species:   Opsin
pid:       PID1929
parent:    n_os_milR_97
paralog:   
locus:     JAAVMX010000003.1:11850903-11851190
matures:   ['AGUAUGUUUUUCUGAUU', 'UUAGAAAGUUAUAGUA']
srr:       SRR12952906
genome:    /Users/jax/+Genomes/Fungal_genomes/Opsin.GCA_012934285.1_ASM1293428v1_genomic.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952906.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952906.cram JAAVMX010000003.1:11850903-11851190

0 out of bounds
3 alignments
3 proper strand
2 stranded perfect matches

        *********************                                                                                                                                                                                                                                       ********************        
UUAUGUCUUAAGUAUGUUUUUCUGAUUUUUCUUGUAAAGUAAUGCUUUUUAAAUCCGAUCGUCGUUUUCUUUCUUCUUUCUUAUUCGUAUGUGUGUGUGCGUAUGUAUAUAUGUUCUUCUUUAUUUAAUCUAGGCAUUCUAGUCUUCUUAUAAUAGUUAGAAGCUCUCCUUUGCAUAGUAUAAUCGUAUAAAGUAUAGCUAUCGAAAGAGUUAUAGUAGAGUCUUUAGUUAUCUUCUAGGUUGCUAUUGCUAAUGCAUAAAGAAUUAGAAAGUUAUAGUAAGGUAUAA
.(((((((((..((((.(((((((((((((..((((.((((((((..((((....(((...)))......................(((((....(((((.((((((.....(..((((((((((......((((......))))......)))))..)))))..).....)))))))))))..))))).(((.(((((((....((((.((......)).)))))))))))))).))))..)).))))))..))))..))))))))))))).)))).))))))))).
----------AGUAUGUUUUUCUGAUU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=17 a=0 c
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUAGAAAGUUAUAGUA-------- l=16 a=0 c*
-----------------------------------------------------UCCGAUCGUCGUUUUCUUUC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=20 a=1 ma
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUAGAAAGUUAUAGUA-------- l=16 a=0 ma*

-----------------------------------------------------UCCGAUCGUCGUUUUCUUUC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=20 a=1 (ma)
-------------------------------------------------UAAAUCCGAUCGUCGUUUU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=19 a=1 
------------UAUGUUUUUCUGAUUUgUCUUGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=1 

mb-00010
ax-1011011
ku-01
ss-100111111100
fn-011
