species:   Fugra
pid:       PID0646
parent:    Fg-HN-milR11
paralog:   
locus:     CM000575.1:2257626-2257769
matures:   ['UGGCAUGUUGGACAAAAGGUGUA', 'UCAUCUUCUGUCAAGGCUAUGCUGUU']
srr:       SRR3055827_1
genome:    /Users/jax/+Genomes/Fungal_genomes/Fugra.AACM00000000.2_scaffolds.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Wang2016-nz.SRR3055827_1.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Wang2016-nz.SRR3055827_1.cram CM000575.1:2257626-2257769

3 out of bounds
6 alignments
6 proper strand
4 stranded perfect matches

        *************************                                                                          ****************************         
UUUCGGACGGUGGCAUGUUGGACAAAAGGUGUAUGUUUUGGGGGGUCAGACGGUGACAUCGGAUGGGUUCCGGGUGUUUUUUGUUGCUGGGUAUGGUAAAUUGAACUUAUCAUCUUCUGUCAAGGCUAUGCUGUUGGUAGAGAG
((((...((((((((((((.((((.((((((((.((((.......(((..(((((((((((((.....)))))........))))))))....)))......)))).)).)))))).))))..))).)))))))))...)))).
----------UGGCAUGUUGGACAAAAGGUGUA--------------------------------------------------------------------------------------------------------------- l=23 a=1 c
-------------------------------------------------------------------------------------------------------------UCAUCUUCUGUCAAGGCUAUGCUGUU--------- l=26 a=0 c*
----------UGGCAUGUUGGACAAAAGGUGUA--------------------------------------------------------------------------------------------------------------- l=23 a=1 ma
-------------------------------------------------------------------------------------------------------------UCAUCUUCUGUCAAGGCUAUGCUGUU--------- l=26 a=0 ma*

----------UGGCAUGUUGGACAAAAGGUGUA--------------------------------------------------------------------------------------------------------------- l=23 a=1 (c,ma)
----------UGGCAUGUUGGACAAAAGGUGUAa-------------------------------------------------------------------------------------------------------------- l=24 a=1 
-----------GGCAUGUUGGACAAAAGGUGa---------------------------------------------------------------------------------------------------------------- l=21 a=1 
-----------GGCAUGUUGGACAAAAGGUGU---------------------------------------------------------------------------------------------------------------- l=21 a=1 
-------------------------------------UUGGGGGGUCAGACGGUGA---------------------------------------------------------------------------------------- l=19 a=1 
-------------------------------------------------------------------------------------------UAUGGUAAAUUGAACUUAUCA-------------------------------- l=21 a=1 

mb-01011
ax-1011011
ku-01
ss-110111111100
fn-011
