species:   Rhirr
pid:       PID1182
parent:    Locus_828
paralog:   
locus:     scaffold_81:370577-371186
matures:   ['CGAGGAUCGAGAGCUUGCACGUCA', 'ACGCGCAACUUCUCUUUCCUUUGC']
srr:       ERR2841786
genome:    /Users/jax/+Genomes/Fungal_genomes/Rhirr.Rhiir2_1_AssemblyScaffolds.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Silvestri2019-js.ERR2841786.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Silvestri2019-js.ERR2841786.cram scaffold_81:370577-371186

0 out of bounds
685 alignments
671 proper strand
650 stranded perfect matches

                        **************************                                                                                                                                                                                                                                                                                     **************************                                                                                                                                                                                                                                                                 
GAAACCUUUCCUUUCCUUUCGCGUUGACGCGCAACUUCUCUUUCCUUUGCUUUCAUCUUUUUUCUUUUCUUUUUUUUUCUCGUUCCUAAGACCCUCUAUUUAUAUACAAAAUUGCAAGUUACUGUGUUUCGUGAACGUAAUAACGUAACUAUAAAAGGGUAUGGUGGUUUUGGUGAUUUUGUAUAGUUAUGCGGGCAGCUUUUGACGAAAAACCGCGGCAGCUGCUGCAAAAAGGGUAAAUAGCAAACUGACCAACUUUUAAUUAUAUUGCUAAUUUUUAGAAUUGUGUUAAUAGGAACAAGAAUAGCAAGAAAAAGAAUCAUGAAAGCCGAGGAUCGAGAGCUUGCACGUCAACGCGCAAAGAAAAGGUGAUUUCGGUUAAGUUUUAAAGUUUACAAAAGGGUGUUCUCGAGGUAAUUUAUGAUAAAAAUUAUUUAUUAUCAAUGACAUCUUUUUCUUUUGAAAUGUCGUCUUUCAUGAUAAUUCGAUAAAAAACUAUUUAUUAAAAGAUCAAUGAUUUCUUUUUCUUUUAUUUUAUUACUCACAAUAGCAAUGCCCAAGUAAGUCGACUACCAGACGUUGCGUACUCCUAGGAAAGGGACGGCGAUCA
....((.((((((((((..((((((((((.((((.(((((..(((((.((((((((..(((((..((((((.....((((.(((((((..(((((.......(((((((((((((...((((........))))((((....)))).((((((......)))))).......)))))))))))))....(((((.(((((.(((.((......))))).))))))))))...)))))...........(((((((.((((((..((.......))..))))))))).)))).))))))).))))....)))))))))))..)))))))).)))))..))))).)))).)))))))))).((((((((((.((((..((((...(((((((((((..(((((((((((.....((((((..(((((....)))))..))))))...)))))))))))...(((((.((((((.....)))))).)))))....))))).....))))))))))...)))).))))))))))...................(((((((...(((......)))....).))))))........)))))))))).))......
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=293 c
--------------------------ACGCGCAACUUCUCUUUCCUUUGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=129 c*
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=293 ma
--------------------------ACGCGCAACUUCUCUUUCCUUUGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=129 ma*

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGUGAUUUCGGUUAAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=17 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGCGCAAAGAAAAGGUG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=18 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGCGCAAAGAAAAGGUGAUUUCG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=3 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGCGCAAAGAAAAGGUGAUUUCGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=12 a=1 
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGAGCUUGgACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=13 a=1 
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGAUCGAGAGCUUGCAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=18 a=1 
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=15 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACa-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=21 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=21 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=23 a=35 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUu------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=23 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=293 (c,ma)
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGaCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGgUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGcCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCuCGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=3 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCgCGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUCAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=20 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUaGAGAGCUUGCACGUCAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUCAg---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=2 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGAGGAUCGAGAGCUUGCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=10 
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCCGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=27 a=1 
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGCCGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=28 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAAGCCGAGGAUCGAGAGCUUGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAAGCCGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=30 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAAAGCCGAGGAUCGAGAGCUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAAAGCCGAGGAUCGAGAGCUUG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=24 a=1 
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCAUGAAAGCCGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=34 a=2 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAAAGAAUCAUGAAAGCCGAGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=23 a=1 
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAGAAAAAGAAUCAUGAAAGCCGAGGAUCGAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=33 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAAACCGCGGCAGCUG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=17 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------UGGUGGUUUUGGUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=14 a=1 
--------------------------------------------------------------------------------------------------------UACAAAAUUGCAAGUUACUGUGUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=1 
-----------------------------------UUCUCUUcCCUUUGCUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=17 a=1 
----------------------------------CUUCUCUUUCCUUUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=15 a=1 
--------------------------ACGCGCAACUUCUCUU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=16 a=1 
--------------------------ACGCGCAACUUCUCUUUCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=19 a=2 
--------------------------ACGCGCAACUUCUCUUUCCU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=20 a=4 
--------------------------ACGCGCAACUUCUCUUUCCUU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=21 a=8 
--------------------------ACGCGCAACUUCUCUUUCCUUU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=22 a=11 
--------------------------ACGCGCAACUUCUCUUUCCUUUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=103 
--------------------------ACGCGCAACUcCUCUUUCCUUUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=1 
--------------------------ACGCGCAACUUCUCUUUCCUUUa--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=2 
--------------------------ACGCGCAACUUCUCUUUCCUUUGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=129 (c*,ma*)
--------------------------ACGCGCAACUUCUCUUUCCUUUGa-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=2 
--------------------------gCGCGCAACUUCUCUUUCCUUUGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=1 
--------------------------ACGCGCAACUUCUCUUUCCUUUGCU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=2 
--------------------------ACGCGCAACUUCUCUUUCCUUUGCa------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 
GAAACCUUUCCUUUCCUUUCG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=21 a=1 
GAAACCUUUCCUUUCCUUUCGCGUU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=3 
GAAACCUUUCCUUUCCUUUCGCGUUG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=26 a=2 

mb-11111
ax-1110111
ku-11
ss-111101111111
fn-111
