New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_pgi = 143516454 (1.020)3 (0.060) 3/256 NT 5.4% intergenic (‑156/+21) ttcC/uspF pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related/stress‑induced protein, ATP‑binding protein
?NC_000913_3_pae_pgi = 1435170 53 (1.060)intergenic (‑162/+15) ttcC/uspF pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related/stress‑induced protein, ATP‑binding protein

AAAGCGACTCAATTCGTTATATGGCATCAGAAGAGTATGCGTCATGCCGGAACGCCCAGCATAAGAAATCTGATATAAAAAACTGTGGCGTGTATGGTACGGATTAGAGGGGAAAATGTCAGCACATTTGCGAAATGAATCAAAAAGCCCGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/1435012‑1435164
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcccgcaCATTGCTGCGGGCTTTTTG  <  NC_000913_3_pae_pgi/1435170‑1435152
                                                                                                                                                                            
AAAGCCACTCAATTCGTGATATGGCATCAGAAGATGATGCGTCATGCCGGAAAGCCCAGCATAAGAAATCTGATATAAAAAACTGTGGCGTGTATGGTACGGATTAGAGGGGAAAATGTCAGCACATTTGCGAAATGGATCAAAAAGCC                         <  1:623937/149‑1
  AGCGACTCAATTCGTTATATTGCATCGAAAGAGTATGCGGCATGCCGGAACGCCCAGTATAAGAAATCTGATATAAAAAACTGTGGCGTGTATGGTACGGATTAGAGGGGAAAATGGCAGCACATTTTCGAAATGAATCAAAAAGCCCG                       <  2:372683/149‑1
    CGACTCAATTCGTTATATGGCATCAGAAGATTATGCGTCATGCCGGAACGCCCAGCATAAGAAATCTGATATAAAAAACTGTGGCGTGTATGATACGGATTAGAGGGGAAAATGTCAGCACATTTTCGAAATAAATCAAAAAGCCCGCt                     >  2:260508/1‑148
                      cGCATAAGAAGAGTATGCGTGAGGCCGGAAAGCACAGTATAAGAAATCTGATATAAAAAGCTGTGGCGTGTATGGTACGGATTAGAGGGGAAAATGTCAGCACATTTGCGAAATGAAGCAAAAAGCCCGCACATTGCCGCGGGCTTTTT   <  2:21973/148‑1
                                                                                               GGTACGGATTAGAGGGGAAAATGTCAGCACATTTGCGAAATGAATCAAAAAGCCCGCACATTGCTGCGGGCTTTTTG  <  1:31964/77‑1
                                                                                               GGTACGGATTAGAGGGGAAAATGTCAGCACATTTGCGAAATGAATCAAAAAGCCCGCACATTGCTGCGGGCTTTTTG  >  2:31964/1‑77
                                                                                                                                                                            
AAAGCGACTCAATTCGTTATATGGCATCAGAAGAGTATGCGTCATGCCGGAACGCCCAGCATAAGAAATCTGATATAAAAAACTGTGGCGTGTATGGTACGGATTAGAGGGGAAAATGTCAGCACATTTGCGAAATGAATCAAAAAGCCCGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/1435012‑1435164
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcccgcaCATTGCTGCGGGCTTTTTG  <  NC_000913_3_pae_pgi/1435170‑1435152

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.