New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 2298464	NA (NA)	6 (0.090)	4/262	NT	5.5%	noncoding (569/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
	?	CP009273	= 2298494	109 (1.560)					noncoding (599/655 nt)	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences	REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences

CCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGgttgga‑t‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/2298320‑2298464 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTTGGA‑TGCGGCGTAACCGCCTTATCCAACCTACGGGGTGGAGCACTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAACCGGCTTGGGCGTTAGATGTCGGATGCGGCGTAACCGCCTTATCCGACCTACGGGGTGGA  <  CP009273/2298494‑2298340                                                                                                                                                                                                                                                                                                               CCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTG                                                                                                                                                          <  2:1027994/149‑1  CTACACCGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGACCAAGCCGGTTGCGTGATGCGACGCTCGCGCATCTTATCAGGCGGACGCCGCTGTGAAGTGCTCCACCACGTAGGTGGG                                                                                                                                                         >  2:741997/1‑149   TACACCGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGA                                                                                                                                                        <  1:886328/149‑1    cCACCGCTGTGACCTTCTCCCCCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGA‑T                                                                                                                                                      <  2:610329/148‑1        CGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTCCACCGCTGTGAAATGCTCCACCCCGTAGGTCGGctcagg                                                                                                                                                   >  1:817472/1‑143                  TGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACCTCTAAAGCCCAGTCCTGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTCCTCCACCCCGTAGGTTGGA‑TCCGGCGcttccgcc                                                                                                                                        >  1:549510/1‑141                           CCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGA‑TGCGGCGTAACCGCCTTATCCAAC                                                                                                                               <  1:655377/149‑1                                  TCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGA‑TGCGGCGTAACCGCCTTATCCAACCTACGGG                                                                                                                        <  1:611154/149‑1                                  TCGGATAAGGCGGCCACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTTGGA‑TGCGGCGTAACCGCCTTATCCAACCTACGGG                                                                                                                        <  1:1083294/149‑1                                                                                      TGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTT                                                                                                                                                           <  2:1168335/63‑1                                                                                      TGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTT                                                                                                                                                           >  2:205789/1‑63                                                                                      TGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTT                                                                                                                                                           <  1:205789/63‑1                                                                                                                         CGCTGTGAAGTGCTCCACCCCGTAGGTTGGACAGCGCGGTGA‑CGCCGCATCCAACCTACGGGGTGGAGCCCTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAACCGGCCTGGGCGTTAGATCTCGGACGCGG                                 >  2:267558/1‑149                                                                                                                                           CCCGTAGGTTGGA‑TAAGGCGGTTACGCCGCATCCAACCTACGGGGAGGGGCACTTCACAGAGGCGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAGCCGGCTTGGGCGTTAGATGTCGGATGCGGCGTAACCGCCTTATCCGA               >  1:962370/1‑149                                                                                                                                                  gtgGGA‑TGCGGCGTAACCGCCTTATCCAACCCACGGGGTGGAGCACTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAACCGGCTTGGGCGTTAGATGTCGGATGCGGCGTAACCGCCTTATCCGACCTACGG        <  1:217217/146‑1                                                                                                                                                         TGCGGCGTAACCGCCTTATCCAACCTACGGGGTGGAGCACTTCACAGCGGTGTAGGCCTGATAAGACGCGCTAGCGTCGCATCAGGCAACCGGCTTGGGCGTTAGATGTCGGATGCGGCGTAACCGCCTTATCCGACCTACGGGGTGGA  >  1:1075822/1‑149                                                                                                                                                         TGCGGCGGACCCGCCGTATCCAACCTACGGGGTGGAGCACTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAACCGGCTTGGGCGTTAGATGTCGGATGCGGCGTAACCGCCTTATCCGACCTACGGGGTGGA  <  2:1083294/149‑1                                                                                                                                                         TGCGGCGCATCCGCCGCATCCAACCTACGGGGGGGAGCACTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAACCGGCTTGGGCGTTAGATGTCGGATGCGGCGTAACCGCCTTATCCGACCTACGGGGTGGA  <  2:611154/149‑1                                                                                                                                                                                                                                                                                                               CCTACACCGCTGTGAAGTGCTCCACCCCGTAGGTCGGATAAGGCGGTTACGCCGCATCCGACATCTAACGCCCAAGCCGGTTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACACCGCTGTGAAGTGCTCCACCCCGTAGgttgga‑t‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/2298320‑2298464 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTTGGA‑TGCGGCGTAACCGCCTTATCCAACCTACGGGGTGGAGCACTTCACAGCGGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCAACCGGCTTGGGCGTTAGATGTCGGATGCGGCGTAACCGCCTTATCCGACCTACGGGGTGGA  <  CP009273/2298494‑2298340

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.