New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4409174 =	NA (NA)	4 (0.050)	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	4409235 =	59 (0.670)					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

ATGCACGGCACCGTCGCTTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATGTAGGCCGGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4409475‑4409174 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atgtaggccggataaACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGTCAGTATCAGGA  >  NC_000913/4409235‑4409519                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ATGCACGGCACCGTCGCTTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTAT                                                                                                                                                                                                                                                                                                            >  2:574825/1‑289     ACGGCACCGTCGCTTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATGTAG                                                                                                                                                                                                                                                                                                        <  1:63407/289‑1     ACGGCACCGTCGCGTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGTGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGCTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATGTAG                                                                                                                                                                                                                                                                                                        <  1:599514/289‑1      CGGCACCGTCGCTTTTCTCGTCGCGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGTCTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGTCCTCCAGCAGGGCATGCACTGCGTGGATGCCGTACTTCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTTCCTGTTGCACTACCTTTATCCGTCCTACATGATCTCTGCCATATATTTATTTTGCGTGATTATGTAta                                                                                                                                                                                                                                                                                                       >  2:870313/1‑287       GGCACCGTCGCTTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATGTAGGC                                                                                                                                                                                                                                                                                                      <  1:903280/289‑1                   TTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATGTAGGCCGGATAAACGTA                                                                                                                                                                                                                                                                                          <  2:711995/289‑1                                                              acagGAGACTCAAGGGCGTGAATCAGCGCTAGCAGACTGTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAGCGTTCAGGGGCGCGCTCCAGCAGTTCTTGCACTGGGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGAAATATATTGAATTGGCGTGATTATGTAGGCCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCG                                                                                                                                                                                                                                                <  2:34318/284‑1                                                                             GCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATGTAGGCCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAAGGATTTA                                                                                                                                                                                                                                      >  1:34318/1‑283                                                                                           tcACAGACGTTCGACTTCACGGCCTTGTAAAAGAAAGCTTTCCTGAACCCGTTCAAGGGCGCGCGCCAGCAGTGCCTTCACTCCGTGGATGCCGTAGATCATTTCTCTCATTACTGTACTCGTTGTTGACGTTTTGCCTGATGCGCTACCTTTATCCGGCCTACATGATCTCGGCAATATATGGAATTTGCGTGATTATGTAGGCCGGATAAACGTAGTGCATCAGGCAACACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGG                                                                                                                                                                                                                  <  2:434230/287‑1                                                                                                  CGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATG                                                                                                                                                                                                                                                                                                           <  1:316253/193‑1                                                                                                  CGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATG                                                                                                                                                                                                                                                                                                           >  2:316253/1‑193                                                                                                                           TAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATTCCCTACGTTTATCCAGCCTACATGATCTCTGCAATATATTTAATTTGCGTGATTATGTAGGCCGGATAAACGTAGTGCATCAGACAAAACGTAAACAACGAGTACATTAATGAGCGACAATATTTACGGCATCCACG                                                                                                                                                                                                                           >  1:104954/1‑248                                                                                                                                                                                                                                                                                                ATGTAGGCCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACG              >  2:128607/1‑288                                                                                                                                                                                                                                                                                                ATGTAGGCCGGATAAACGTAGGGCAACAGGCAAAACGTAAACAACGAGGACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGT             <  1:436639/289‑1                                                                                                                                                                                                                                                                                                     GGCCGGAAAAACGAAGGGCATAAGGCAAAACGTAAACAACGAGTACATTAATGGGCGAAAGGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGTCAGT         <  2:14525/288‑1                                                                                                                                                                                                                                                                                                       CCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGTCAGTATC      >  1:43357/1‑289                                                                                                                                                                                                                                                                                                       CCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGTCAGTAT       <  2:43357/288‑1                                                                                                                                                                                                                                                                                                          GATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCCGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCCCGACGAGAAAAGCGACGGTGCCGTCCACCAGGGCATTATCGCCCGCTGGACGCCAGGCACTCAGTAACAGG   >  2:397163/1‑289                                                                                                                                                                                                                                                                                                           ATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCC                                                                                                                        >  2:304056/1‑171                                                                                                                                                                                                                                                                                                           ATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCC                                                                                                                        <  1:304056/171‑1                                                                                                                                                                                                                                                                                                           ATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTATTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCACTTGGTAACCCGCCAAGATCTCGACGAGAAAAGCGACGGTCGCGTGCACCATGGCATTATCGCCCGCGTGAAGCCAGAACGTCAGTATCAGGA  >  1:661553/1‑289                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ATGCACGGCACCGTCGCTTTTCTCGTCGAGATATTGGCGGTTTGCCAACTGGATAACCACGCCCTGAGACTCAAGGGCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATGTAGGCCGGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/4409475‑4409174 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atgtaggccggataaACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAAACGTCTGTTACCGCTGATTCACGCCCTTGAGTCTCAGGGCGTGGTTATCCAGTTGGCAAACCGCCAATATCTCGACGAGAAAAGCGACGGTGCCGTGCATCAGGGCATTATCGCCCGCGTGAAGCCAGGACGTCAGTATCAGGA  >  NC_000913/4409235‑4409519

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ 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.