New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	2304471 =	53 (1.120)	6 (0.130)	6/272	5.5	12.1%	noncoding (55/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
	?	NC_000913_3_vch_tpiA	= 2347207	37 (0.820)					noncoding (48/203 nt)	REP164 (repetitive extragenic palindromic) element; contains 5 REP sequences	REP164 (repetitive extragenic palindromic) element; contains 5 REP sequences
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAACCGGCTCGGGCGTTGGATGTCGGATGCGGCGTGACCGCCTTGTCTGACCTACGGGGTGCCGCACTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_vch_tpiA/2304624‑2304471 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcaggcCTACAAACCGAGCCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATCTCAATATCAGATCTTACATGCGCCGCTTTCGCAGCCATCGTCCTGGATTGACGGCACCAGATCGTCTTGTGCGTCTTCAGCGCCGTCACGGGTGTT  <  NC_000913_3_vch_tpiA/2347207‑2347061                                                                                                                                                                                                                                                                                                               GCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAACCGGCTCGGGCGTTGGATGTCGGATGCGGCGTGACCGCCTTGTCTGACCTACGGGGTGCCGCACTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCAT                                                                                                                                                          <  2:772613/149‑1         GGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAACCGGCTCGGGCGTTGGATGTCGGATGCGGCGTGACCGCCTTGTCTGACCTACGGGGTGCCGCACTTCACAGCGGTGTAGGGAAGACACGCCTCGCCAGCGTCGCCTCCGGCCac                                                                                                                                                  >  2:345942/1‑147                                                                                                          ACTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC                                                                                                                                                     >  1:215740/1‑49                                                                                                          ACTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC                                                                                                                                                     <  2:215740/49‑1                                                                                                               ACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAG                                                                                                                                                       <  1:672096/42‑1                                                                                                               ACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAG                                                                                                                                                       >  2:672096/1‑42                                                                                                                           GCCTGATAAGACGCGCCAGCGTCGCATCAGGCCTACAAACCGAGCCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATCTCAATATCAGATCTTACATGCGCCGCTTTCGCAGCCATCGTCCTGGATTGACGGCACCAGATCGTC                                >  2:147343/1‑149                                                                                                                            CCTGATAAGACGCGCCAGCGTCGCATCAGGCCTACAAACCGAGCCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATCTCAATATCAGATCTTACATGCGCCGCTTTCGCAGCCATCGTCCTGGATTGACGGCACCAGATCGTCT                               >  1:259343/1‑149                                                                                                                                 TAAGACGCGCCAGCGTCGCATCAGGCCTACAAACCGAGCCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATCTCAAT                                                                                             >  1:387264/1‑82                                                                                                                                 TAAGACGCGCCAGCGTCGCATCAGGCCTACAAACCGAGCCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATCTCAAT                                                                                             <  2:387264/82‑1                                                                                                                                             GCGTCGCATCAGGCCTACAAACCGAGCCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATCTCAATATCAGATCTTACATGCGCCGCTTTCGCAGCCATCGTCCTGGATTGACGGCACCAGATCGTCTTGTGCGTCTTCAGCGCC              <  2:259343/149‑1                                                                                                                                                         GCCTACAAACCGAGCCGTAGGCCGGATAAGGCGTTAACGCCGCATCCGGCATCTCAATATCAGATCTTACATGCGCCGCTTTCGCAGCCATCGTCCTGGCTTTACGGCACCCGATCGTCTTGTGCGTCTTCAGCCCCGTCACGGCTGTT  >  2:342182/1‑149                                                                                                                                                                                                                                                                                                               GCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAACCGGCTCGGGCGTTGGATGTCGGATGCGGCGTGACCGCCTTGTCTGACCTACGGGGTGCCGCACTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_vch_tpiA/2304624‑2304471 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcaggcCTACAAACCGAGCCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATCTCAATATCAGATCTTACATGCGCCGCTTTCGCAGCCATCGTCCTGGATTGACGGCACCAGATCGTCTTGTGCGTCTTCAGCGCCGTCACGGGTGTT  <  NC_000913_3_vch_tpiA/2347207‑2347061

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