species:   Pechr
pid:       PID0227
parent:    milR-13
paralog:   
locus:     CM002798.1:8239273-8239341
matures:   ['UAGGACUUGAUCGCGUGAGAC', 'UCUCGCCGCGUUUCUUCACUAAG']
srr:       SRR1705825
genome:    /Users/jax/+Genomes/Fungal_genomes/Pechr.GCA_000710275.1_ASM71027v1_genomic.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Dahlmann2015-ew.SRR1705825.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Dahlmann2015-ew.SRR1705825.cram CM002798.1:8239273-8239341

36 out of bounds
263 alignments
205 proper strand
137 stranded perfect matches

********************                         *********************** 
UAGGACUUGAUCGCGUGAGACAGACCAUGGCCCAUCGAGUCGAGAUCUCGCCGCGUUUCUUCACUAAGG
(((((...((.((((((((((.(((((((...))).).)))..).))))).))))..)).)).)))...
UAGGACUUGAUCGCGUGAGAC------------------------------------------------ l=21 a=29 c
---------------------------------------------UCUCGCCGCGUUUCUUCACUAAG- l=23 a=0 c*
UAGGACUUGAUCGCGUGAGA------------------------------------------------- l=20 a=70 ma
-----------------------------------------------UCGCCGCGUUUCUUCACUAAG- l=21 a=0 ma*

UAGGACUUGAUCGC------------------------------------------------------- l=14 a=1 
UAGGACUUGAUCGCGUGA--------------------------------------------------- l=18 a=6 
UAGGACUUGAUCGCGUGAGA------------------------------------------------- l=20 a=70 (ma)
UAGGACUUGAUCGCGUGAGg------------------------------------------------- l=20 a=2 
UgGGACUUGAUCGCGUGAGA------------------------------------------------- l=20 a=1 
UAGGACUUGAUCGCGUGAGAa------------------------------------------------ l=21 a=38 
UAGGACUUGAUCGCGUGAGAC------------------------------------------------ l=21 a=29 (c)
UgGGACUUGAUCGCGUGAGAC------------------------------------------------ l=21 a=2 
UAGGACUUGAUCGCGUGAGACc----------------------------------------------- l=22 a=16 
UAGGACUUGAUCGCGUGAGACu----------------------------------------------- l=22 a=2 
UAGGACUUGAUCGCGUGAGAaA----------------------------------------------- l=22 a=1 
UAGGACUUGAUCGCGUGAGACA----------------------------------------------- l=22 a=1 
-AGGACUUGAUCGCGUGAGA------------------------------------------------- l=19 a=1 
-AGGACUUGAUCGCGUGAGACA----------------------------------------------- l=21 a=1 
-AGGACUUGAUCGCGUGAGACAGACC------------------------------------------- l=25 a=1 
-------------CGUGAGACAG---------------------------------------------- l=10 a=3 
-------------CGUGAGACAGAC-------------------------------------------- l=12 a=1 
---------------UGAGACAGACCAUGGCC------------------------------------- l=17 a=2 
---------------UGAGACAcACCAUGGCCC------------------------------------ l=18 a=1 
---------------UGAGACAGACCAUGGCCC------------------------------------ l=18 a=2 
---------------UGAGACAGACCAUGGCCCc----------------------------------- l=19 a=1 
-----------------AGACAGACCAUGGCCCAUCGAGUCGAGA------------------------ l=28 a=2 
----------------------GACCAUGGCCC------------------------------------ l=11 a=1 
----------------------GACCAUGGCCCAUCGAGUCGAGA------------------------ l=23 a=9 
----------------------GACCAUGGCCCAUCGAGgCGAGA------------------------ l=23 a=1 
-------------------------CAUGGCCCAUCGAGUCGAGA------------------------ l=20 a=1 
---------------------------UGGCCCAUCGAGUCGAGAcC---------------------- l=20 a=1 
---------------------------UGGCCCAUCGAGUCGAGAUC---------------------- l=20 a=1 
----------------------------------UCGAGUCGAGAUCUCGCC----------------- l=18 a=2 
----------------------------------UCGAGUCGAGAUCUCGCCGC--------------- l=20 a=2 
-----------------------------------CuAGUCGAGAUCUCGCC----------------- l=17 a=1 
-----------------------------------CGAGUCGAGAUCUCGCC----------------- l=17 a=1 
-----------------------------------------------UCGCCGCGUcUCUUCACU---- l=18 a=1 

mb-01111
ax-1011011
ku-01
ss-111110101100
fn-101
