species:   Opsin
pid:       PID1941
parent:    n_os_milR_61
paralog:   
locus:     JAAVMX010000003.1:8139576-8139768
matures:   ['UAUUUAUUUAAUGCCACGGAGGGGU', 'UCCUUAAUGUGGGCUUAUUGUUUG']
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 JAAVMX010000003.1:8139576-8139768

0 out of bounds
4 alignments
4 proper strand
3 stranded perfect matches

         ***************************                                                                                                                          **************************         
UUAUAUAGUCUUAUUUAUUUAAUGCCACGGAGGGGUUAACUCCUUAAUGUAGGCUUAUUUAUUGCCACGGAGGGGUUUGCUCCUUAAUGUAGGCUUAUUUAAUGCCACGGAGGGGUUUGCUCCUUAAUGUGGGCUUGUUUGAUGCCACGGAGGGGUUUGCUCCUUAAUGUGGGCUUAUUGUUUGGCUAGCUAA
.....(((((..((.....(((..((((((((((((.((((((((..(((.((((((.......((((((((((((..(((((((..(((.(((.........)))))))))))))..)))))))..))))).......))).)))))))))))))).)))))))..)))))..)))..))..))))).....
-----------UAUUUAUUUAAUGCCACGGAGGGGU------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 c
----------------------------------------------------------------------------------------------------------------------------------------------------------------UCCUUAAUGUGGGCUUAUUGUUUG--------- l=24 a=0 c*
-----------UAUUUAUUUAAUGCCACGGAGGGGU------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 ma
----------------------------------------------------------------------------------------------------------------------------------------------------------------UCCUUAAUGUGGGCUUAUUGUUUG--------- l=24 a=0 ma*

-----------UAUUUAUUUAAUGCCACGGAGGGGU------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 (c,ma)
--------------------------------uGGUUAACUCCUUAAUGUAGGCUUA---------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 
---------------------------------------------------------------------------------------------------------------------------------UGGGCUUGUUUGAUGCCACGGA------------------------------------------ l=22 a=1 
--------------------------------------------------------------------------------------------------------------------------------------------------------------------UAAUGUGGGCUUAUUGUUUGGCUAG---- l=25 a=1 

mb-01111
ax-1001001
ku-01
ss-100011101100
fn-011
