New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	3986604 =	48 (1.320)	4 (0.120)	4/264	4.6	8.3%	noncoding (173/207 nt)	glmZ	sRNA antisense activator of glmS mRNA, Hfq‑dependent
	?	NC_000913_3_pae_tpiA	3986634 =	44 (1.310)					noncoding (203/207 nt)	glmZ	sRNA antisense activator of glmS mRNA, Hfq‑dependent
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ACGCAGAGCCGTTTACGGTGCTTATCGTCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGG  >  NC_000913_3_pae_tpiA/3986488‑3986780                                                                                                                                                   |                                                                                                                                                    aCGCAGAGCCGTTTACGGTGCTTATCGTCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACCGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGttttt                                                                                                                                                   >  1:501217/1‑149 (MQ=255)  cGCAGAGCCGTTTACGGTGCTTATCGTCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAAAGCAGGCGtttttt                                                                                                                                                  >  1:476785/1‑149 (MQ=255)   gCATAGCCGTTTACGGTTCTTATCGTCCACTGAAAGATGTCGATTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGttttttt                                                                                                                                                 <  2:13335/149‑1 (MQ=255)   gCAGAGCCGTTTACGGTGCTTATCGTCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACACCGTTGAGTGAAGCACACACTTGTTTTCATACAAACCTGTTCTAACGCCTGCTCCCTAATAAGAGCAGACGtttagta                                                                                                                                                 >  1:369144/1‑145 (MQ=255)    acgagCCGTTTACGGTCCTTATCGTCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTTTGTGAAGCTCCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTa                                                                                                                                                <  1:165958/147‑1 (MQ=255)     agagCCGTTTACGGTGCTTATCGTCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTAt                                                                                                                                               <  1:590758/149‑1 (MQ=255)     agagCCGTTTACGGTGCTTATCGTCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTAt                                                                                                                                               <  2:306766/149‑1 (MQ=255)                 ggTGCTTATCGTCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCACCTTGTTGTCATACAGACCCGTTTTAACGCCTGCTTCGTAATAAGAGCAGGCGTTTTTTTATTTT‑TCAAGaaag                                                                                                                                  >  1:555154/1‑147 (MQ=255)                         tCGTCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAAGGCCTGCTCCGTAATAAGAGCAGGCGTTTATTTAGGTA‑TCAGGAAGGCCCCGCAg                                                                                                                          >  2:11200/1‑149 (MQ=255)                            tCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGGAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTg                                                                                                                       >  1:205076/1‑149 (MQ=255)                            tCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTg                                                                                                                       >  2:505819/1‑149 (MQ=255)                              cACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCt                                                                                                                     >  1:496475/1‑149 (MQ=255)                                       aTGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCgg                                                                                                            <  1:329761/149‑1 (MQ=255)                                           ggCTTATGCCTCATCAGACACCATGGTCACAAGTTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCGCCGTAATAATAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGATGTGCTTGCCTCCGGGTga                                                                                                        <  2:216045/148‑1 (MQ=255)                                              ttATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGaa                                                                                                     <  2:317778/149‑1 (MQ=255)                                              tgaTGCCTCAGCAGACACCATGGGCACAACGTTGAGTGAAGCAGCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑ACAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGaa                                                                                                     <  2:476785/147‑1 (MQ=255)                                                   gctggtgaGACACGATGGGCACAGCGTTGAGTGAAGCGCCCACTTGGTGTCATACAGGCCTGTTTTAACGGCTGCGCCGTAATAAGAGCGGGCGGTGTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAac                                                                                                <  1:10710/142‑1 (MQ=255)                                                                  tGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAg                                                                                                                          <  2:158627/108‑1 (MQ=255)                                                                  tGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAg                                                                                                                          >  1:158627/1‑108 (MQ=255)                                                                    gACACAACGTTGAGCGAAGCCCCCACTTGTTGCCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTAtt                                                                               <  1:277565/149‑1 (MQ=255)                                                                      cacaACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCt                                                                             <  1:429852/149‑1 (MQ=255)                                                                      cacaACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATCTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTATTGTGGCGGGTTATTCt                                                                             <  1:560451/149‑1 (MQ=255)                                                                       acaACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGAGCCCGGAGGTGCTTGCCTCCGTGTAAGAAGGAACGACCGTTGCGGGTTATTCtc                                                                            >  2:123838/1‑148 (MQ=255)                                                                          aCGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCaa                                                                         <  2:501217/149‑1 (MQ=255)                                                                           cGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAAc                                                                        >  1:269929/1‑149 (MQ=255)                                                                               gAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTACCTACGGGTGAGCAGGAACAACACAGGAGGGGTATTGTGAAACGtga                                                                    >  1:531456/1‑147 (MQ=255)                                                                                  tGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACa                                                                 >  2:622687/1‑149 (MQ=255)                                                                                          ccACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCTGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACACCAAACCg                                                         >  2:514050/1‑149 (MQ=255)                                                                                            aCTTGTTGTCATACAGACGTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCTGGTTATTCTGCAACGTTAACATCAAACCGTc                                                       <  1:275517/149‑1 (MQ=255)                                                                                              ttgttgTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTcgc                                                     <  1:383636/149‑1 (MQ=255)                                                                                              ttgttgTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACCTTAAAATCAAACCgagtc                                                     >  1:484087/1‑145 (MQ=255)                                                                                               tgttgtCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAACCCGTcgcg                                                    >  1:260298/1‑149 (MQ=255)                                                                                                 ttgtCATACAGACCTGTTTTAACGCCTGCCCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGAc                                                  >  2:524243/1‑149 (MQ=255)                                                                                                   gtCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGc                                                >  1:465698/1‑149 (MQ=255)                                                                                                            aCCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTGAACATCAAACCATCCGGACGCATACATGCa                                       >  1:518459/1‑149 (MQ=255)                                                                                                            aCCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGGTATTCTGCAACGTTAAAATCAAACCGTCGCGACGCATAGCTGCa                                       >  1:518466/1‑149 (MQ=255)                                                                                                                           tGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGc                                                                           >  2:70290/1‑98 (MQ=255)                                                                                                                           tGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGc                                                                           <  1:70290/98‑1 (MQ=255)                                                                                                                                cGTAATAAGAGCAGGCGTTTTTTTATTTC‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGGGAGAATGAGCTACTGTGGCGGGTTATTCTGCGACGTTAACATCAAACCGTCGCGCCTCATAGCTGCAGCTCCTTCCGGCTTGGGcgg                   >  2:37401/1‑147 (MQ=255)                                                                                                                                 ggaataaGAGCATGGGTTTTTGTATGTA‑TCAGGAAGGCACTGGAGGTGCTTGCCTCCGGGGGAGAAGTAACTACTGTGGCGGGTTATTCTGCACCGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCCTCTTCCGGGTTGTGCAGt                  <  2:512609/147‑1 (MQ=255)                                                                                                                                 gTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGt                  <  1:414513/149‑1 (MQ=255)                                                                                                                                 gTAATAAGAGCAGGCGTTTTTTTATGTA‑TAAGGAAGGCGCCGGAGGTGCTGGCCTCCGGGGGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGt                  >  2:189097/1‑149 (MQ=255)                                                                                                                                 gTAATAAGAGCAGGCGCTTTTTTACCAACCCATGAA‑GCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCTGGTTATTCTGCAACGTTAACATCAAACCGCCGCGACGCCTAGCTGCAGCTTATTCCGGCTTTTGCAGt                  >  2:462899/1‑149 (MQ=255)                                                                                                                                     taaGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTCCTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCGGt              >  1:159600/1‑149 (MQ=255)                                                                                                                                         ggCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAg          <  1:382372/148‑1 (MQ=255)                                                                                                                                                gTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAACTTCTTCCGACTTGTGAAATCTGTCCAGCacgacg   >  1:178511/1‑149 (MQ=255)                                                                                                                                                gTTTTTTGATGTA‑TCAGAAAAGCCCCGGAGGAGCTTGCCTCCGGGTGAGAAGGAACTACTATGGCGGGTTACTCTGCAACGTTAACATCCAACCGTCGCGACGCATAGCTACATCTTCTTCCGGATTGTGCAGTATGTCCACcgcgcgc   >  2:58312/1‑146 (MQ=255)                                                                                                                                                 tttttttATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCATCGCGTCgg  >  1:400660/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                    ACGCAGAGCCGTTTACGGTGCTTATCGTCCACTGACAGATGTCGCTTATGCCTCATCAGACACCATGGACACAACGTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTA‑TCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGG  >  NC_000913_3_pae_tpiA/3986488‑3986780

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ 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.