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

TTTTCGCCGCATCCGACATTCGCACACGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAAAGGGATTTCTAACTCATTGATAAATTTGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATT  >  NC_000913/111447‑111731                                                                                                                                                   |                                                                                                                                            ccattttgctccaaacgttgtcagctgatcgacctcggagaatgggctgctgaagaaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGc                                                                                                                                            <  1:674790‑M1/2‑1 (MQ=255)    ttttgctccaaacgttgtcagctgatcgacctcggagaatgggctgctgaagaaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTg                                                                                                                                         >  2:674790‑M1/144‑148 (MQ=255)              aacgttgtcagctgatcgacctcggagaatgggctgctgaagaaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTg                                                                                                                                         <  1:1260‑M1/5‑1 (MQ=255)              aacgttgtcagctgatcgacctcggagaatgggctgctgaagaaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTg                                                                                                                                         >  2:1260‑M1/134‑138 (MQ=255)                             aTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAAAGGGATTTCTAACTCATTGATAAATTTGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCa                                                                                                                >  3:1128549/1‑148 (MQ=255)                                   tcggagaatgggctgctgaagaaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGa                                                                                                                                        >  2:473938‑M1/113‑118 (MQ=255)                                   tcggagaatgggctgctgaagaaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGa                                                                                                                                        <  1:473938‑M1/6‑1 (MQ=255)                                   cggagaatgggctgctgaagaaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacaagatGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑a                                                                                                         <  1:166672‑M1/36‑1 (MQ=255)                                    cggagaatgggctgctgaagaaaaacgaatccctagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTg                                                                                                                                         >  3:1001764‑M1/112‑116 (MQ=255)                                    cggagaatgggctgctgaagaaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTg                                                                                                                                         <  4:1001764‑M1/5‑1 (MQ=255)                                                        aaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGcc                                                                                                                                           <  4:608544‑M1/3‑1 (MQ=255)                                                        aaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGcc                                                                                                                                           <  2:42138‑M1/3‑1 (MQ=255)                                                        aaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGcc                                                                                                                                           >  3:608544‑M1/92‑94 (MQ=255)                                                        aaaaacgaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGcc                                                                                                                                           >  1:42138‑M1/92‑94 (MQ=255)                                                              gaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGa                                                                                                                                        <  3:434345‑M1/6‑1 (MQ=255)                                                              gaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGa                                                                                                                                        <  1:882‑M1/6‑1 (MQ=255)                                                              gaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGa                                                                                                                                        >  2:882‑M1/86‑91 (MQ=255)                                                              gaatccccagcagtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGa                                                                                                                                        >  4:434345‑M1/86‑91 (MQ=255)                                                                               cTCATTGATAAATTTGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACg                                                                                                       <  1:287723/106‑1 (MQ=255)                                                                               cTCATTGATAAATTTGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACg                                                                                                       >  2:287723/1‑106 (MQ=255)                                                                               cTCATTGATAAATTTGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCa                                                             <  4:1128549/148‑1 (MQ=255)                                                                                tCATTGATAAATTTGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTc                                                                                                                            <  4:234693/85‑1 (MQ=255)                                                                                tCATTGATAAATTTGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTc                                                                                                                            >  3:234693/1‑85 (MQ=255)                                                                                atctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGATGCGACGCTGTCCGCGTCTTATCa                                                                                                                >  3:531854‑M1/68‑97 (MQ=255)                                                                                atctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGATGCGACGCTGTCCGCGTCTTATCa                                                                                                                <  4:531854‑M1/30‑1 (MQ=255)                                                                                atctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGATGCGACGCTGTCCGCGTCTTATCa                                                                                                                >  2:79488‑M1/68‑97 (MQ=255)                                                                                atctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGATGCGACGCTGTCCGCGTCTTATCa                                                                                                                <  1:79488‑M1/30‑1 (MQ=255)                                                                                       tAAATTTGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGt                                                                        <  4:164703/129‑1 (MQ=255)                                                                                       tAAATTTGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGt                                                                        >  3:164703/1‑129 (MQ=255)                                                                                           tttGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATg                                                                                     <  3:33348/112‑1 (MQ=255)                                                                                           tttGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATg                                                                                     >  4:33348/1‑112 (MQ=255)                                                                                            ttGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCg                                                >  4:580354/1‑148 (MQ=255)                                                                                                      gagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGATGCGACGCTGTCCGCGTCTTa                                                                                                                   <  3:736516‑M1/27‑1 (MQ=255)                                                                                                      gagcgaagaaccaaagcagtgacatttgtctgatgccgcacgtagGCCTGATGCGACGCTGTCCGCGTCTTa                                                                                                                   >  4:736516‑M1/46‑72 (MQ=255)                                                                                                         tCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGAt                                                                                                                                       <  2:348817/49‑1 (MQ=255)                                                                                                         tCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGAt                                                                                                                                       >  1:348817/1‑49 (MQ=255)                                                                                                         tCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGtt                                                                       >  1:1099449/1‑112 (MQ=255)                                                                                                         tCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGtt                                                                       <  2:1099449/112‑1 (MQ=255)                                                                                                         tCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCAc                                   >  4:551746/1‑148 (MQ=255)                                                                                                          cGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATg                                                                                     <  3:174305/97‑1 (MQ=255)                                                                                                          cGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATg                                                                                     >  4:174305/1‑97 (MQ=255)                                                                                                            gATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGttct                                                                     >  2:89678/1‑111 (MQ=255)                                                                                                            gATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGttct                                                                     <  1:89678/111‑1 (MQ=255)                                                                                                             atgcggCGTGAACGCCTTATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGttcttc                                                                   <  2:449033/108‑1 (MQ=37)                                                                                                              tAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCActgctg                              <  3:580354/148‑1 (MQ=255)                                                                                                              tAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCAGAAAGATCGCCActgctg                              >  1:1080137/1‑148 (MQ=255)                                                                                                               aaGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCAGAAAGATCGCCACTGCTgg                             <  2:1080137/148‑1 (MQ=255)                                                                                                                     ttCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCActgc                                >  3:1073321/1‑139 (MQ=255)                                                                                                                     ttCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCActgc                                <  4:1073321/139‑1 (MQ=255)                                                                                                                        aCGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGtt                    <  3:551746/148‑1 (MQ=255)                                                                                                                         cgccgcATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGTATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGaa                                             <  3:603165/122‑1 (MQ=255)                                                                                                                         cgccgcATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGTATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGaa                                             >  4:603165/1‑122 (MQ=255)                                                                                                                              cATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCt                                                                             >  2:1054285/1‑85 (MQ=255)                                                                                                                              cATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCt                                                                             <  1:1054285/85‑1 (MQ=255)                                                                                                                                    aCATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCg                                       >  3:617294/1‑117 (MQ=255)                                                                                                                                    aCATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCg                                       <  4:617294/117‑1 (MQ=255)                                                                                                                                           gcacgtagGCCTGATAAGACGCGGACAGCGTCGCATCAGGCATCTTGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCAtt  <  2:166672‑M1/140‑1 (MQ=255)                                                                                                                                             caAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGAt                                         <  2:237816/106‑1 (MQ=255)                                                                                                                                             caAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGAt                                         >  1:237816/1‑106 (MQ=255)                                                                                                                                               aGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCActgct                               >  3:622344/1‑114 (MQ=255)                                                                                                                                               aGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCActgct                               <  4:622344/114‑1 (MQ=255)                                                                                                                                                 aTGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCtt                                                                            <  4:491305/67‑1 (MQ=255)                                                                                                                                                 aTGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCtt                                                                            >  3:491305/1‑67 (MQ=255)                                                                                                                                                   |                                                                                                                                            TTTTCGCCGCATCCGACATTCGCACACGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAAAGGGATTTCTAACTCATTGATAAATTTGTTTTTGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTTGCACAAGATGCCTGATGCGACGCTGTCCGCGTCTTATCAGGCCT‑ACGTGCGGCATCAGACAAATGTCACTGCTTTGGTTCTTCGCTCCAGTCATCGCTTTCGGAAAGATCGCCACTGCTGGGGATTCGTTTTTCTTCAGCAGCCCATT  >  NC_000913/111447‑111731

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ 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.