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
                                                                            GCGTGAATCAGCGGTAACAGACGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATGTAGGCCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAAGGATTTA                                                                                                                                                                                                                                      >  1:34318/1‑283
                                                                                          tcACAGACGTTCGACTTCACGGCCTTGTAAAAGAAAGCTTTCCTGAACCCGTTCAAGGGCGCGCGCCAGCAGTGCCTTCACTCCGTGGATGCCGTAGATCATTTCTCTCATTACTGTACTCGTTGTTGACGTTTTGCCTGATGCGCTACCTTTATCCGGCCTACATGATCTCGGCAATATATGGAATTTGCGTGATTATGTAGGCCGGATAAACGTAGTGCATCAGGCAACACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGG                                                                                                                                                                                                                  <  2:434230/287‑1
                                                                                                 CGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATG                                                                                                                                                                                                                                                                                                           <  1:316253/193‑1
                                                                                                 CGTTTATCTTCACGGCCTTTTAAAATAAAGACTTCCTGAAAACGTTCAGGGGCGCGCTCCAGCAGGGCCTGCACTGCGTGGATGCCGTAAATCATTTCGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATGATCTCTGCAATATATTGAATTTGCGTGATTATG                                                                                                                                                                                                                                                                                                           >  2:316253/1‑193
                                                                                                                                                                             CGTGGATGCCGTAAATATTGTCGCTCATTAATGTACTCGTTGTTTACGTTTTGTCTGATGCACTACGTTTATCCGGCCTACATAATCACGCAAATTAAATATATTGCAGAGATCATGTAGGCTGGATAAACGTAGGGAATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACGCAGTGCAGGCCCTGCTGGAGCGCGCCCCTGAACGTTTTCAGGAAGTCTTTA                                                                                                                                                                        <  1:104954/248‑1
                                                                                                                                                                                                  CGCTCATTAATGTACTCGTTGTTTACGTTTTGCCTGATGCACTACGTTTATCCGGCCTACATAATCACGCCAATTCAATATATTTCAGAGATCATGTAGGCCGGATAAACGTAGTGCATCAGGCAAAACGTAAACAACGAGTACATTAATGAGCGAAATGATTTACGGCATCCACCCAGTGCAAGAACTGCTGGAGCGCGCCCCTGAACGCTTTCAGGAAGTCTTTATTTTAAAAGGCCGTGAAGATAACAGTCTGCTAGCGCTGATTCACGCCCTTGAGTCTCctgt                                                                                                           >  2:34318/1‑284
                                                                                                                                                                                                                                                                                                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.