species:   Fugra
pid:       PID0753
parent:    Fg-JS-milR58
paralog:   
locus:     CM000577.1:1733657-1733823
matures:   ['GCGAAGAGAGGGGG', 'UGCUUUCUUUGCGG']
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 CM000577.1:1733657-1733823

2 out of bounds
9 alignments
7 proper strand
6 stranded perfect matches

         ****************                                                                                                                    ****************          
CUUUUCGUUCAUGCUUUCUUUGCGGCGGGAUCAUGGAGAGGGCGUCGGUCCAUAACUCAUUCGCAGGUCGGGCUGUUGGGUUGAGGAUUGGCACCAAACUCGGCUCGCGAAAAUGGAAUCGUAGGCCGAGAAGACAAACAUUGGCGAAGAGAGGGGGAGACGAGGGG
(((((((((..(.((((((((((.(...............((.((((((((.(((((((...((((......))))))))))).)))))))).))...(((((((.((((........)))).)))))))...........).)))))))))).)...)))))))))
-----------------------------------------------------------------------------------------------------------------------------------------------GCGAAGAGAGGGGG---------- l=14 a=0 c
-----------UGCUUUCUUUGCGG---------------------------------------------------------------------------------------------------------------------------------------------- l=14 a=0 c*
----------------------CGGCGGGAUCAUGGAGAGGGCGU-------------------------------------------------------------------------------------------------------------------------- l=23 a=1 ma
-----------UGCUUUCUUUGCGG---------------------------------------------------------------------------------------------------------------------------------------------- l=14 a=0 ma*

----------------------CGGCGGGAUCAUGGAGAGGGCGU-------------------------------------------------------------------------------------------------------------------------- l=23 a=1 (ma)
--------------------------------------------------------------GCAGGUCGGGCUGUUGGGUUGAGGAUUGGCA-------------------------------------------------------------------------- l=31 a=1 
----------------------------------------------------------------AGGUCGGGCUGUUGGGUUGAGGAUUGGCA-------------------------------------------------------------------------- l=29 a=1 
--------------------------------------------------------------------CGGGCUGUUGGGUUGAGGAUUGGC--------------------------------------------------------------------------- l=24 a=1 
---------------------------------------------------------------------GGGCUGUUGGGUUGAGGAUUGGCAC------------------------------------------------------------------------- l=25 a=1 
-------------------------------------------------------------------------UGUUGGGUUGAGGAUUGGCAa------------------------------------------------------------------------- l=21 a=1 
---------------------------------------------------------------------------------UGAGGAUUGGCACCAAACUCGG---------------------------------------------------------------- l=22 a=1 

mb-00010
ax-1011011
ku-01
ss-100110111100
fn-001
