New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	703315 =	11 (0.270)	4 (0.110)	3/294	NT	13.7%	noncoding (90/165 nt)	RIP63 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site	RIP63 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site
	?	CP009273	3505933 =	40 (1.050)					noncoding (64/90 nt)	REP250 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP250 (repetitive extragenic palindromic) element; contains 2 REP sequences

ATCAAACAGGGCTTTGCTGAACCGTCGCTGAAAGATGCGGTTGCGGGTAAAGCATTCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAACAGCAAACAATCCAAAACGCCGCGTTCAGCGGCGTTTTTTCTGCTTTTCTTCGCGAATTAATTCCGCTTCGCAATTTATCCATAAAATAAATTTAAAATAACAAAACATAATTA  >  CP009273/703043‑703510                                                                                                                                                                                                                                                                                 |                                                                                                                                                                                                    tcgaaggaaagatgtatggtcatctgaaaggtgaagtgcgtgatgccgtttccggtatgctgactgaagtgcaggaatgctatcaccgtttccgcaacgatgaagccttcctgcaacaggtgatgaaagatgacgcggaaaaagccagcgcgcacgcttcccgtacgctaaaagcggtgtacgaagcgattggttttgtggcgaagccggaattcactattgctggcaaattgcgctttgttcatgccggatgcggcgtgaatgccttatccg                                                                                                                                                                                                     >  1:733528‑M1/273‑273 (MQ=255)       gacagatgtatggtcatctgaaaggtgaagtggctgatgccgtttccggtatgctgactgaagtgcaggaacgctatcaccgtttccgcaacgatgaagccttcctgcaacaggtgatgaaagatggcgcggaaaaagccagcgcgcacgcttcccgtacgctaaaagcggtgtacgaagcgattggttttgtggcgaagccgtaattcactattgctggcaaattgcgctttgttcatgccggatgcggcgtgaacgccttatccGGCCTACa                                                                                                                                                                                              >  1:17150‑M1/267‑274 (MQ=255)                                                              gactgaattgcaggaacgctatcaccgtttccgcaacgatgaagccttcctgcaacaggggatgaaagatggcgcggaaaaagccagcgcgcacgcttcccgtacgctaaaagcggtgtacgaagcgattggttttgtggcgaagccgtaattcactattgctggcaaattgcgctttgttcatgccggatgcggcgtgaacgccttatccg                                                                                                                                                                                                     >  2:722115‑M1/212‑212 (MQ=255)                                                                    gcgattggtACGTCTGCCTCGGTTGCCGCCATTCTACGGTGGTATAACCGTTAGTTAACCGCTCCGTTGGGCTGCGTTATACCTGGGCGAAAGGAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCTTTTACCTCGCATCCGGCAAGGAACAGACAAACAGTTTCAATCGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCa                                                                                                                                <  2:174443/267‑1 (MQ=37)                                                                                         aTAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGAtct                                                                                                                                                                                        >  2:223945/1‑198 (MQ=255)                                                                                             ccgccATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGc                                                                                                                                                                                    <  1:223947/198‑1 (MQ=255)                                                                                                                                   ccGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAACAGCAAACAATCCAAAAAGCCGCGTTCAGCGGCGTTTTTTCTGCTTttctt                                                                 >  1:85223/1‑275 (MQ=255)                                                                                                                                     gTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAgg                                                                                                                                                                                                    <  1:621849/142‑1 (MQ=255)                                                                                                                                       tGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGaaa                                                                                                                    <  1:365723/220‑1 (MQ=255)                                                                                                                                                tGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAACAGCAAACAATCCAAAACGCCGCGTTCAGCGGCGTTTTTTCTGGTTTTCTACCCGAATTAATTc                                                    >  2:132271/1‑275 (MQ=255)                                                                                                                                                tGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAACAGCAAACAATCAAAAACGCCGCGTCCAGCGGCGTTTTTTCTGCTTTTGTCCTCGcattattt                                                     >  2:137557/1‑274 (MQ=255)                                                                                                                                                                         tAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCt                                                                                                                                                                                                 >  1:84499/1‑109 (MQ=255)                                                                                                                                                                             tttAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACAt                                                                                                                                                                                             <  2:84498/109‑1 (MQ=255)                                                                                                                                                                                 aGTTTCGCTATGCCGGATGGGTCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAACAGCAAACAATCCAAAACGCCGCGTTCAGCGGCGTTTTTTCTGCTTTTCTTCGCGAATTAATTCCGCTTCGCAATTTATCCATAAAATAAATTTaa                    <  1:137558/274‑1 (MQ=255)                                                                                                                                                                                            gCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAACAGCAAACAAGCCAAAACGCCGCGTTCAGCGGCGTTTTTTCTGCTTTTCTTCGCGAATTAATTCCGCTTCGCAATTTATCCATAAAATAAATTTAAAATAACAAAACa        >  1:414168/1‑275 (MQ=255)                                                                                                                                                                                              ttggttttgtggcgaagccgtaattcactattgctggcaaattgcgctttgttcatgccggatgcggcgtgaacgccttatccGGcc                                                                                                                                                                                                  <  2:118629‑M1/4‑1 (MQ=255)                                                                                                                                                                                                  ttttgtggcgaagccgtaattcactattgctggcaaattgcgctttgttcatgccggatgcggcgtgaacgccttatccGGCCTACa                                                                                                                                                                                              >  1:118630‑M1/80‑87 (MQ=255)                                                                                                                                                                                                    gggCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGcc                                                                                                                                                                                                  <  2:305733/81‑1 (MQ=255)                                                                                                                                                                                                                 gCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAACAGCAAACAATCCAAAACGCCGCGTTCAGCGGCGTTTTTTCTGCTTTTCTTCGCGAATTAATTCCGCTTCGCAATTTATCCATAAAATAAATTTAAAATAACAAAACATAATta  >  1:417397/1‑260 (MQ=255)                                                                                                                                                                                                                                tgacaaaatgcgctttgttcatgccggatgcggcgtgaacgccttatccGGCCTACATGATCTCTGCAATATATTgaa                                                                                                                                                                         <  1:696459‑M1/29‑2 (MQ=255)                                                                                                                                                                                                                                 ggcaaattgcgctttgttcatgccggatgcggcgtgaacgccttatccGGcc                                                                                                                                                                                                  <  2:47689‑M1/4‑1 (MQ=255)                                                                                                                                                                                                                                    aaaatgcgctttgttcatgccggatgcggcgtgaacgccttatccGGCCTACATGATCTCTGCAATATATTGAATTTg                                                                                                                                                                     >  2:696445‑M1/46‑78 (MQ=255)                                                                                                                                                                                                                                     aattgcgctttgttcatgccggatgcggcgtgaacgccttatccGGCCTACa                                                                                                                                                                                              >  1:47690‑M1/45‑52 (MQ=255)                                                                                                                                                                                                                                                gttcatgccggatgcggcgtgaacgccttatccGGc                                                                                                                                                                                                   >  2:630318‑M1/34‑36 (MQ=255)                                                                                                                                                                                                                                                          gatgcggcgtgaacgccttatccGGCCTACATGATCTCTGCAATATATTGAg                                                                                                                                                                         <  2:331072‑M1/29‑1 (MQ=255)                                                                                                                                                                                                                                                              cggcgtgaacgccttatccGGCCTACATGATCTCTGCAATATATTGAGTTTg                                                                                                                                                                     >  1:331078‑M1/20‑52 (MQ=255)                                                                                                                                                                                                                                                                                 |                                                                                                                                                                                                    ATCAAACAGGGCTTTGCTGAACCGTCGCTGAAAGATGCGGTTGCGGGTAAAGCATTCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGGCGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAATTTTAAGTTTCGCTATGCCGGATGGGGCGTTTACGTCGCATCCGGCAAGGAACAGACAAACAGTTTCAAACGCTAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATGATCTCTGCAATATATTGAGTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAACAGCAAACAATCCAAAACGCCGCGTTCAGCGGCGTTTTTTCTGCTTTTCTTCGCGAATTAATTCCGCTTCGCAATTTATCCATAAAATAAATTTAAAATAACAAAACATAATTA  >  CP009273/703043‑703510

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 35 ≤ 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.