New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	446776 =	28 (0.970)	7 (0.260)	7/266	2.4	21.2%	intergenic (‑110/+39)	yajR/cyoE	putative transporter/protoheme IX farnesyltransferase
	?	NC_000913_3_pae_tpiA	446800 =	26 (0.970)					intergenic (‑134/+15)	yajR/cyoE	putative transporter/protoheme IX farnesyltransferase

CGCGCGCCTCTCACCTGGCGTCATTTTATAATCGTTCATTACCACCTCTGTTTTAAATTCGCGACTAGTGTAAAGCGGCAAACGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAATCAACGGACATCATCACCGAGAGGGCAGTGATGGCGATGATAGAGAAGCCGAACAGCTTGCG  >  NC_000913_3_pae_tpiA/446628‑446922                                                                                                                                                     |                                                                                                                                                   agttgctgatgacagaatctgggcgcgcaagctgttcggcttctctatcatcgccatcactgccctctcggtgatgatgtccgttgattttatggtaccggactcgcatacgctgctggctgctgtgtggtaacaaaacctctctatta                                                                                                                                                    <  2:2076‑M1/1‑1 (MQ=255)    gcgcCTCTCACCTGGCGTCATTTTATAATCGTTCATTACCACCTCTGTTTTAAATTCGCGACTAGTGTAAAGCGGCAAACGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGaaaaa                                                                                                                                                 >  2:292170/1‑149 (MQ=255)     cgcCTCTCACCTGGCGTCATTTTATAATCGTTCATTACCACCTCTGTTTTAAATTCGCGACTAGTGTAAAGCGGCAAACGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGaaaaaa                                                                                                                                                <  2:177972/149‑1 (MQ=255)                       gcgcgcaagctgttcggcttctctatcatcgccatcactgccctctcggtgatgatgtccgttgattttatggtaccggactcgcatacgctgctggctgctgtgtggtaacaaaccctctccattAAAAAGGTGCCGTAGCCCCtttt                                                                                                                              >  1:485324‑M1/127‑149 (MQ=255)                        ttttATAATCGTTCATTACCACCTCTGTTTTAAATTCGCGACTAGTGTAAAGCGGCAAACGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGCAAAAAGGTGCTACGGCACCttttt                                                                                                                             <  1:437961/149‑1 (MQ=255)                           tataATCGTTCATTACCACCTCTGTTTTAAATTCGCGACTAGTGTAAAGCGGCAAACGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAAt                                                                                                                          >  1:17253/1‑149 (MQ=255)                                 tgttcggcttctctatcatcgccatcactgccctctcggtgatgatgtccgttgattttatggtaccggactcgcatacgctgctggctgctgtgtggtaacaaaacctctctattAAAAAGGTGCCGTAGCACCTTTTTAATagagag                                                                                                                    >  1:280541‑M1/117‑149 (MQ=255)                                 cGTTCATTACCTCCTCTGTTTTAAATTCGCGACTAGTGTAAAGCGGCAAACGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATagagag                                                                                                                    <  1:224866/149‑1 (MQ=255)                                   ttCATTAGCACCTCTGTTTTAAATTCGCGACGAGTGTAAAGCGGCAAACGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGt                                                                                                                  <  2:180122/149‑1 (MQ=255)                                       ttACCACCTCTGTTTTAAATTCGCGACTAGTGTAAAGCGGCAAACGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTg                                                                                                              >  1:475788/1‑149 (MQ=255)                                                    cgccatcactgccctctcggtgatgatgtccgttgattttatggtaccggactcgcatacgctgctggctgctgtgtggtaacaaaacctctctattAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACAcagca                                                                                                 >  1:2076‑M1/98‑149 (MQ=255)                                                      tAAATTCGCGACTAGTGTAAAGCGGCAAACGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACAcagcagc                                                                                               <  1:325133/149‑1 (MQ=255)                                                             tgccctctcggtgatgatgtccgttgattttatggtaccggactcgcatacgctgctggctgctgtgtggtaacaaaacctctctattAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGtttt                                                                                                               <  1:430785‑M1/38‑1 (MQ=255)                                                             tgccctctcggtgatgatgtccgttgattttatggtaccggactcgcatacgctgctggctgctgtgtggtaacaaaacctctctattAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGtttt                                                                                                               >  2:430785‑M1/89‑126 (MQ=255)                                                             gcgACTAGTGTTAAGCGGCAAACGAATGGGGGAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACAcagcagccagcagc                                                                                        <  2:223370/149‑1 (MQ=255)                                                                   aGTGTAAAGCGGCAAACGAATGGGGGAAACATGCAGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGc                                                                                  <  1:26448/149‑1 (MQ=255)                                                                                aaaCGAATGGGGTAAACATGCGGATCTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAAGTGCCGTAGCACCTTTTTAATAGAGAGGTTTGATTACCACACAGCCGCCAGCAGCGTATGCGAGTACAGAACCa                                                                     >  2:88249/1‑149 (MQ=255)                                                                                   cGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATaa                                                                  <  2:152902/149‑1 (MQ=255)                                                                                    ttgattttatggtaccggactcgcatacgctgctggctgctgtgtggtgacaaaacctctctattAAAAAGGTGCCGTAGCACCTTTTTa                                                                                                                            <  2:26023‑M1/25‑1 (MQ=255)                                                                                    ttgattttatggtaccggactcgcatacgctgctggctgctgtgtggtgacaaaacctctctattAAAAAGGTGCCGTAGCACCTTTTTa                                                                                                                            >  1:26023‑M1/66‑90 (MQ=255)                                                                                     aagggggTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATaaaa                                                                <  2:178449/146‑1 (MQ=255)                                                                                     aaTGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATaaaa                                                                <  1:480073/149‑1 (MQ=255)                                                                                          ggTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACGATAAAATCAAc                                                           >  1:193784/1‑149 (MQ=255)                                                                                                  tGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAATCAACGGAcatca                                                   <  1:292170/149‑1 (MQ=255)                                                                                                   gCGGATTTTTTAGTAAATATTTCGACTGGGATATGTTTATAATGTTAAGCAAAAAGGTACCGTAGGACCTTTTTAATAGTAAGGATTTGTTACCAAACAACAACACACAGCCTATGCCAGTAAGATACGATTAAAGAAACGCAaatcac                                                  >  2:223602/1‑148 (MQ=255)                                                                                                              gctgtatatTCCGAGGGGGATATGTTTCGAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGGGGTGTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAGTCAACGGAGATCATCACCGAGAggg                                       <  2:25976/144‑1 (MQ=255)                                                                                                                 aaaTATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAATCAACGGACATCATCACCGAGAGGGCAg                                    <  1:51059/149‑1 (MQ=255)                                                                                                                      tttCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAATCAACGGACATCATCACCGAGAGGGCAGTGATg                               >  2:305417/1‑149 (MQ=255)                                                                                                                              gggATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAATCAACGGACATCATCACCGAGAGGGCAGTGATGGCgatgat                       <  1:128635/149‑1 (MQ=255)                                                                                                                                  tatGTTTCTAATGCTAAGAAAAAAGGTGTCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAGTCAACGGACATCATCACCGAGAGGGCAGTGATGGCGATGATagag                   <  2:318315/149‑1 (MQ=255)                                                                                                                                      tttCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCACCCAGCAGCGTATGCGAGTCCGGTACCATAAACTCAACGGACATCACCACAGAGATGGCAATGATGGCGATGGTagagcaac               >  2:78798/1‑145 (MQ=255)                                                                                                                                         cTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAATCAACGGACATCATCACCGAGAGGGCAGTGATGGCGATGATAGAGaa                 >  2:201639/1‑144 (MQ=255)                                                                                                                                         cTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAATCAACGGACATCATCACCGAGAGGGCAGTGATGGCGATGATAGAGaa                 <  1:201639/144‑1 (MQ=255)                                                                                                                                               gtAAGGAAAAAGGTGGCGTAGCACGTTTTTAATAGAGAGGTTTTGTTACCACACAGCGGCCAGCAGCGTATGCGAGGCCGGTACCATAAAATCAACGGAGATCATCACCGAGAGGGCAGTGATGGCGATGATAGAGAAGCCGAACAGCt      <  2:323349/148‑1 (MQ=255)                                                                                                                                                 aaGAAAAAAGGTGCCGTAGCACCTTTATACGCGAAAAGATTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAATCAACGGACATCATCGCCGGAAGGGCAGTGATGGAGATAGTAGAGAGGCCaaaagactgg    >  2:487899/1‑142 (MQ=255)                                                                                                                                                   gAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAATCAACGGACATCATCACCGAGAGGGCAGAGATGGCGATGATAGAGAAGCCGAACAGcataga  >  2:133792/1‑144 (MQ=255)                                                                                                                                                     |                                                                                                                                                   CGCGCGCCTCTCACCTGGCGTCATTTTATAATCGTTCATTACCACCTCTGTTTTAAATTCGCGACTAGTGTAAAGCGGCAAACGAATGGGGTAAACATGCGGATTTTTTAGTAAATATTTCGAGAGGGATATGTTTCTAATGCTAAGAAAAAAGGTGCCGTAGCACCTTTTTAATAGAGAGGTTTTGTTACCACACAGCAGCCAGCAGCGTATGCGAGTCCGGTACCATAAAATCAACGGACATCATCACCGAGAGGGCAGTGATGGCGATGATAGAGAAGCCGAACAGCTTGCG  >  NC_000913_3_pae_tpiA/446628‑446922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.