New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_pgi 4218555 =63 (1.190)6 (0.130)
+AAAACGCCTTATCCA
5/240 NT 9.7% noncoding (120/132 nt) REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences
?NC_000913_3_pae_pgi = 4253262 NA (NA)noncoding (102/130 nt) RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site

GAGGAATCGACCATACTGAGCATCGAAGCCTTGCAAAATGGTTTGAGCAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGCCGGATGCGGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/4218670‑4218555
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGCCG  <  NC_000913_3_pae_pgi/4253262‑4253202
                                                                                                                    |||||||||||||||                                                             
GAGGAATCGACCATACTGAGCATCGAAGCCTTGCAAAATGGTTTGAGCAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGCCGGATGCGGCGAAAACGCCTTATCCAGCCTTCCATAATCTGCAA                                             >  1:346582/1‑149
GAGGAATCGACCATACTGAGCATCGAAGCCTTGCAAAATGGTTTGAGCAATCAATAATTCCAGGCCAAGCGGCATTTAGAGCCCTCATCAGGAGCAGAGAATTGCCGGGTGCGGCGCAAGCGCCTTATCCAGCCGTCCATAATCTGCAA                                             >  2:531166/1‑149
 AGGAATCGACCATACTGAGCATCGAAGCCTTGCAAAATGGTTTGAGCAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGCCGGATGCGGCGAAATCGCCTTATCAAGCCTTTCATAATCTGCAAA                                            >  1:153076/1‑149
             TACTGAGCATCGAAGCCTTGCAAAATGGTTTGAGCAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGCCGGATGCGGCGAAAACGCCTTAACCAGCCTTCCATAATCTGCAAATACAATAAATTG                                >  1:362620/1‑149
                                         TTTGAGCAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGCCGGATGCGGCGAAAACGCCTTATCCAGACTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGC    <  1:948790/149‑1
                                           TGAGCAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGCCGGATGCGGCGAAAACGCCTTATCCAGCCTTCCATAATCTGCAAATTCAATACATTGCGATGTGTTGTGTAGGCCTAAAAAGCGCCG  >  2:763349/1‑149
                                                                                                                    |||||||||||||||                                                             
GAGGAATCGACCATACTGAGCATCGAAGCCTTGCAAAATGGTTTGAGCAATCAATAATTCCAGGCCACGCGGCATTTAGCGCCCTCATCAGGAGCAGAGAATTGCCGGATGCGGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/4218670‑4218555
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCCTTCCATAATCTGCAAATTCAATAAATTGCGATGTGTTGTGTAGGCCTGAGAAGCGCCG  <  NC_000913_3_pae_pgi/4253262‑4253202

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.