species:   Opsin
pid:       PID1933
parent:    n_os_milR_56
paralog:   
locus:     JAAVMX010000003.1:6939813-6939873
matures:   ['UGCUGCUGCGGCGACUCAUCCGG', 'GGAAUAGUUAUGUAGCCGGCGUU']
srr:       SRR12952899
genome:    /Users/jax/+Genomes/Fungal_genomes/Opsin.GCA_012934285.1_ASM1293428v1_genomic.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952899.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952899.cram JAAVMX010000003.1:6939813-6939873

4 out of bounds
47 alignments
43 proper strand
28 stranded perfect matches

*************************           *************************
GAUGCUGCUGCGGCGACUCAUCCGGAGGAGCAGCCGCGGGAAUAGUUAUGUAGCCGGCGUU
((((((((((((..((((..(((.(.((.....)).).)))..)))).))))).)))))))
--UGCUGCUGCGGCGACUCAUCCGG------------------------------------ l=23 a=5 c
--------------------------------------GGAAUAGUUAUGUAGCCGGCGUU l=23 a=0 c*
--UGCUGCUGCGGCGACUCAUCCGG------------------------------------ l=23 a=5 ma
--------------------------------------GGAAUAGUUAUGUAGCCGGCGUU l=23 a=0 ma*

--UGCUGCUGCGGCGACUCAc---------------------------------------- l=19 a=1 
--UGCUGCUGCGGCGACUCAcC--------------------------------------- l=20 a=3 
--UGCUGCUGCGGCGACUCAUC--------------------------------------- l=20 a=5 
--UGCUGCUGCGGCGACUCAUCCa------------------------------------- l=22 a=1 
--UGCUGCUGCGGCGACUCAUCCGG------------------------------------ l=23 a=5 (c,ma)
--UGCcGCUGCGGCGACUCAUCCGG------------------------------------ l=23 a=1 
--UGCUGCUGCGGCGACUCAUCCGGA----------------------------------- l=24 a=5 
--UGCUGCUGCGGCGACUCAUCCGGu----------------------------------- l=24 a=1 
--UGCUGCUGCGGCGACUCAUCCGGAGG--------------------------------- l=26 a=3 
---GCUGCUGCGGCGACUCAUCCGG------------------------------------ l=22 a=2 
-----UGCUGCGGCGACUCAUC--------------------------------------- l=17 a=2 
-----UGCUGCGGCGACUCAUCu-------------------------------------- l=18 a=1 
-----UGCUGCGGCGACUCAUCCGGA----------------------------------- l=21 a=3 
-----UGCUGCGGCGACUCAUCCGGAG---------------------------------- l=22 a=1 
-----UGCUGCGGCGACUCAUCCGGAc---------------------------------- l=22 a=1 
-----UGCUGCGGCGACUCAUCCGGAGc--------------------------------- l=23 a=1 
-----UGCUGCGGCGACUCAUCCGGAGa--------------------------------- l=23 a=1 
--------UGCGGCGACUCAUCCGGAG---------------------------------- l=19 a=1 
--------UGCGGCGACUCAUCCGGAGG--------------------------------- l=20 a=1 
--------UGCGGCGACUCAUCCGGAGcAGC------------------------------ l=23 a=4 

mb-01011
ax-1011011
ku-01
ss-111111111100
fn-111
