species:   Fugra
pid:       PID0647
parent:    Fg-HN-milR12
paralog:   
locus:     CM000575.1:3418672-3418918
matures:   ['UGUGACGGUUGGGUUUCUAA', 'GGGUGUAACUGUUACAAGUC']
srr:       SRR2970501_1
genome:    /Users/jax/+Genomes/Fungal_genomes/Fugra.AACM00000000.2_scaffolds.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Wang2016-nz.SRR2970501_1.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Wang2016-nz.SRR2970501_1.cram CM000575.1:3418672-3418918

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

             **********************                                                                                                                                                                                    **********************          
UGUGGCCUAACGGUUGGGUGUAACUGUUACAAGUCUAAAUAAGAGCUAUUAAUAUAUAAUAGAUAAGAUUUCUAAAAGAUAAACUAAUUUAUAUUAAGUUUAUAUUAAUAGAUAUAUAAGGCAUUAUUAAGUAAUAGUAAAGUAUUAUAUCUCUUAAUAGUAAAUAGAGUAAAUUAAGCGUAUUUAGGUAAAGAAGUCUUAUUAAUAGCUAGUAAGCUGUGACGGUUGGGUUUCUAAAUAGGUAAAC
....(((((....(((((..(((((((((((.(.((...((..(((((((((((...........((((((((...(((((..(((((((((.....(((((((((((.(((((((....((.((((((.....)))))).))..))))))).))))).))))))...))))))).))..)))))......)))))))))))))))))))..))))))))))))))))....))))).)))))....
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUGACGGUUGGGUUUCUAA---------- l=20 a=6 c
---------------GGGUGUAACUGUUACAAGUC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=20 a=0 c*
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUGACGGUUGGGUUUCUAA---------- l=20 a=6 ma
---------------GGGUGUAACUGUUACAAGUC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=20 a=0 ma*

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUGACGGUUGGGUUUCUAA---------- l=20 a=6 (c,ma)
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGACGGUUGGGUUUCUAAAcAGG----- l=23 a=1 

mb-00011
ax-1011111
ku-01
ss-111111111110
fn-111
