New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 173588	NA (NA)	5 (0.050)	4/164	NT	NA	noncoding (85/85 nt)	REP13 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP13 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913	2443819 =	NA (NA)					noncoding (31/80 nt)	REP171 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP171 (repetitive extragenic palindromic) element; contains 2 REP sequences

AGCGTTTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/173483‑173588 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atccgacCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAAAC  >  NC_000913/2443819‑2443915                                                                                                                                                                                                             AGCGTTTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCA                                                                                                         >  2:2764256/1‑100  GCGTTTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCAT                                                                                                        >  2:3115564/1‑100   CGTTTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATC                                                                                                       >  2:1413632/1‑100    GTTTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATGCGGCGTGAACGCCTTATCC                                                                                                      <  2:1443660/100‑1    GTTTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCC                                                                                                      <  1:3115592/100‑1      TTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGA                                                                                                    >  1:1889494/1‑100       TACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAC                                                                                                   >  2:2962523/1‑100       TACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAC                                                                                                   >  1:895723/1‑100       TACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAC                                                                                                   >  1:2813381/1‑100       TACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAC                                                                                                   >  2:1955523/1‑100       TACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAC                                                                                                   >  2:2155901/1‑100        ACGCGACAACGGATGCCCGATGCGACGCGGGCGCGTCGTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAC                                                                                                   <  2:1928189/99‑1         CGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATGCGGCGTGAACGCCTTATCCGACC                                                                                                  <  1:2267649/99‑1                                                                        CGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACG                                  >  1:1278627/1‑100                                                                            GGTCGGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGC                              >  2:1154902/1‑100                                                                               CGGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGAGGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAAC                           >  2:1994249/1‑100                                                                               CGGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAAC                           >  2:774/1‑100                                                                                GGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACT                          >  2:94494/1‑100                                                                                                    ATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTTCTGTGACGCCTGCTG      <  1:2886232/100‑1                                                                                                    ATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTG      <  1:2383894/100‑1                                                                                                     nCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGA     >  2:484685/2‑100                                                                                                     TCCGACCTACGTGTGACGTGTAGGCCTGATAAGATGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGTCTGCTGA     <  2:894247/100‑1                                                                                                     TCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTca     <  1:3005950/100‑3                                                                                                     TCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGA     >  2:2032488/1‑100                                                                                                       CGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTTCTGAAA   >  1:426767/1‑100                                                                                                        GACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAAAC  <  2:2878323/100‑1                                                                                                        GACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAAAC  <  1:787112/100‑1                                                                                                                                                                                                             AGCGTTTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/173483‑173588 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atccgacCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAAAC  >  NC_000913/2443819‑2443915

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.