New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 173588	NA (NA)	10 (0.070)	5/164	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                                                                                                         >  2:4037318/1‑100    GTTTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATGCGGCGTGAACGCCTTATCC                                                                                                      <  2:3972719/100‑1     TTTATGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATGCGGCGTGAACGCCTTATCC                                                                                                      <  2:845065/99‑1     TTTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCG                                                                                                     <  1:143805/100‑1     TTTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCG                                                                                                     <  1:831289/100‑1      TTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGA                                                                                                    >  2:545848/1‑100      TTACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGA                                                                                                    >  1:2591741/1‑100       TACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAC                                                                                                   >  1:3399901/1‑100       TACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCACGAATCGTAGGTCGGATAAGGCGATCACGCCGCATCCGAC                                                                                                   >  1:1642684/1‑100        ACGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATGCGGCGTGAACGCCTTATCCGACC                                                                                                  <  2:75093/100‑1         CGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGGTCGGATGCGGCGTGAACGCCTTATCCGACCT                                                                                                 <  2:2175048/100‑1         CGCGACAACGGATGCCCGATGCGACGCTGGCGCGTCTTATCGGGCCTACAAACGGCCCCGAATCGTAGCTCGGATAAGGCGTTCACGCCGCATCCGAC                                                                                                   >  2:733747/1‑98                                                                          TAGGTCGGATAAGGCGTTCACGCCGCATCCGGCCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCC                                >  1:895527/1‑100                                                                          TAGGTCGGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCC                                >  2:722504/1‑100                                                                            GGTCGGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGC                              >  1:994235/1‑100                                                                             GTCGGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCA                             >  1:2338404/1‑100                                                                             GTCGGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCA                             >  1:225776/1‑100                                                                                GGATAAGGCGTTCACGCCGCATCCGACCTATGTGTGACGTGTAGGCCTGATAAGACGCGAGAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACT                          >  2:1870628/1‑100                                                                                GGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACT                          >  1:3600806/1‑100                                                                                GGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACT                          >  2:587097/1‑100                                                                                GGATAAGGCGTTCACGCCGCATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAAC                           >  1:2458143/1‑99                                                                                 GATAAGGCGTTCACGCCTTATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTT                         >  1:2318668/1‑100                                                                                                    ATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTG      >  1:2131579/1‑100                                                                                                    ATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTG      >  1:3159415/1‑100                                                                                                    ATCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTG      <  2:641687/100‑1                                                                                                     TCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGA     <  2:1688062/100‑1                                                                                                     TCCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGA     <  2:1937061/100‑1                                                                                                      CCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAA    <  2:1023658/100‑1                                                                                                      CCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAA    >  2:2491275/1‑100                                                                                                      CCGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAA    <  1:2697684/100‑1                                                                                                       CGACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAAA   >  1:1484828/1‑100                                                                                                        GACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAAAC  <  2:3897183/100‑1                                                                                                        GACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAAAC  <  1:79033/100‑1                                                                                                        GACCTACGTGTGACGTGTAGGCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAAAC  >  1:3386030/1‑100                                                                                                          CCTACGTGTGACGTGTAGTCCTGATAAGACGCGATAAGCGTCGCATCAGGCATGCTGCTCCAGACGCCGCAACTTACTGCTGTGACGCCTGCTGAAAC  <  2:88531/98‑1                                                                                                                                                                                                             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.