species:   Rhsol
pid:       PID0505
parent:    Rhi-milR-132
paralog:   
locus:     KB317837.1:9796-9886
matures:   ['UGAUGGGACUUCCUGAGUGG', 'AGGACUUGGGAGGAUUAUUGGG']
srr:       SRR1994873
genome:    /Users/jax/+Genomes/Fungal_genomes/Rhsol.AFRT00000000.1_scaffolds.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Lin2016-hq.SRR1994873.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Lin2016-hq.SRR1994873.cram KB317837.1:9796-9886

3 out of bounds
41 alignments
34 proper strand
31 stranded perfect matches

        ***********************                          *************************         
AGCGAACCCCUGAUGGGACUUCCUGAGUGGGUGCCCAACGCUUUGAACCAGGAUUUGCCCAGGACUUGGGAGGAUUAUUGGGAAGAAACAA
........((((((((..(((((((((((((((.((..............))...)))))...)))))))))).)))))))).........
----------UGAUGGGACUUCCUGAGUGG------------------------------------------------------------- l=20 a=1 c
------------------------------------------------------------AGGACUUGGGAGGAUUAUUGGG--------- l=22 a=0 c*
----------UGAUGGGACUUCCUGAGUGGG------------------------------------------------------------ l=21 a=6 ma
-----------------------------------------------------------CAGGACUUGGGAGGAUUAUUGGG--------- l=23 a=2 ma*

----------UGAUGGGACUUCCUGAGUGG------------------------------------------------------------- l=20 a=1 (c)
----------UGAUGGGACUUCCUGAGUGGG------------------------------------------------------------ l=21 a=6 (ma)
----------UGAUGGGACUUCCUGAGUGGGU----------------------------------------------------------- l=22 a=2 
----------UGAUGGGACUUCCUGAGUGGGUG---------------------------------------------------------- l=23 a=1 
----------UGAUGGGACUUCCUGAGUGGGUGC--------------------------------------------------------- l=24 a=1 
-----------GAUGGGACUUCCUGAGUGGGUGC--------------------------------------------------------- l=23 a=1 
-------------UGGGACUUCCUGAGUGGGU----------------------------------------------------------- l=19 a=2 
-------------UGGGACUUCCUGAGUGGGUG---------------------------------------------------------- l=20 a=2 
-------------UGGGACUUCCUGAGUGGGUGCC-------------------------------------------------------- l=22 a=2 
-------------------------------UGCCCgACGCUUUGAACCAGG--------------------------------------- l=21 a=1 
-----------------------------------------UUUGAACCAGGAUUUGCCCAGu---------------------------- l=22 a=1 
-----------------------------------------UUUGAACCAGGAUUUGCCCAGc---------------------------- l=22 a=1 
-----------------------------------------UUUGAACCAGGAUUUGCCCAGG---------------------------- l=22 a=1 
-----------------------------------------------CCAGGAUUUGCCCAGGACUUGG---------------------- l=22 a=1 
-----------------------------------------------------------CAGGACUUGGGAGGAUUAUUGG---------- l=22 a=4 
-----------------------------------------------------------CAGGACUUGGGAGGAUUAUUGGG--------- l=23 a=2 (ma*)
-----------------------------------------------------------CAGGACUUGGGAGGAUUAUUGGGA-------- l=24 a=2 
------------------------------------------------------------AGGACUUGGGAGGAUUAUUGGGA-------- l=23 a=3 

mb-01111
ax-1111011
ku-01
ss-111111111101
fn-111
