New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	4218566 =	70 (1.320)	9 (0.170) +T	9/268	NT	11.5%	noncoding (131/132 nt)	REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences
	?	NC_000913_3_pae_pgi	= 4253287	NA (NA)					noncoding (127/130 nt)	RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site	RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site

ACCGGAGGTCACTTCGAGGAATCGACCATACTGAGCATCGAAGCCTTGCAAAATGGTTTGAGCAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/4218685‑4218566 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGATGCGGCGAAAACGCCTTATCCGGCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGCCGCGCATCAGGCAACCCAGAAGAAAGCCGGATGATCATCCGGCTTTTTTACATCATCAGAAA  <  NC_000913_3_pae_pgi/4253287‑4253142                                                                                                                         |                                                                                                                                                   ACCGGAGGTCACTTCGAGGAATCGACCATACTGAGCATCGAAGCCTTGCAAAATGGTTTGAGCAATCAATAATGCCAGGCCACGCGGCATTTAGCGCCCTCATAAAAAGCTGCGAGGGGTTGGATGCGGCGAAAACGCATTATCCGTCC                                                                                                                        >  1:939064/1‑149                   ctactGACCATACTTAGCATGTAAGCCTTGCAAAATGGTTTGAGCAATCAATAATTCCAGTCGACGCGGTATTTAGCGCCCTTATCAGGAGCAGTGAAGTGCTGGATGCGGCGAAAATTCCTTATCCGGCCTTCCATACTCTGCAAATT                                                                                                      <  2:187220/144‑1                                           GCCTTGCAAAATGGTTTGACACATCAATAATTCCAGGCCACGCGGCATTTAGCGTCCTTTTCAGGAGCAGAGAATTGCTGGATGCGGCGAAAACGCCTTATCCGGCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTA                                                                              <  1:379235/149‑1                                                          TTGAGCAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGCTGGATGCGGCGAAAACGCCTTATCCGGCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGCC                                                               <  1:892285/149‑1                                                               CAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGCTGGATGCGGCGAAAACGCCTTATCCGGCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGCCGCGCA                                                          >  1:829268/1‑149                                                                                                       tgAGGAGCAGAGAATTGCTGGATGCGGCGAAAACGACTTATCCGGCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGGTGTGTAGGCCTGAGAAGCGCCGCGCATCAGGCAACCCAGAAGAAAGCCGGATGATCATCCGGCTTT                  <  1:853638/147‑1                                                                                                              cataaAATTGCTGCATGCGGCGAAAACGCCTTATTCGGCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGCCGCGCATCAGGCAACCCAGAAGAAAGCCGGATGATCATCCGGCTTTTTTACAT           <  1:130721/144‑1                                                                                                                 gGAATTGCTGGATGCGGCGAAAACGCCTTATCCGGCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTAGGCCTGGGAAGCGCCGCGCATCAGGCCACCCAGAAGAAAGCCGGATGATCATCCGGCTTTTTTACATCAT        <  2:283137/148‑1                                                                                                                   AATTGCTGGATGCGGTGAGAACGCCTTATCCGGCCTTCCATAATCTGCAAATTCAATCAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGCCGCGCATCAGGCAACCCAGAAGAAAGCCGGATGATCATCCGGCTTTTTTACATCATCA      <  2:320592/149‑1                                                                                                                      TGCTGGATGCGGCGAAAACGCCTGATGCGGCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGCCGCGCATCAGGCAACCCAGAAGAAAGCCGGATGATCATCCGGCTTTTTTACATCATCAGAA   <  1:953204/149‑1                                                                                                                       GCTGGATGCGGCGAAAACGCTTTTTTCGGCTTTCCTTAATCTGCTAATTCAATGAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGCCGCGCATCAGGCAACCCAGAAGAAAGCCGGATGATCATCCGGCTTTTTTACATCATCAGAAA  <  1:36628/149‑1                                                                                                                         |                                                                                                                                                   ACCGGAGGTCACTTCGAGGAATCGACCATACTGAGCATCGAAGCCTTGCAAAATGGTTTGAGCAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/4218685‑4218566 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGATGCGGCGAAAACGCCTTATCCGGCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGCCGCGCATCAGGCAACCCAGAAGAAAGCCGGATGATCATCCGGCTTTTTTACATCATCAGAAA  <  NC_000913_3_pae_pgi/4253287‑4253142

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.