New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	= 4296174	20 (0.710)	7 (0.260)	5/270	3.1	29.8%	noncoding (310/600 nt)	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
	?	NC_000913_3_vch_tpiA	= 4296190	14 (0.520)					noncoding (326/600 nt)	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites	RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites
Rejected: Coverage evenness skew score above cutoff.

CTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTG  >  NC_000913_3_vch_tpiA/4296033‑4296271                                                                                                                                              |                                                                                                  cTGATTTGGCGTGATTTGTTAGGTCGGATAGGGCGTTTACGCCGTATCCGACATCAAGGCCTGATGCGAGGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGt                                                                                            <  2:127577/149‑1 (MQ=11)  tGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGCTTTTGTAGGTCGGATAAGGCGtt                                                                                           >  1:208282/1‑149 (MQ=37)            tGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATCAGGTGTTTCTGCCGCAt                                                                                 >  2:387842/1‑149 (MQ=255)                   gTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTTCTATAGCTTCATTTTCTAGGTCGCATACGGCCTTTATGCCGGCTCCgcgat                                                                          >  2:78140/1‑145 (MQ=14)                       gTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACCCCAACCAGCGCATTATCCTGCATTATCGTGATTTTCTGGATCGGACAATGCCTTTAAGCCCAATTCGAccccatg                                                                      >  2:272116/1‑143 (MQ=2)                       gTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAAc                                                                      >  2:492222/1‑149 (MQ=38)                        tCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCATTAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACctcaatg                                                                     <  2:318267‑M2/149‑8 (MQ=255)                        tCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACg                                                                     <  1:301438/149‑1 (MQ=37)                             tAAGGCGTTTACGCCGCGTCATGTATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGa                                                                <  2:470038/149‑1 (MQ=11)                                 gCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCg                                                            >  2:369688/1‑149 (MQ=39)                                 gCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCGGATGCg                                                            >  2:329238/1‑149 (MQ=255)                                  ggTTTCCGCCGCACAAGAAATCAGCGCCTGATGCGACGCGTGCGGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCGTTATTTAGGGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGa                                                           <  2:171238/148‑1 (MQ=11)                                  cGTTTACGCCGCACCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGa                                                           <  1:57396/149‑1 (MQ=38)                                     ttACGCCGCATCCCACATCACCGCTTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACCGCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGAATAGAGTTTTATTCCGCATCCGACATCAACGCCTGATGCGACGc                                                        <  1:248060/149‑1 (MQ=11)                                         gccgcATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTaa                                                    >  2:487978/1‑149 (MQ=34)                                              aTCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGt                                               >  2:192380/1‑149 (MQ=35)                                                  gACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAg                                                                                                <  2:198980/96‑1 (MQ=38)                                                      tCAACGCCTGATGCGACGTCTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACACCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAg                                       <  1:418888/149‑1 (MQ=11)                                                        aaCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGc                                                                    <  1:229208/118‑1 (MQ=32)                                                        aaCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTACCGCGTCTTATCAgcc                                     >  2:249333/1‑147 (MQ=17)                                                         aCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGcc                                    <  1:487978/149‑1 (MQ=31)                                                                                                                 ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACctacaaaatcacgctaaatcaggctattgcgctgtctggcgtaggcctgataagacgcg                 >  1:317866‑M2/1‑53 (MQ=255)                                                                                                                 ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACctacaaaatcacgctaaatcaggctattgcgctgtctggcgtaggcctgataagacgcg                 <  2:317964‑M2/112‑60 (MQ=255)                                                                                                                 ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACctacaaaatcacgctaaatcaggctattgcgctgtctggcgtaggcctgataagacgcg                 <  2:317866‑M2/112‑60 (MQ=255)                                                                                                                 ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACctacaaaatcacgctaaatcaggctattgcgctgtctggcgtaggcctgataagacgcg                 >  1:317964‑M2/1‑53 (MQ=255)                                                                                                                                         tCGGATAAGGCGTTTATGCCGCATCCGACctacaaaatcacgctaaatcaggctattgcgctgtctggcgtaggcctgataagacgcggcaagcgtcgcatca  <  2:196167‑M2/103‑75 (MQ=255)                                                                                                                                         tCGGATAAGGCGTTTATGCCGCATCCGACctacaaaatcacgctaaatcaggctattgcgctgtctggcgtaggcctgataagacgcggcaagcgtcgcatca  >  1:196167‑M2/1‑29 (MQ=255)                                                                                                                                              |                                                                                                  CTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTG  >  NC_000913_3_vch_tpiA/4296033‑4296271

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.