New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	= 349845	14 (0.800)	3 (0.170)	3/274	2.3	17.6%	noncoding (241/365 nt)	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
	?	NC_000913_3_vch_pgi	= 349969	NA (NA)					noncoding (365/365 nt)	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences	REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences
Rejected: Frequency below/above cutoff threshold.

ACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGCGTTCCGGCGGGCAATACGGCGCTCTGCACC  >  NC_000913_3_vch_pgi/349834‑350113                                                                                                                                        |                                                                                                                                                 aCTGAACTGTAGGTCGGATAAGACGCATAGGGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGAcc                                                                                                                                     <  2:179274/149‑1 (MQ=255)        tGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACaaa                                                                                                                              <  1:223161/149‑1 (MQ=255)           aGGGCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGGCGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGa                                                                                                                           <  2:207042/149‑1 (MQ=255)             gTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCATCGCGACCCTCCACATGATa                                                                                                                         >  2:261843/1‑149 (MQ=11)                 caaaaGACGCATTGCGTCGCCTCCGACAACCGATGCCTGATGCGCAGCCGGCGCCACGTATCAGGCCTACGGGGTGAACTGCACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACaa                                                                                                                     <  1:90114/146‑1 (MQ=17)                          actAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGTATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGa                                                                                                            <  1:9845/147‑1 (MQ=255)                                       ccGAGAACCGATGCCTGATGCGCCGCTGACGGGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGCGCGac                                                                                               <  2:261127/149‑1 (MQ=255)                                       ccGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGac                                                                                               <  2:261402/149‑1 (MQ=255)                                                 aTGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATcc                                                                                     <  1:261843/149‑1 (MQ=255)                                                            gccgcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGt                                                                          <  2:157786/149‑1 (MQ=255)                                                                                         ggTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCtgt                                             <  1:214754/149‑1 (MQ=255)                                                                                          gTGAACCGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCAACAACAATCTCGACCCAACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGAACCCCTGTCAATAAACGGCAAAAAACtgcg                                            <  2:314278/149‑3 (MQ=37)                                                                                                          gTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGCGTTc                            <  2:117257/149‑1 (MQ=255)                                                                                                              gATAAGACGCATAGCGTCGCATCCGACctacagttcagttcaccccgtaggcctgataagtcgcgtcagcggcgcatcaggcatcggttgtcggatgcgacgctatgcgtcttatccgacctacagttcagtgcaccccgtaggcctga                        <  2:288928‑M2/149‑123 (MQ=255)                                                                                                               aTAAGACGCATAGCGTCGCATCCGACctacagttcagtgcaccccgtag                                                                                                                           <  1:33244‑M2/49‑24 (MQ=255)                                                                                                               aTAAGACGCATAGCGTCGCATCCGACctacagttcagtgcaccccgtag                                                                                                                           >  2:33244‑M2/1‑26 (MQ=255)                                                                                                                      gCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAAc                                                          <  2:2058/107‑1 (MQ=255)                                                                                                                      gCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAAc                                                          >  1:2058/1‑107 (MQ=255)                                                                                                                                    ccGACctacagttcagtgcaccccgtaggcctgataagtcgcgtcagcggcgcatcaggcatcggttgtcggatgcgacgctatgcgtcttatccgacctacagttcagtgcaccccgtaggcctgataagtcacgtcagcggcgcatc  <  1:276323‑M2/149‑145 (MQ=255)                                                                                                                                        |                                                                                                                                                 ACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTACAAATGATAACAATGACGAGGACAACATGAGCGACACAACGATCCTGCAAAACAGTACCCATGTCATTAAACCGAAAAAATCTGTGGCACTTTCTGGCGTTCCGGCGGGCAATACGGCGCTCTGCACC  >  NC_000913_3_vch_pgi/349834‑350113

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.