New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	= 3252144	NA (NA)	5 (0.090)	5/266	7.8	NA	noncoding (80/98 nt)	RIP234 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP234 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913_3_vch_tpiA	= 3252155	NA (NA)					noncoding (91/98 nt)	RIP234 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP234 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
Rejected: Coverage evenness skew score above cutoff.

GATGTTCGCTTCGGTTAAAAAAAGGCACCTTACGAGGTGCCTCTGATAATTAGCTAAGTGCATGTTGTTCATGTCGGATGTGGCATGAACGCCTTATCTGACATACAAAACATTGTACATTCAATAGATTGCATAACCCGCGCAGACCAGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_vch_tpiA/3251993‑3252144 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagatGCGCTACGCTTATCTGGTCTGCGCGGGTTATGCAATCTATTGAATGTACAATGTTTTGTATGT  <  NC_000913_3_vch_tpiA/3252155‑3252093                                                                                                                                                                                                                         gagtTTCGCTTCGGTTAAAAAAAGGCACCTTACTAGGTGCCTCTGATAATTAGCTAAGTGCATGTTGTTCATGTCGGATGTGGCATGAACGCCTTATCTGACATACAAAACATTGTACATTCAAGAGATTGCATAACCCGCGCAGACCA                                                                    <  1:416753/145‑1      TCGCTTCGGTTAAAAAAAGGCACCTTACGAGGTGCCTCTGATAATTAGCTAAGTGCATGTTGTTCATGTCGGATGTGGCATGAACGCCTTATCTGACATACAAAACATTGTACATTCAATAGATTGCATAACCCGCGCAGACCAGATGC                                                               >  2:221242/1‑149                                               TAATTAGCTAAGTGCATGTTGTTCATGTCGGATGTGGCATGAACGCCTTATCTGACATACAAAACATTGTACATTCAATAGATTGCATAACCCGCGCAGACCAGATGCGCTACGCTTATCTGGTCTGCGCGGGTTATGCAATCTATTGA                      <  1:221242/149‑1                                                                   ctttATGTCGGATGAGGCATGAACGCCTTATCGGACATACAAAACATTATACATTCAATAGATTACATAACCCGCGCAGACCAGATGCGCTACGCTTATCTGGTCTGCGCGGGTTATGCAATCTATTGAATGTACAATGTTTTGTATGT  <  2:943714/145‑1                                                                                      TGAACGCCTTATCTGACATACAAAACATTGTACATTCAATAGATTGCATAACCCGCGCAGACCAGATGCGCTACGCTTATCTGGT                                               <  1:459336/85‑1                                                                                      TGAACGCCTTATCTGACATACAAAACATTGTACATTCAATAGATTGCATAACCCGCGCAGACCAGATGCGCTACGCTTATCTGGT                                               >  2:459336/1‑85                                                                                                                                                                                                                         GATGTTCGCTTCGGTTAAAAAAAGGCACCTTACGAGGTGCCTCTGATAATTAGCTAAGTGCATGTTGTTCATGTCGGATGTGGCATGAACGCCTTATCTGACATACAAAACATTGTACATTCAATAGATTGCATAACCCGCGCAGACCAGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_vch_tpiA/3251993‑3252144 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagatGCGCTACGCTTATCTGGTCTGCGCGGGTTATGCAATCTATTGAATGTACAATGTTTTGTATGT  <  NC_000913_3_vch_tpiA/3252155‑3252093

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.