New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	3908414 =	NA (NA)	5 (0.110)	5/242	NT	9.1%	noncoding (28/64 nt)	REP283 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP283 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913_3_pae_pgi	= 4613614	50 (1.050)					noncoding (98/388 nt)	REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences

TTTTGCGAAGAATAAACACGGTTGATATTGCTGACACGGTTTTCCCCTCACCCTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTGCCGGATGCGGCGTGAACGCCTGATCCGGCCTACGGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/3908573‑3908414 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atccggcctacggtTCGGCACAAACCTGTAGGCATGATAAGACGCGTTAAGCGTCGCATCAGGCATTGTGCGCCAACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGGCACGTTAAACAACGTATACGTGTTATTAAGCAACGCTTGCGCAATC  <  NC_000913_3_pae_pgi/4613614‑4613469                                                                                                                                                                                                                                                                                                                    TTTTGCGAAGAATAAACACGGTTGATATTGCTGACACGGTTTTCCCCTCACCCTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTGCCGGATGCGGCGTGAACGCCTGATC                                                                                                                                                               <  1:322099/149‑1          GAATAACCAAGGGTGATGTTGCTGAGACGGTTTTCCCCGTCCCCTAACCCGCTCCCCTGAGGGGCGAGGGGACCGACCGATCGCCTTTTTGACTTTGTACACGGTTAACACTTTGCCGGATGCGGCGTGAACGCCTGATCCGGCCTACG                                                                                                                                                      <  2:416952/149‑1                                               CTCACCCTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTGCCGGATGCGGCGTGAACGCCTGATCCGGCCTACGGTTCGGCACAAACCTGTAGGCATGATAAGACGCGTTA                                                                                                                 >  1:9480/1‑149                                                                           GAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTGCCGGATGCGGCGTGAACGCCTGATCCGGCCTACGGTTCGGCACAAACCTGTAGGCATGATAAGACGCGTTAAGCGTCGCATCAGGCATTGTGCGCCAAC                                                                                     <  2:9480/149‑1                                                                                                                         acggcgGGATGGGGGGGGAACGCCTGATCCGGCCTACGGTTCGGCACAAACCTGTAGGCATGATAAGACGCGTTAAGCGTCGCATCAGGCATTGTGCGCCAACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGGCACGTTAAA                                       <  2:688246/143‑1                                                                                                                                        ggaAACGCCTGATCCGGCCTACGGTTCGGCACAAACCTGTAGGCATGATAAGACGCGTTAAGCGTCGCATCAGGCATTGTGCGCCAACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGGCACGTTAAACAACGTATACGTGTT                        <  2:773864/146‑1                                                                                                                                             CGCCTGACACGGCCTAGGGTTCGGCACAAACCTGTAGGCATGATAAGACGGGTTAAGCGTCACATCAGGCATTGTGCGCCAACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGGCACGTTAAACAACGTATACGTGTTATTAA                   <  2:684831/149‑1                                                                                                                                                    TCCGGCCTACGGTTCGGCACAAACCTGTAGGCATGATAAGACGCGTTAAGCGTCGCATCAGGCATTGTGCGCCAACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGGCACGTTAAACAACGTATACGTGTTATTAAGCAACGC            >  1:291568/1‑149                                                                                                                                                       gtcttatGGTTCGGCACAAACCTGTAGGCATGATAAGACGCGTTAAGCGTCGCATCAGGCATTGTGCGCCAACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGGCACGTTAAACAACGTATACGTGTTATTAAGCAACGCTTG         <  1:767101/142‑1                                                                                                                                                              GGTTCGGCACAAACCTGTAGGCATGATAAGAAGCGTTAAGCGTCGCATCAGGCATTGTGCGCCAACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGGCACGTTAAACAACGTATACGTGTTATTAAGCAACGTTTGCGCAATC  <  1:978681/149‑1                                                                                                                                                                                                                                                                                                                    TTTTGCGAAGAATAAACACGGTTGATATTGCTGACACGGTTTTCCCCTCACCCTAACCCTCTCCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTTTGCCGGATGCGGCGTGAACGCCTGATCCGGCCTACGGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/3908573‑3908414 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atccggcctacggtTCGGCACAAACCTGTAGGCATGATAAGACGCGTTAAGCGTCGCATCAGGCATTGTGCGCCAACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGGCACGTTAAACAACGTATACGTGTTATTAAGCAACGCTTGCGCAATC  <  NC_000913_3_pae_pgi/4613614‑4613469

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.