hCoV-19/USA/WI-UW-13/2020|EPI_ISL_417516|2020-03-15	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||X|||||||||||||
hit  22460 TTTAGAGTCCTACCAACAGAATCT  22483
hCoV-19/USA/WA-UW-2249/2020|EPI_ISL_426130|2020-03-24	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||X|||||||||||||||||||||
hit  22508 TTCAGAGTCCAACCAACAGAATCT  22531
hCoV-19/USA/WA-S388/2020|EPI_ISL_434148|2020-03-27	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/USA/UT-02223/2020|EPI_ISL_436923|2020-04-15	95.83%	1	1
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||||||X|||
hit  22510 TTTAGAGTCCAACCAACAGAGTCT  22533
hCoV-19/USA/UT-02222/2020|EPI_ISL_436922|2020-04-15	95.83%	1	1
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||||||X|||
hit  22497 TTTAGAGTCCAACCAACAGAGTCT  22520
hCoV-19/USA/UT-02024/2020|EPI_ISL_454730|2020-04-17	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           |||||||||||X||||||||||||
hit  22514 TTTAGAGTCCAGCCAACAGAATCT  22537
hCoV-19/USA/NY-PV09028/2020|EPI_ISL_421599|2020-03-21	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22450 TTTAGAGTCCAACCAATAGAATCT  22473
hCoV-19/USA/NY-NYUMC598/2020|EPI_ISL_444715|2020-04-03	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/USA/NY-NYUMC402/2020|EPI_ISL_430429|2020-04-13	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           |||||||||||X||||||||||||
hit  22514 TTTAGAGTCCAGCCAACAGAATCT  22537
hCoV-19/India/S48/2020|EPI_ISL_455668|2020-05-05	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/India/S34/2020|EPI_ISL_455663|2020-05-02	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/India/S25/2020|EPI_ISL_455655|2020-04-30	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/SHEF-C584B/2020|EPI_ISL_441979|2020-04-11	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||X|||||||||||||
hit  22514 TTTAGAGTCCGACCAACAGAATCT  22537
hCoV-19/England/NOTT-110D23/2020|EPI_ISL_448410|2020-04-29	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-110989/2020|EPI_ISL_441878|2020-04-30	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-110154/2020|EPI_ISL_441477|2020-04-12	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-110145/2020|EPI_ISL_441476|2020-04-11	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-110136/2020|EPI_ISL_441475|2020-04-11	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-110127/2020|EPI_ISL_441474|2020-04-11	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-110084/2020|EPI_ISL_441465|2020-04-15	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-10FFD6/2020|EPI_ISL_441461|2020-04-14	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-10FFB8/2020|EPI_ISL_441460|2020-04-06	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-10FE15/2020|EPI_ISL_441448|2020-04-09	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-10FCDF/2020|EPI_ISL_441437|2020-04-08	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/NOTT-10FCC0/2020|EPI_ISL_432709|2020-04-08	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/England/CAMB-83CE3/2020|EPI_ISL_443372|2020-04-16	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||X|||||||||||
hit  22460 TTTAGAGTCCAAGCAACAGAATCT  22483
hCoV-19/England/CAMB-81BCA/2020|EPI_ISL_443083|2020-04-12	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||X|||||||||||
hit  22460 TTTAGAGTCCAAGCAACAGAATCT  22483
hCoV-19/England/CAMB-8159F/2020|EPI_ISL_442525|2020-04-10	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||X|||||||||||
hit  22460 TTTAGAGTCCAAGCAACAGAATCT  22483
hCoV-19/England/CAMB-80949/2020|EPI_ISL_443045|2020-04-10	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||X|||||||||||
hit  22460 TTTAGAGTCCAAGCAACAGAATCT  22483
hCoV-19/England/CAMB-7C1FD/2020|EPI_ISL_434010|2020-04-14	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||X|||||||||||
hit  22514 TTTAGAGTCCAAGCAACAGAATCT  22537
hCoV-19/England/CAMB-1AA2F2/2020|EPI_ISL_443682|2020-04-16	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||X|||||||||||
hit  22460 TTTAGAGTCCAAGCAACAGAATCT  22483
hCoV-19/England/20134082104/2020|EPI_ISL_423183|2020-03-21	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           |||||||||||X||||||||||||
hit  22514 TTTAGAGTCCAGCCAACAGAATCT  22537
hCoV-19/England/20122028104/2020|EPI_ISL_465746|2020-03-17	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||||||||X|||||||
hit  22514 TTTAGAGTCCAACCAATAGAATCT  22537
hCoV-19/Bosnia_and_Herzegovina/02-Banja_Luka/2020|EPI_ISL_462990|2020-04-29	95.83%	1	0
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           |||||||X||||||||||||||||
hit  22484 TTTAGAGGCCAACCAACAGAATCT  22507
hCoV-19/USA/MDH-7761/2020|EPI_ISL_454429|2020-03-12	87.50%	3	2
fwd      1 TTTAGAGTCCAACCAACAGAATCT     24
           ||||||||||X||||||||XX|||
hit  22508 TTTAGAGTCCCACCAACAGCCTCT  22531

--> 41192 of 41227 covered (99.92%)
--> 35 of 41227 missed (0.08%) with at least 1 mismatch (35 fwd)
--> 3 of 41227 missed (0.01%) with at least 1 mismatch in 3' region (3 fwd)
--> 1 of 41227 missed (0.00%) with at least 2 mismatches in 3' region (1 fwd)
