Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	W3110S.gb	2755178	2755324	147	40 [0]	[0] 11	intA	integrase

AGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGC  >  W3110S.gb/2755116‑2755177                                                              | agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTTGTGGAATGTGAAGAAAACCAGc  <  1:1238910/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:828904/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1015517/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:376239/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:635847/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:644874/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:677047/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:678963/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:722795/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:7395/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:793068/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:323375/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:887781/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:897413/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:921848/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:92914/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:944206/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:951566/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:973371/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:988762/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1545394/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1289718/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1297809/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1327436/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1332061/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:134013/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:149005/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1512186/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1148399/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:157842/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1599330/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1619387/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:195891/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:216222/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1024029/62‑1 (MQ=255) agGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:23865/62‑1 (MQ=255)    ccAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:472078/59‑1 (MQ=255)         aCCAATACCTTCTTGTTAGTTGCCGAGCGTTTGTGGAATGTGAAGAAAACCAGc  <  1:236681/54‑1 (MQ=255)               aCCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:1537160/48‑1 (MQ=255)                      tGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc  <  1:553750/41‑1 (MQ=255)                                                              | AGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGC  >  W3110S.gb/2755116‑2755177

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑