New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	= 2549563	NA (NA)	5 (0.160)	5/270	3.6	18.5%	noncoding (98/98 nt)	RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	NC_000913_3_vch_tpiA	= 4235454	22 (0.710)					noncoding (4/77 nt)	REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_vch_tpiA/2549409‑2549563 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atccggcCTACATATCGACGATGATTAACCGCGCCACGCTTTATAGCGGTTAATCAGACCATTGGTCGAGCTATCGTGGCTGCTGATTTCTTTATCATCTTTCAGCTCTGGCAGAATACGGTTCGCCAGCTGTTTACCCAGTTCCACGCCC  <  NC_000913_3_vch_tpiA/4235454‑4235311                                                                                                                                                                                                                                                                                                             AAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCA                                                                                                                                                        >  1:429605/1‑149        CAGTCAGTGAGGTTACTGACGGGTCTAAGAGTGCTGACAACCGCAAAACTGCCTGATGCGCTGCGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATGCGGCGTGAACGCCTTATCCGGCC                                                                                                                                                 <  1:455505/149‑1                                                                                                                              GCCGGATAAGGCGTTCACGCCGCATCCGGCCTACATGAATACTAGGATTAACCGCGCCACGCTTTATAGCGGTTAATCAGACCATTGGTCGAGCTATCGTGGCTGCTGATTTCTTTATCATCTTTCAGCTCTGGCAGAATACGGTTCGC                           >  1:137079/1‑149                                                                                                                                 GGATAAGGCGTTCACGCCGCATCCGGCCTACATATCGACGATGATTAACCGC                                                                                                                         <  1:41827/52‑1                                                                                                                                 GGATAAGGCGTTCACGCCGCATCCGGCCTACATATCGACGATGATTAACCGC                                                                                                                         >  2:41827/1‑52                                                                                                                                             CACGCCGCATCCGGCCTACATATCGACGATGATTAACCGCGCCACGCTTTATAGCGGTTAATCAGACCATTGGTCGAGCTATCGTGGCTGCTGATTTCTTTATCATCTTTCAGCTCTGGCAGAATACGGTTCGCCAGCTGTTTACCCAG            <  2:137079/149‑1                                                                                                                                                     ATCCGGCCTACATATCGACGATGATTAACCGCGCCACGCTTTATAGCGGTTAATCAGACCATTGGTCGAGCTATCGTGGCTGCTGATTTCTTTATCATCTTTCAGCTCTGGCAGAATACGGTTCGCCAGCTGTTTACCCAGTTCCACGC    <  1:383659/149‑1                                                                                                                                                     ATCCGGCCTACATATCGACGATGATTAACCGCGCCACGCTTTATAGCGGTTAATCAGACCATTGGTCGAGCTATCGTGGCTGCTGATTTCTTTATCATCTTTCAGCTCTGGCAGAATACGGTTCGCCAGCTGTTTACCCAGTTCCACGC    >  2:130724/1‑149                                                                                                                                                       CCGGCCTACATATCGACGATGATTAACCGCGCCACGCTTTTATGCGGCTATTTTGATCTTTGGTCGAGCTATCGTGGCTGCTGATTTCTTTATCATCTTTCAGCTCTGGCAGAAGACGGTTCGCCAGCTGTTTACCCAGTTCCACGCCC  <  1:16346/149‑1                                                                                                                                                           CCTACATATCGACGATGATTAACCGCGCCACGCTTTATAGCGGTTAATCAGACCATTGGTCGAGCTATCGTGGCTGCTGATTTC                                                               >  1:375511/1‑84                                                                                                                                                           CCTACATATCGACGATGATTAACCGCGCCACGCTTTATAGCGGTTAATCAGACCATTGGTCGAGCTATCGTGGCTGCTGATTTC                                                               <  2:375511/84‑1                                                                                                                                                                                                                                                                                                             AAAAGGCCAGTCAGTAATGTTACTGGCTGGTCTGAGAGTGCTGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGAGCCCACAATATATTGAATTAGCACGATTTCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_vch_tpiA/2549409‑2549563 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atccggcCTACATATCGACGATGATTAACCGCGCCACGCTTTATAGCGGTTAATCAGACCATTGGTCGAGCTATCGTGGCTGCTGATTTCTTTATCATCTTTCAGCTCTGGCAGAATACGGTTCGCCAGCTGTTTACCCAGTTCCACGCCC  <  NC_000913_3_vch_tpiA/4235454‑4235311

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ 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.