New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 2796251	13 (0.750)	5 (0.310)	5/254	1.5	26.9%	coding (578/663 nt)	csiR	transcriptional repressor of csiD
	?	NC_000913_3_pae_pgi	= 2796261	15 (0.930)					coding (588/663 nt)	csiR	transcriptional repressor of csiD

ATTTGCTGCAAATGCGTGAACGGTTGTTTGATCTGGCGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCG  >  NC_000913_3_pae_pgi/2796110‑2796398                                                                                                                                              |                                                                                                                                                    aTTTGCTGCAAATGCGTGAACGTTTGTTTGATCTTGCGGCGCGTTATCGTTTTATCTGGCTTCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGCACTGGCGCGcgcggtat                                                                                                                                             <  1:147758‑M1/150‑9 (MQ=255)      ttgtaaaTGCGTGAACGGTTGTTTGATCTGGCGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAAGGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACcgcgcgc                                                                                                                                        <  1:93/146‑1 (MQ=255)      ctgcAAATGCGTGAACGGTTGTTTGATCTGGCGGCGCGTTATCGTTTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGcgc                                                                                                                                        >  3:32229‑M2/1‑147 (MQ=255)          aaaTGCGTGAACGGTTGTTTGATCTGGCGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGcgcgcca                                                                                                                                    >  4:29204‑M2/1‑143 (MQ=255)            aTGCGTGAACGGTTGTTTGATCTGGCGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGcgcggtatctcgcgccagt                                                                                                                                  <  4:59052‑M1/150‑20 (MQ=255)            aTGCGTGAACGGTTGTTTGATCTGGCGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGcgcgccagt                                                                                                                                  >  1:145008‑M2/1‑141 (MQ=255)                                 cTGGCGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTa                                                                                                             <  2:65240/150‑1 (MQ=255)                                   ggcggcGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACt                                                                                                           >  1:178629/1‑150 (MQ=255)                                              aTCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGcgcgccagtaccgccgcagtcagggtctggtgctgatcgtgtt                                                                                                >  3:84984‑M2/1‑107 (MQ=255)                                                 gATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGcgcggtatctcgcgccagtaccgccgcagtcagggtctggtgctga                                                                                                       <  1:105242‑M1/140‑47 (MQ=255)                                                 gATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGcgcggtatctcgcgccagtaccgccgcagtcagggtctggtgctga                                                                                                       >  2:105242‑M1/1‑94 (MQ=255)                                                                  cgAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGAtg                                                                            <  1:177987/150‑1 (MQ=255)                                                                            gttCGGTGGAAATTCTGGAGGATAGACGCGATCAGCACCGGAGCCTGACTGCGGCGGTACTGGCGCGAGATACCGTGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAAtt                                                                  <  2:64549/149‑1 (MQ=255)                                                                                tcatgAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAact                                                              <  3:123790/146‑1 (MQ=255)                                                                                                    aaCACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGcgcggtatctcgcgccagtaccgccgcagtcagggtctggtgctgatcgtgtttatcctccagcatttccaccgaaagcaccgttcgccgcagccagataaatcgat                                          >  3:84984‑M1/1‑43 (MQ=255)                                                                                                     acacGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAaca                                         >  1:63621/1‑150 (MQ=255)                                                                                                           tCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGcgcgccagtaccgccgcagtcagggtctggtgctgatcgtgtttatcctccagcatttccaccgaaagcaccgttcgccgcagccagataaatc                                             <  1:105242‑M2/140‑95 (MQ=255)                                                                                                           tCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGcgcgccagtaccgccgcagtcagggtctggtgctgatcgtgtttatcctccagcatttccaccgaaagcaccgttcgccgcagccagataaatc                                             >  2:105242‑M2/1‑46 (MQ=255)                                                                                                           tCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAACACTTGcc                                   >  4:79622/1‑150 (MQ=255)                                                                                                                    gACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAACACTTGCCCCGGATaaa                          >  3:114669/1‑150 (MQ=255)                                                                                                                       ccTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGAtggctg                                                                        <  2:135302/101‑1 (MQ=255)                                                                                                                       ccTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGAtggctg                                                                        >  1:135302/1‑101 (MQ=255)                                                                                                                                 gcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCt             >  3:19917/1‑150 (MQ=255)                                                                                                                                      aCTGGCGCGcgcggtatctcgcgccagtaccgccgcagtcagggtctggtgctgatcgtgtttatcctccagcatttccaccgaaagcaccgttcgccgcagccagataaatcgataacgcgccgccagatcaaacaaccgttcacgcat        >  1:145008‑M1/1‑9 (MQ=255)                                                                                                                                      aCTGGCGCGAGATACCGCGcgcgccagtaccgccgcagtcagggtctggtgctgatcgtgtttatcctccagcatttccaccgaaagcaccgttcgccgcagccagataaatcgataacgcgccgccagatcaaacaaccgttcacgcat        <  4:59052‑M2/150‑132 (MQ=255)                                                                                                                                        tGGCGCGcgcggtatctcgcgccagtaccgccgcagtcagggtctggtgctgatcgtgtttatcctccagcatttccaccgaaagcaccgttcgccgcagccagataaatcgataacgcgccgccagatcaaacaaccgttcacgcattt      >  4:29204‑M1/1‑7 (MQ=255)                                                                                                                                          gcgcGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAAGTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCAt    >  4:35500/1‑150 (MQ=255)                                                                                                                                            gcgcgcggtatctcgcgccagtaccgccgcagtcagggtctggtgctgatcgtgtttatcctccagcatttccaccgaaagcaccgttcgccgcagccagataaaacgataacgcgccgccagatcaaacaaccgttcacgcatttgcag  >  3:32229‑M1/1‑3 (MQ=255)                                                                                                                                              |                                                                                                                                                    ATTTGCTGCAAATGCGTGAACGGTTGTTTGATCTGGCGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCG  >  NC_000913_3_pae_pgi/2796110‑2796398

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.