGCCCTTGAGTCTCctgt                                                                                                           >  1:34318/1‑284                                                                                                                                                                                                                                                                                                 ATGTAGGCCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACG              >  1:128607/1‑288                                                                                                                                                                                                                                                                                                 ATGTAGGCCGGATAAACGTAGGGCAACAGGCAAAACGTAAACAACGAGGACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGT             <  2:436639/289‑1                                                                                                                                                                                                                                                                                                      GGCCGGAAAAACGAAGGGCATAAGGCAAAACGTAAACAACGAGTACATTAATGGGCGAAAGGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGTCAGT         <  1:14525/288‑1                                                                                                                                                                                                                                                                                                        CCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGTCAGTATC      >  2:43357/1‑289                                                                                                                                                                                                                                                                                                        CCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGTCAGTAT       <  1:43357/288‑1                                                                                                                                                                                                                                                                                                           GATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCCGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCCCGACGAGAAAAGCGACGGTGCCGTCCACCAGGGCATTATCGCCCGCTGGACGCCAGGCACTCAGTAACAGG   >  1:397163/1‑289                                                                                                                                                                                                                                                                                                           GATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGaatcagcggtaa                                                                                           <  1:157103/201‑13                                                                                                                                                                                                                                                                                                           GATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGaatcagcggtaa                                                                                           >  2:157103/1‑189                                                                                                                                                                                                                                                                                                            ATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCC                                                                                                                        <  2:304056/171‑1                                                                                                                                                                                                                                                                                                            ATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCC                                                                                                                        >  1:304056/1‑171                                                                                                                                                                                                                                                                                                            ATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTATTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCACTTGGTAACCCGCCAAGATCTCGACGAGAAAAGCGACGGTCGCGTGCACCATGGCATTATCGCCCGCGTGAAGCCAGAACGTCAGTATCAGGA  >  2:661553/1‑289                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ATGCACGGCACCGTCGCTTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGC‑GTGATTATGTAGGCCGGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4409476‑4409175 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atgtaggccggataaACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGTCAGTATCAGGA  >  NC_000913/4409236‑4409520

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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.