New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 1435164	54 (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.