species:   Opsin
pid:       PID1933
parent:    n_os_milR_56
paralog:   
locus:     JAAVMX010000003.1:6939813-6939873
matures:   ['UGCUGCUGCGGCGACUCAUCCGG', 'GGAAUAGUUAUGUAGCCGGCGUU']
srr:       SRR12952901
genome:    /Users/jax/+Genomes/Fungal_genomes/Opsin.GCA_012934285.1_ASM1293428v1_genomic.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952901.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952901.cram JAAVMX010000003.1:6939813-6939873

56 out of bounds
49 alignments
44 proper strand
23 stranded perfect matches

*************************           *************************
GAUGCUGCUGCGGCGACUCAUCCGGAGGAGCAGCCGCGGGAAUAGUUAUGUAGCCGGCGUU
((((((((((((..((((..(((.(.((.....)).).)))..)))).))))).)))))))
--UGCUGCUGCGGCGACUCAUCCGG------------------------------------ l=23 a=9 c
--------------------------------------GGAAUAGUUAUGUAGCCGGCGUU l=23 a=0 c*
--UGCUGCUGCGGCGACUCAUCCGG------------------------------------ l=23 a=9 ma
--------------------------------------GGAAUAGUUAUGUAGCCGGCGUU l=23 a=0 ma*

-AUGCUGCUGCGGCGACUCAUCCGGA----------------------------------- l=25 a=1 
--UGCUGCUGCGGCGACUCAU---------------------------------------- l=19 a=1 
--UGCUGCUGCGGCGACUCAUC--------------------------------------- l=20 a=1 
--UGCUGCUGCGGCGACUCAUCCG------------------------------------- l=22 a=1 
--UGCUGCUGCGGCGACUCAUCCa------------------------------------- l=22 a=1 
--UGCUGCUGCGGCGACUCAUCCGG------------------------------------ l=23 a=9 (c,ma)
--UGCUGCUGCGGCGACUCAUCCGu------------------------------------ l=23 a=3 
--UGCUGCUGCGGCGACUCAUCCGa------------------------------------ l=23 a=1 
--UGCUGCUGCGGCGACUCAUCCGGA----------------------------------- l=24 a=8 
--UGCUGCUGCGGCGACUCAUCCGGu----------------------------------- l=24 a=4 
--UGCUGCUGCGGCGACUCAUCCGGg----------------------------------- l=24 a=4 
--UGCUGCUGCGGCGACUCAUCCGGAG---------------------------------- l=25 a=1 
--UGCUGCUGCGGCGACUCAUCCGGAu---------------------------------- l=25 a=1 
--UGCUGCUGCGGCGACUCAUCCGGAGu--------------------------------- l=26 a=1 
-----UGCUGCGGCGACUCAUCCGu------------------------------------ l=20 a=1 
-----UGCUGCGGCGACUCAUCCGGA----------------------------------- l=21 a=1 
-----UGCUGCGGCGACUCAUCCGGAGu--------------------------------- l=23 a=1 
-----UGCUGCaGCGACUCAUCCGGAGG--------------------------------- l=23 a=1 
--------UGCGGCGACUCAUCCGGAGcAG------------------------------- l=22 a=1 
--------UGCGGCGACUCAUCCGGAGcAGC------------------------------ l=23 a=1 
--------UGCGGCGACUCAUCCGGAGcAGCA----------------------------- l=24 a=1 

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