New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3216644	NA (NA)	9 (0.090)	6/164	NT	NA	noncoding (44/78 nt)	REP228 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP228 (repetitive extragenic palindromic) element; contains 2 REP sequences
	?	NC_000913	= 3216674	NA (NA)					noncoding (74/78 nt)	REP228 (repetitive extragenic palindromic) element; contains 2 REP sequences	REP228 (repetitive extragenic palindromic) element; contains 2 REP sequences

TAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACgccggat‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3216546‑3216644 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCCGGATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTGCA  <  NC_000913/3216674‑3216569                                                                                                                                                                                                               TAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACG                                                                                                           <  2:2917312/100‑1  AATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAAATGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGC                                                                                                          >  2:1784865/1‑100   ATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCC                                                                                                         <  1:2487274/100‑1    TGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCG                                                                                                        >  2:1242035/1‑100    TGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCG                                                                                                        >  2:1859186/1‑100    TGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCG                                                                                                        >  2:2005230/1‑100    TGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCG                                                                                                        >  2:2569217/1‑100     GATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGG                                                                                                       >  1:1013054/1‑100     GATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGG                                                                                                       <  2:2027518/100‑1     GATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGG                                                                                                       <  2:2891861/100‑1     GATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGG                                                                                                       <  2:833994/100‑1     GATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGG                                                                                                       <  1:1080587/100‑1      ATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGGCGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGA                                                                                                      >  1:1728988/1‑100      ATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGA                                                                                                      <  1:2730843/100‑1      ATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCCCCTCTTCTCAGGCATCATTACTCAACGCC                                                                                                         >  1:944871/1‑97       TTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGAT                                                                                                     >  1:1489974/1‑100         GTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCCACGCCGGAT                                                                                                     >  1:1264264/1‑98                       ATGCAAGCGAGTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATAAGGCGTTCACGCCGC                                                                                     <  1:284967/100‑1                             GCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATAAGGCGTTCACGCCGCATCCGG                                                                               <  2:887159/100‑1                               GATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATAAGGCGTTCACGCCGCATCCGGCG                                                                             <  1:2101321/100‑1                                ATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCGTCATTACTCAACGCCGGATAAGGCGTTCACGCCGCATCCGGCGT                                                                            <  2:410008/100‑1                                ATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATAAGGCGTTCACGCCGCATCCGGCGT                                                                            <  1:2153920/100‑1                                ATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATAAGGCGTTCACGCCGCATCCGGCGT                                                                            <  2:1951175/100‑1                                ATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTGCTCAGGCATCATTACTCAACGCCGGATAAGGCGTTCACGCCGCATCCGGCGT                                                                            <  1:1399302/100‑1                                  TTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATAAGGCGTTCACGCCGCATCCGGCGTTG                                                                          <  2:1638650/100‑1                                        AACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACGCCGGATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAAT                                                                    <  2:1673732/100‑1                                                                                                    GCCGGATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGTTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATC         <  1:639192/99‑1                                                                                                    GCCGGATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCG        <  1:1076650/100‑1                                                                                                    GCCGGATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCG        <  1:880471/100‑1                                                                                                     CCGGATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGC       >  1:2569202/1‑100                                                                                                     CCGGATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGC       <  2:2512829/100‑1                                                                                                       gtATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGC       <  1:254442/96‑1                                                                                                        GATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTG    <  1:2598495/100‑1                                                                                                        GATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTG    <  1:2921850/100‑1                                                                                                        GATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTG    <  1:1266242/100‑1                                                                                                         ATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTGC   <  2:2190031/100‑1                                                                                                         ATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTGC   <  1:1989274/100‑1                                                                                                         ATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTGC   <  2:554369/100‑1                                                                                                          TAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTGCA  >  2:2300005/1‑100                                                                                                          TAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTGCA  >  2:1586559/1‑100                                                                                                          TAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTGCA  >  2:2725995/1‑100                                                                                                          TAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTGCA  >  1:2953691/1‑100                                                                                                                                                                                                               TAATGATTGTTAATCATGATAAATGCAAGCGATTTGTAGAACTGATATGTCTATAGTCTGATAAGACGAACCGCCTCTTCTCAGGCATCATTACTCAACgccggat‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3216546‑3216644 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCCGGATAAGGCGTTCACGCCGCATCCGGCGTTGAGTAATGATGCCTGAGAAGAGGCGGTTCGTCTTATCAGACTATAGACATATCAGTTCTACAAATCGCTTGCA  <  NC_000913/3216674‑3216569

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.