species:   Rhirr
pid:       PID1181
parent:    Locus_818
paralog:   
locus:     scaffold_81:287993-288405
matures:   ['UGAGAGAUCUUUACUUGCAG', 'GCAAGUAAGAGAUCUCUCAAU']
srr:       ERR2841789
genome:    /Users/jax/+Genomes/Fungal_genomes/Rhirr.Rhiir2_1_AssemblyScaffolds.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Silvestri2019-js.ERR2841789.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Silvestri2019-js.ERR2841789.cram scaffold_81:287993-288405

0 out of bounds
5 alignments
4 proper strand
2 stranded perfect matches

                                                                                                                                 *********************            **********************                                                                                                                                                                                                                                     
GGAACGAAAACGUAAUGCGGACGAAACCGUAUUUGACGCCAAUUGGUAAAAUUCAUUAUUUAUUAUAAUCUUUUUUUUUUUUGCAACGUUAAUUUUAAUGUUUGACCAUCUUUAUUCUUCCACAAACGUAUUGAGAGAUCUUUACUUGCAGAAAAAUUCUUCGGCAAGUAAGAGAUCUCUCAAUACGUUUGUGGAAUCUCAUCAAGACCAUGCAUCACAGCGAGUAAAGAUCUCAGUACGUCUGUGGAAUCUCGAGACCAUGCAGACUGUCGCCAUCUUUACCGGAGAAUUGAUUAUAAGGAAUAUAAUAAAAAAAAUAAUAUCAAUAAAUAUUCACCACCCAAAUUUUGUUACAAAUAUCUUAAAGAAAUUGGGGAAAUAGUCAUAAUAUUUAGUCAUAGUAAUAUUUAGUU
...(((....)))(((((((......)))))))(((((((....))).........(((((.((((((((..((((((......(((((((....)))))))(((..((((((((((((((((((((((((((((((((((((((((((.(((......))).)))))).))))))))))))))))))))))))))...............((......)))))))))))).)))(((((((((((...((....))...))))))).)).))..........))))))..)))))))).))))).............(((((......))))).....(((((.((((................)))).))))).(((((.......))))).))))...............
-----------------------------------------------------------------------------------------------------------------------------------UGAGAGAUCUUUACUUGCAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=20 a=0 c
-------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAAGUAAGAGAUCUCUCAAU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=21 a=0 c*
-----------------------------------------------------------------------------------------------------------------------------------UGAGAGAUCUUUACUUGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=19 a=1 ma
--------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAGUAAGAGAUCUCUCAAU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=20 a=0 ma*

------------UAAUGCGGAuGAAACCG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=17 a=1 
-----------------------------------------------------------------------------------------------------------------------------------UGAGAGAUCUUUACUUGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=19 a=1 (ma)
-------------------------------------------------------------------------------------------------------------------------------------------------------------------cCAAGUAAGAGAUCUCUCAAU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=21 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUCGAGACCAUG------------------------------------------------------------------------------------------------------------------------------------------------------- l=12 a=1 

mb-01111
ax-1010001
ku-01
ss-100000111100
fn-001
