species:   Scscl
pid:       PID1601
parent:    Ssc-milR-77
paralog:   
locus:     NW_001820819.1:818042-818128
matures:   ['UUCAAGUCCUUCGGCUCUUUCU', 'AAAGAGCCCGAGACUGAUCA']
srr:       SRR12527894
genome:    /Users/jax/+Genomes/Fungal_genomes/Scscl.GCF_000146945.2_ASM14694v2.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Xia2020-rh.SRR12527894.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Xia2020-rh.SRR12527894.cram NW_001820819.1:818042-818128

3 out of bounds
18 alignments
16 proper strand
13 stranded perfect matches

     ***********************                             *************************     
CUUUUGCUAGUAAAAGAGCCCGAGACUGAUCAAUGACUCCUUCAAGGAUACGUCUUUCAAGUCCUUCGGCUCUUUCUUCCAUUUCCU
............((((((((.((((((((...(((..((((...))))..)))...)).))).))).))))))))............
-------------------------------------------------------UUCAAGUCCUUCGGCUCUUUCU---------- l=22 a=1 c
------------AAAGAGCCCGAGACUGAUCA------------------------------------------------------- l=20 a=0 c*
-------UAGUAAAAGAGCCCGAGACUG----------------------------------------------------------- l=21 a=2 ma
-----------------------------------------------------------AGUCCUUCGGCUCUUUCUUCCAU----- l=23 a=0 ma*

--UUUGCUAGUAAAAGAGCCCGAG--------------------------------------------------------------- l=22 a=1 
-------UAGUAAAAGAGCCCGAGACUG----------------------------------------------------------- l=21 a=2 (ma)
----------UAAAAGAGCCCGAGACUGAUCAA------------------------------------------------------ l=23 a=2 
--------------------------UGAUCAAUGACUCCUUCAAGGA--------------------------------------- l=22 a=1 
--------------------------UGAUCAAcGACUCCUUCAAGGA--------------------------------------- l=22 a=1 
--------------------------UuAUCAAUGACUCCUUCAAGGA--------------------------------------- l=22 a=1 
---------------------------------UGACUCCUUCAAGGAUACGUCU-------------------------------- l=22 a=2 
---------------------------------UGACUCCUUCAAGGAUACGUCUU------------------------------- l=23 a=1 
-----------------------------------------UCAAGGAUACGUCUUUCAAGUCC----------------------- l=23 a=1 
-------------------------------------------------------UUCAAGUCCUUCGGCUCUUUa----------- l=21 a=1 
-------------------------------------------------------UUCAAGUCCUUCGGCUCUUUCU---------- l=22 a=1 (c)
--------------------------------------------------------UCAAGUCCUUCGGCUCUUUCUU--------- l=22 a=2 

mb-01011
ax-1001011
ku-01
ss-111111101100
fn-111
