species:   Cocin
pid:       PID1285
parent:    cci-milR-30
paralog:   
locus:     scaffold_45:38266-38321
matures:   ['AGGACGAGGACGAGGACGAGGAC', 'UUUUGUUCUGUUUUUGGAUACCCUCG']
srr:       SRR9972088
genome:    /Users/jax/+Genomes/Fungal_genomes/Cocin.Copci_AmutBmut1_AssemblyScaffolds.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Lau2020-gn.SRR9972088.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Lau2020-gn.SRR9972088.cram scaffold_45:38266-38321

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

***********************    **************************** 
AGGACGAGGACGAGGACGAGGACGCUAGUUUUUGUUCUGUUUUUGGAUACCCUCGG
....(((((((.(((((((((((....))))))))))))))))))...........
AGGACGAGGACGAGGACGAGGAC--------------------------------- l=23 a=2 c
-----------------------------UUUUGUUCUGUUUUUGGAUACCCUCG- l=26 a=0 c*
AGGACGAGGACGAGGACGAGGAC--------------------------------- l=23 a=2 ma
-----------------------------UUUUGUUCUGUUUUUGGAUACCCUCG- l=26 a=0 ma*

AaGACGAGGACGAGGACGAGGAC--------------------------------- l=23 a=1 
AGGACGAGGACGAGGACGAGGAC--------------------------------- l=23 a=2 (c,ma)

mb-00011
ax-1001011
ku-01
ss-111111101010
fn-011
