New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	111593 =	35 (0.370)	8 (0.090)	8/186	NT	17.5%	noncoding (164/200 nt)	RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site	RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site
	?	NC_000913	111626 =	43 (0.500)					noncoding (197/200 nt)	RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site	RIP8 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site

AATGGGCTGCTGAAGAAAAACGAATCCCCAGCAGTGGCGATCTTTCCGAAAGCGATGACTGGAGCGAAGAACCAAAGCAGTGACATTTGTCTGATGCCGCACGT‑AGGCCTGATAAGACGCGGACAGCGTCGCATCAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/111731‑111593 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcaggcCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCGAGGTCGATCAGCTGACAACGTTTGGAGCAAAATGG  >  NC_000913/111626‑111771                                                                                                                                                                                                                                                                                                 AATGGGCTGCTGAAGAAAAACGAATCCCCAGCAGTGGCGATCTTTCCGAAAGCGATGACTGGAGCGAAGAACCAAAGCAGTGACATTTGTCTGATGCCGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGC                                                                                                                                            <  2:166672/148‑1     GGCTGCTGAAGAAAAACGAATCCCCAGCGGTGGCGATCTTTCAGAAAGCGATGCCTGGAGCGAAGAACCAAAGCAGTGACATTTGTCTGATGCCGCACGT‑AGGCCTGATGCGACGCTGTCCGCGTCTTATCAG                                                                                                                                                       <  3:715687/133‑1     GGCTGCTGAAGAAAAACGAATCCCCAGCAGTGGCGATCTTTCCGAAAGCGATGACTGGAGCGAAGAACCAAAGCAGTGACATTTGTCTGATGCCGCACGT‑AGGCCTGATGCGACGCTGTCCGCGTCTTATCAG                                                                                                                                                       >  4:715687/1‑133                                         TCTTTCCGAAAGCGATGACTGGAGCGAAGAACCAAAGCAGTGACATTTGTCTGATGCCGCACGT‑AGGCCTGATAAGACGCGGACAGCGTCGCATC                                                                                                                                                         >  4:1057722/1‑95                                         TCTTTCCGAAAGCGATGACTGGAGCGAAGAACCAAAGCAGTGACATTTGTCTGATGCCGCACGT‑AGGCCTGATAAGACGCGGACAGCGTCGCATC                                                                                                                                                         <  3:1057722/95‑1                                                                   AAGAACCAAAGCAGTGACATTTGTCTGATGCCGCACGT‑AGGCCTGATAAGACGCGGACAGCGTCGCAT                                                                                                                                                          <  4:1137872/68‑1                                                                   AAGAACCAAAGCAGTGACATTTGTCTGATGCCGCACGT‑AGGCCTGATAAGACGCGGACAGCGTCGCAT                                                                                                                                                          >  3:1137872/1‑68                                                                          AAAGCAGTGACATTTGTCTGATGCCGCACGT‑AGGCCTGATAAGACGCGGACAGCGTCGCATCA                                                                                                                                                        <  1:232902/63‑1                                                                          AAAGCAGTGACATTTGTCTGATGCCGCACGT‑AGGCCTGATAAGACGCGGACAGCGTCGCATCA                                                                                                                                                        >  2:232902/1‑63                                                                                                        T‑AGGCCTGATAAGACGCGGACAGCGTCGCATCAGGCATCTTGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCG                                     <  1:166672/148‑1                                                                                                               TGATAAGACGCGGACAGCGTCGCATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGAT                                                                                 <  4:531854/97‑1                                                                                                               TGATAAGACGCGGACAGCGTCGCATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGAT                                                                                 <  1:79488/97‑1                                                                                                               TGATAAGACGCGGACAGCGTCGCATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGAT                                                                                 >  3:531854/1‑97                                                                                                               TGATAAGACGCGGACAGCGTCGCATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGAT                                                                                 >  2:79488/1‑97                                                                                                                  TAAGACGCGGACAGCGTCGCATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTC                                                                                                       >  4:736516/1‑72                                                                                                                  TAAGACGCGGACAGCGTCGCATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTC                                                                                                       <  3:736516/72‑1                                                                                                                                       TCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCGA                                    >  2:473938/1‑118                                                                                                                                       TCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCGA                                    <  1:473938/118‑1                                                                                                                                       TCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTC                                                               >  2:882/1‑91                                                                                                                                       TCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTC                                                               <  3:434345/91‑1                                                                                                                                       TCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTC                                                               <  1:882/91‑1                                                                                                                                       TCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTC                                                               >  4:434345/1‑91                                                                                                                                        CAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCGAGGTCGATCAGCTGACAACGTTTGGAGCAAAA     >  2:674790/1‑148                                                                                                                                        CAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCGAGGTCGATCAGCTGACAACGTT               >  2:1260/1‑138                                                                                                                                        CAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCGAGGTCGATCAGCTGACAACGTT               <  1:1260/138‑1                                                                                                                                        CAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCG                                     <  4:1001764/116‑1                                                                                                                                        CAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTAGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCG                                     >  3:1001764/1‑116                                                                                                                                          GGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTT                                                         >  3:608544/1‑94                                                                                                                                          GGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTT                                                         <  2:42138/94‑1                                                                                                                                          GGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTT                                                         <  4:608544/94‑1                                                                                                                                          GGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTT                                                         >  1:42138/1‑94                                                                                                                                           GCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCGAGGTCGATCAGCTGACAACGTTTGGAGCAAAATGG  <  1:674790/148‑1                                                                                                                                                                                                                                                                                                 AATGGGCTGCTGAAGAAAAACGAATCCCCAGCAGTGGCGATCTTTCCGAAAGCGATGACTGGAGCGAAGAACCAAAGCAGTGACATTTGTCTGATGCCGCACGT‑AGGCCTGATAAGACGCGGACAGCGTCGCATCAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/111731‑111593 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcaggcCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATTCTCCGAGGTCGATCAGCTGACAACGTTTGGAGCAAAATGG  >  NC_000913/111626‑111771

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.