species:   Opsin
pid:       PID1933
parent:    n_os_milR_56
paralog:   
locus:     JAAVMX010000003.1:6939813-6939873
matures:   ['UGCUGCUGCGGCGACUCAUCCGG', 'GGAAUAGUUAUGUAGCCGGCGUU']
srr:       SRR12952898
genome:    /Users/jax/+Genomes/Fungal_genomes/Opsin.GCA_012934285.1_ASM1293428v1_genomic.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952898.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952898.cram JAAVMX010000003.1:6939813-6939873

10 out of bounds
58 alignments
53 proper strand
32 stranded perfect matches

**************************         **************************
GAUGCUGCUGCGGCGACUCAUCCGGAGGAGCAGCCGCGGGAAUAGUUAUGUAGCCGGCGUU
((((((((((((..((((..(((.(.((.....)).).)))..)))).))))).)))))))
--UGCUGCUGCGGCGACUCAUCCGG------------------------------------ l=23 a=4 c
--------------------------------------GGAAUAGUUAUGUAGCCGGCGUU l=23 a=0 c*
--UGCUGCUGCGGCGACUCAUCCGGA----------------------------------- l=24 a=13 ma
-------------------------------------GGGAAUAGUUAUGUAGCCGGCGUU l=24 a=0 ma*

--UGCUGCUGCGGCGACUCAUC--------------------------------------- l=20 a=4 
--UGCUGCUGCaGCGACUCAUC--------------------------------------- l=20 a=1 
--UGCUGCUGCGGCGACUCAUa--------------------------------------- l=20 a=1 
--UGCUGCUGCGGCGACUCAUCa-------------------------------------- l=21 a=1 
--UGCUGCUGCGGCGACUCAUCC-------------------------------------- l=21 a=4 
--UGCUGCUGCGGCGACUCAUCu-------------------------------------- l=21 a=1 
--UGCUGCUGCGGCGACUCAUuC-------------------------------------- l=21 a=2 
--UGCUGCUGCGGCGACUCAUCCG------------------------------------- l=22 a=1 
--UGCUGCUGCGGCGACUCAUCCGG------------------------------------ l=23 a=4 (c)
--UGCUGCUGCGGCGACUCAUCCcG------------------------------------ l=23 a=2 
--UGCUGCUGCGGCGACUCAUCCGGA----------------------------------- l=24 a=13 (ma)
--UGCUGCUGCGGCGACUCAUCCGGu----------------------------------- l=24 a=2 
--UGCUGCUGCGGCGACUCAUCCGGc----------------------------------- l=24 a=2 
--UGCUGCUGCGGCGACUCAUCCGGAGc--------------------------------- l=26 a=3 
-----UGCUGCGGCGACUCAUC--------------------------------------- l=17 a=1 
-----UGCUGCGGCGACUCAUCCGG------------------------------------ l=20 a=3 
-----UGCUGCGGCGACUCAUCCGa------------------------------------ l=20 a=2 
-----UGCUGCGGCGACUCAUCCGGg----------------------------------- l=21 a=1 
-----UGCUGCGGCGACUCAUCCGaA----------------------------------- l=21 a=1 
-----UGCUGCGGCGACUCAUCCGGA----------------------------------- l=21 a=1 
-----UGCUGCGGCGACUCAUCCGGAG---------------------------------- l=22 a=1 
--------UGCGGCGACUCAUCCGGAGc--------------------------------- l=20 a=1 
-----------------UCAUCCGGAGGAGCAGCCGCGGu--------------------- l=23 a=1 

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