species:   Opsin
pid:       PID1875
parent:    n_os_milR_9
paralog:   
locus:     JAAVMX010000009.1:1184375-1184434
matures:   ['UGACGGCGUUGGCAGCCGGGCCGG', 'GGGCCAGCACGGGCAACGUCUUCGUC']
srr:       SRR12952903
genome:    /Users/jax/+Genomes/Fungal_genomes/Opsin.GCA_012934285.1_ASM1293428v1_genomic.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952903.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952903.cram JAAVMX010000009.1:1184375-1184434

0 out of bounds
74 alignments
74 proper strand
13 stranded perfect matches

   ******************************************************   
GUGCCGGGCCAGCACGGGCAACGUCUUCGUCUAUGACGGCGUUGGCAGCCGGGCCGGCAU
(((((((.((.((...(.(((((((.((......)).))))))).).)).)).)))))))
---------------------------------UGACGGCGUUGGCAGCCGGGCCGG--- l=24 a=1 c
-----GGGCCAGCACGGGCAACGUCUUCGUC----------------------------- l=26 a=0 c*
-------------------------------UAUGACGGCGUUGGCAGCCGGGC------ l=23 a=5 ma
-----GGGCCAGCACGGGCAACGUCUUCGUC----------------------------- l=26 a=0 ma*

---------------------------------UGACGGCGUUGGCAGCCGGG------- l=20 a=2 
---------------------------------UGACGGCGUUGGCAGCCGGGu------ l=21 a=2 
---------------------------------UGACGGCGUUGGCAGCCGGGCC----- l=22 a=1 
---------------------------------UuACGGCGUUGGCAGCCGGGCCG---- l=23 a=1 
---------------------------------UGACGGCGUUGGCAGCCGGGCCGa--- l=24 a=3 
---------------------------------UGACGGCGUUGGCAGCCGGGCCGG--- l=24 a=1 (c)
-------------------------------UAUGACGGCGUUGGCAGC----------- l=18 a=2 
-------------------------------UAUGACGGCGUUGGCAGCCGG-------- l=21 a=1 
-------------------------------UAUGACGGCGUUGGCAGCCGGGu------ l=23 a=3 
-------------------------------UAUGACGGCGUUGGCAGCCGGGC------ l=23 a=5 (ma)
------------------------------uUAUGACGGCGUUGGCAGCCGG-------- l=22 a=2 
------------------------------uUAUGACGGCGUUGGCAGCCGGG------- l=23 a=2 
------------------------------uUAUGACGGCGUUGGCAGCCGGGC------ l=24 a=5 
------------------------------uUAUGACGGCGUUGGCAGCCGGGCCG---- l=26 a=1 
-----------------------------UuUAUGACGGCGUUGGCAGC----------- l=20 a=5 
-----------------------------UuUAUGACGGCGUUGGCAGCC---------- l=21 a=1 
-----------------------------UuUAUGACGGCGUUGGCAGCCGG-------- l=23 a=5 
-----------------------------UuUAUGACGGCGUUGGCAGCCGGG------- l=24 a=6 
-----------------------------UuUAUGACGGCGUUGGCAGCCGGGC------ l=25 a=22 
-----------------------------UuUAUGACGGCGUUGGCAGCCGGGCC----- l=26 a=3 
---CCGGGCCAGCAC--------------------------------------------- l=12 a=1 

mb-00011
ax-1001011
ku-01
ss-101111101100
fn-011
