New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	1216552 =	17 (0.380)	38 (0.850)	30/278	0.6	69.1%	coding (184/267 nt)	ariR	RcsB connector protein for regulation of biofilm and acid‑resistance
	?	NC_000913_3_pae_pgi	= 1469240	NA (NA)					intergenic (‑91/‑1)	insC1/ydbA	IS2 repressor TnpA/pseudogene, autotransporter homolog; interrupted by IS2 and IS30

AAGATGAATGAGTTTTCTATAAACTTATACTTAATAATTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/1216679‑1216552 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATC  <  NC_000913_3_pae_pgi/1469240‑1469093                                                                                                                                                                                                                                                                                      AAGATGAATGAGTTTTCTATAAACTTATACTTAATAATTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTC                                                                                                                                 <  1:401132/149‑1        ATGAGTTTGCTATAAACTTATACTTAATAATTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAA                                                                                                                          <  2:634587/149‑1         TGAGTTTTCTATAAACTTATACTTAATAATTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGC                                                                                                                                             <  2:576554/129‑1         TGAGTTTTCTATAAACTTATACTTAATAATTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGC                                                                                                                                             >  1:576554/1‑129                  TATAAACTTATACTTAATAATTAGAAGTTACATATCATCAGCTGTGTATCTCAACACGATTTCCAGTGTTTTTATAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTTGCCCCCTGACTCTCCAGACAAACAATATCcc                                                                                                                >  2:120170/1‑147                           ATACTTAATAATTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAG                                                                                                       <  2:247963/149‑1                              CTTAATAATTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGA                                                                                                    >  2:102920/1‑149                               TTAATAATTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATGAGTAAT                                                                                                   >  2:74538/1‑149                                      TTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAA                                                                                                            >  2:622681/1‑133                                      TTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAA                                                                                                            <  1:622681/133‑1                                      TTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGACCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTA                                                                                            >  1:769641/1‑149                                      TTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTATGGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATGGTCTTA                                                                                            >  1:769601/1‑149                                       TAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAA                                                                                           <  2:636256/149‑1                                             TTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAG                                                                                     <  2:134103/149‑1                                                  TATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTT                                                                                >  2:442728/1‑149                                                   ATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTA                                                                               <  2:750806/149‑1                                                   ATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTA                                                                               <  1:102236/149‑1                                                               GTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTG                                                                   >  2:503701/1‑149                                                                  TCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATAGTAGTTTTTAGTCTAGTCATTGGAG                                                                >  1:45510/1‑149                                                                      AACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA                                                            >  2:443000/1‑149                                                                        CACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGA                                                          >  1:417546/1‑149                                                                        CACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAA                                                              >  1:647732/1‑145                                                                        CACGATTTCCAGTGTTTTTCTAATCACATCAGCTTCGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGTCTAGTCATTGGAGAA                                                              <  2:647732/145‑1                                                                         ACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGAT                                                         >  1:741633/1‑149                                                                               TCCAGTGTTTTTCTAATCACATCCGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGA                                                   <  1:102920/149‑1                                                                                  AGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGT                                                <  2:741633/149‑1                                                                                    cGTTTTTCTAATCACCGCCTCTTTGAGCATATCACCTGTTTTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAAGAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCT                                              <  1:94454/148‑1                                                                                                      AGCTTGTAGAATATCTCTTGATGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCA                            <  1:120170/149‑1                                                                                                         TTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGAC                         >  1:506921/1‑149                                                                                                         TTTGAGAATATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGAC                         >  1:223271/1‑149                                                                                                           TGAAAATATCAATTGTTGTTTATAAACTGGCCACCTGAATCTCCACACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGG                       <  2:45510/149‑1                                                                                                                 TATCACTTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGACGGAGAAACGCAGACGGCGTACC                 >  1:748552/1‑149                                                                                                                       TTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGGTGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACAAAG           >  1:255036/1‑149                                                                                                                       TTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACA              >  2:425816/1‑146                                                                                                                       TTGTTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACA              <  1:425816/146‑1                                                                                                                          TTGTTTCTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAA        >  1:672501/1‑149                                                                                                                                CTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATC  >  1:506383/1‑149                                                                                                                                CTAGACCGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATC  <  1:607386/149‑1                                                                                                                                                                                                                                                                                      AAGATGAATGAGTTTTCTATAAACTTATACTTAATAATTAGAAGTTACATATCATCAGCTGTGTATCGCAACACGATTTCCAGTGTTTTTCTAATCACATCAGCTTTGAGAATATCACTTGTTGTTTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/1216679‑1216552 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATC  <  NC_000913_3_pae_pgi/1469240‑1469093

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.