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

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

                                 ***********************                                                                                    *********************                                
UUAUAUAGUCUUAUUUAUUUAAUGCCACGGAGGGGUUAACUCCUUAAUGUAGGCUUAUUUAUUGCCACGGAGGGGUUUGCUCCUUAAUGUAGGCUUAUUUAAUGCCACGGAGGGGUUUGCUCCUUAAUGUGGGCUUGUUUGAUGCCACGGAGGGGUUUGCUCCUUAAUGUGGGCUUAUUGUUUGGCUAGCUAA
.....(((((..((.....(((..((((((((((((.((((((((..(((.((((((.......((((((((((((..(((((((..(((.(((.........)))))))))))))..)))))))..))))).......))).)))))))))))))).)))))))..)))))..)))..))..))))).....
-----------UAUUUAUUUAAUGCCACGGAGGGGU------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=0 c
----------------------------------------------------------------------------------------------------------------------------------------------------------------UCCUUAAUGUGGGCUUAUUGUUUG--------- l=24 a=0 c*
-----------------------------------UUAACUCCUUAAUGUAGGCUU----------------------------------------------------------------------------------------------------------------------------------------- l=21 a=1 ma
--------------------------------------------------------------UGCCACGGAGGGGUUUGCU---------------------------------------------------------------------------------------------------------------- l=19 a=0 ma*

--------------------------------uGGUUAACUCCUUAAUGUAGGCU------------------------------------------------------------------------------------------------------------------------------------------ l=23 a=1 
-----------------------------------UUAACUCCUUAAUGUAGGCUU----------------------------------------------------------------------------------------------------------------------------------------- l=21 a=1 (ma)
-----------------------------------UUAACUCCUUAAUGUAGGCUUAUc-------------------------------------------------------------------------------------------------------------------------------------- l=24 a=1 
----------------------------------------------------------------------------------------------UUAUUUAAUGCCACGGAGGGGUUUGC------------------------------------------------------------------------- l=26 a=1 
--------------------------------------------------------------------------------------------------------------------------------------------------------------------UAgUGUGGGCUUAUUGUUUGG-------- l=21 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUGGGCUUAUUGUUUGGCU------ l=20 a=1 

mb-00111
ax-1011011
ku-01
ss-110111111100
fn-011
