New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	W3110S.gb	4547364 =	29 (0.570)	5 (0.120)	5/84	NT	15.0%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin
	?	W3110S.gb	4547678 =	33 (0.790)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin

GCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  W3110S.gb/4547442‑4547364 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAG  >  W3110S.gb/4547678‑4547747                                                                                                                                                       GCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTT                                                                                >  1:1778168/1‑71  CTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTT                                                                                <  1:2709947/70‑1     TTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCC                                                                            >  1:46864/1‑71         TCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCA                                                                         <  1:147701/70‑1                      TTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTT                                                           >  1:154960/1‑71                       TTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA                                                                        >  1:3676427/1‑57                         TTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTG                                                                               >  1:3494070/1‑48                                TGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCA                                                                >  1:3860916/1‑56                                 GAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCACAA                                                                        >  1:4427186/1‑47                                                ACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGT                                             >  1:3782906/1‑59                                                     TTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCA                             >  1:3290237/1‑70                                                           ATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCG                       <  1:2125658/70‑1                                                                     TTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCA                                          <  1:676009/41‑1                                                                     TTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCA                                          <  1:3321100/41‑1                                                                      TTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACA            >  1:148382/1‑70                                                                      TTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCG                       >  1:3756672/1‑59                                                                       TGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAA          <  1:2449773/71‑1                                                                       TGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAA          <  1:3132428/71‑1                                                                        GGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTG                                    >  1:3639499/1‑44                                                                         GCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAG                                         >  1:4598822/1‑38                                                                           CCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGT      <  1:2585203/71‑1                                                                           CCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGT      <  1:580793/71‑1                                                                            CCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAA                            <  1:1470725/48‑1                                                                            CCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGT                                        <  1:2286616/36‑1                                                                             CAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTA     >  1:3742190/1‑70                                                                             CAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTA     >  1:1493981/1‑70                                                                             CAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTA     >  1:3186315/1‑70                                                                              AAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTA     >  1:3366873/1‑69                                                                              AAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTA     >  1:1780619/1‑69                                                                              AAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTA     >  1:2345936/1‑69                                                                              AAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACT                         <  1:1900778/49‑1                                                                              AAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGAAGTCAAACTCGTTTACAAAACAAAGTGTA     >  1:2838685/1‑69                                                                               AATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAG  <  1:1741594/71‑1                                                                               AATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTA     >  1:1955960/1‑68                                                                                                                                                       GCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  W3110S.gb/4547442‑4547364 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAG  >  W3110S.gb/4547678‑4547747

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.