species:   Opsin
pid:       PID1903
parent:    n_os_milR_72
paralog:   
locus:     JAAVMX010000008.1:3374360-3374494
matures:   ['UAGGUCUAAAAAAGGUAGUU', 'CUUGCCUUUUGCCUCUU']
srr:       SRR12952903
genome:    /Users/jax/+Genomes/Fungal_genomes/Opsin.GCA_012934285.1_ASM1293428v1_genomic.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952903.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952903.cram JAAVMX010000008.1:3374360-3374494

0 out of bounds
52 alignments
52 proper strand
37 stranded perfect matches

                          *******************                                             **********************                       
CUUAAAGGGCUCGAUAGAUAUCUUCCGGCUUGCCUUUUGCCUCUUUCUUAAGCGUAGCGUAUUAGUCCUUAAGGUCUUUAUCUAGCUUAUAAUAGGUCUAAAAAAGGUAGUUAGAGAUAGUUAAGGCGAUUUAAG
((((((..(((...(((.((((((..((((.(((((((((((......(((((.(((.(((..((.((....)).)).)))))))))))....))))....))))))))))).)))))).))).)))..))))))
--------------------------------------------------------------------------------------------UAGGUCUAAAAAAGGUAGUU----------------------- l=20 a=35 c
----------------------------CUUGCCUUUUGCCUCUU------------------------------------------------------------------------------------------ l=17 a=0 c*
--------------------------------------------------------------------------------------------UAGGUCUAAAAAAGGUAGUU----------------------- l=20 a=35 ma
----------------------------CUUGCCUUUUGCCUCUU------------------------------------------------------------------------------------------ l=17 a=0 ma*

--------------------------------------------------------------------------------------------UAGGUCUAAAAAAGGUAGUU----------------------- l=20 a=35 (c,ma)
--------------------------------------------------------------------------------------------UAGGUCUAAAAAAGGUAGcU----------------------- l=20 a=5 
--------------------------------------------------------------------------------------------UAGGUCUAAAAAAGGUAGgU----------------------- l=20 a=3 
--------------------------------------------------------------------------------------------UAGGUCUAAAAAAGuUAGUUAGAGAU----------------- l=26 a=1 
--------------------------------------------------------------------------------------------UAGGUCUAAAAAAGGUAGUUAGAGAU----------------- l=26 a=1 
--------------------------------------------------------------------------------------------UAGGUCUAAAAAAGGUAGUUgGAGAUA---------------- l=27 a=3 
------------------------------------------------------------------------------------------------UCUAAAAAAGGUAGUUgGAGAUA---------------- l=23 a=2 
--------------------------------------------------------------------------------------------------UAAAAAAGGUAGUU----------------------- l=14 a=1 
--------------------------------------------------------------------------------------------------UAAAAAAGGUAGUUgGAGAUA---------------- l=21 a=1 

mb-01011
ax-1001011
ku-01
ss-111111101110
fn-111
