species:   Opsin
pid:       PID1908
parent:    n_os_milR_50
paralog:   
locus:     JAAVMX010000001.1:21326330-21326786
matures:   ['UGAUCGAUCAUCGCCUCUUUUG', 'AUGGAGGCCUUGCCCGAUUAGC']
srr:       SRR12952904
genome:    /Users/jax/+Genomes/Fungal_genomes/Opsin.GCA_012934285.1_ASM1293428v1_genomic.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952904.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Zhang2021-wd.SRR12952904.cram JAAVMX010000001.1:21326330-21326786

99 out of bounds
126 alignments
103 proper strand
80 stranded perfect matches

 ***********************                                                                                                                                                                                                                                                                                                                                                                                                                         *********************** 
GAAUGGAGGCCUUGCCCGAUUAGCUCGAGAAACUUUAUUUCACGACGGGCGUCAUGCUUGAAGUCAAAGGGCAUGAGCUUGGGCCCAGGAUACCAAGGCAGCGGGCGCGUGGCCUGCAUGCCGAAGUGACGAAGAGUCUGGAGCCGCUGGCUGAUGAAGGAAUUGGGGAAAAUAUUGGAACUCCAAAAGAUUGUUGUGAGAGACAAUAGUUACCGUAGGUGCACAAAGGGACACACCAAGCAAGGUGUAGAGUGUGUAACAAGGAAACAAGGAUGGAUGCUUAGCUAGAAGGCCCUCACGAGAUGUAUGGCGGCGGCACCCGAUUAGUCAGGUGCCCUCGGAUGCUUGUUAAUCCGCUCCGAGCUGUCCGCUUUUCGAAAAUGGAGUUCUUCUCCCCCUCUUAUUUCCCUCUUCAUCAAUCUUCGAUGCACACAUUGAUCGAUCAUCGCCUCUUUUG
....((((((..((..((((((((((.(((..((((...((((..(((((.(((.(((((..(((....))).))))).))))))).((...))..((((((((((.....)))))).)))))..)))).))))..))).))))((..((.((((((((.....(((((((.....(((((((((...(((((((((.....))))))))).((.....((((((.......(((((......)))))....))))))....)).......((.((..((((.......)))))))).(((((.((..((((((((((((.((....)).)))))).(((((.((..........))))))))))))).)).)))))....))))))))).............))))))))))))))).))..))..........))))))..))..))))))....
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUUUG l=22 a=30 c
--AUGGAGGCCUUGCCCGAUUAGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=22 a=0 c*
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUUU- l=21 a=32 ma
---UGGAGGCCUUGCCCGAUUAGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=21 a=0 ma*

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAUUGGAACUCCAAAAGAUUGc----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=22 a=1 
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGGAACUCCAAAAGAUUGUUGUGu------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=24 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACACAUUGAUCGAUCAUCGCCUa----- l=23 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACACAUUGAUCGAUCAUCGCCUCUU--- l=25 a=2 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUU--- l=19 a=4 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUc--- l=19 a=2 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGgUCGAUCAUCGCCUCUU--- l=19 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCgU--- l=19 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUU-- l=20 a=12 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUc-- l=20 a=4 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUgU-- l=20 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUcU-- l=20 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUUU- l=21 a=32 (ma)
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUgU- l=21 a=3 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUUc- l=21 a=2 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUaU- l=21 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUUUG l=22 a=30 (c)
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUUUa l=22 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAcCAUCGCCUCUUUUG l=22 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAUCGCCUCUUUUc l=22 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUCGAUCAcCGCCUCUUUUG l=22 a=1 

mb-01011
ax-1000011
ku-01
ss-101101101110
fn-111
