species:   Rhirr
pid:       PID1182
parent:    Locus_828
paralog:   
locus:     scaffold_81:370577-371186
matures:   ['CGAGGAUCGAGAGCUUGCACGUCA', 'ACGCGCAACUUCUCUUUCCUUUGC']
srr:       ERR2841787
genome:    /Users/jax/+Genomes/Fungal_genomes/Rhirr.Rhiir2_1_AssemblyScaffolds.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Silvestri2019-js.ERR2841787.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Silvestri2019-js.ERR2841787.cram scaffold_81:370577-371186

0 out of bounds
292 alignments
270 proper strand
255 stranded perfect matches

                        *************************                                                                                                                                                                                                                                                                                       *************************                                                                                                                                                                                                                                                                 
GAAACCUUUCCUUUCCUUUCGCGUUGACGCGCAACUUCUCUUUCCUUUGCUUUCAUCUUUUUUCUUUUCUUUUUUUUUCUCGUUCCUAAGACCCUCUAUUUAUAUACAAAAUUGCAAGUUACUGUGUUUCGUGAACGUAAUAACGUAACUAUAAAAGGGUAUGGUGGUUUUGGUGAUUUUGUAUAGUUAUGCGGGCAGCUUUUGACGAAAAACCGCGGCAGCUGCUGCAAAAAGGGUAAAUAGCAAACUGACCAACUUUUAAUUAUAUUGCUAAUUUUUAGAAUUGUGUUAAUAGGAACAAGAAUAGCAAGAAAAAGAAUCAUGAAAGCCGAGGAUCGAGAGCUUGCACGUCAACGCGCAAAGAAAAGGUGAUUUCGGUUAAGUUUUAAAGUUUACAAAAGGGUGUUCUCGAGGUAAUUUAUGAUAAAAAUUAUUUAUUAUCAAUGACAUCUUUUUCUUUUGAAAUGUCGUCUUUCAUGAUAAUUCGAUAAAAAACUAUUUAUUAAAAGAUCAAUGAUUUCUUUUUCUUUUAUUUUAUUACUCACAAUAGCAAUGCCCAAGUAAGUCGACUACCAGACGUUGCGUACUCCUAGGAAAGGGACGGCGAUCA
....((.((((((((((..((((((((((.((((.(((((..(((((.((((((((..(((((..((((((.....((((.(((((((..(((((.......(((((((((((((...((((........))))((((....)))).((((((......)))))).......)))))))))))))....(((((.(((((.(((.((......))))).))))))))))...)))))...........(((((((.((((((..((.......))..))))))))).)))).))))))).))))....)))))))))))..)))))))).)))))..))))).)))).)))))))))).((((((((((.((((..((((...(((((((((((..(((((((((((.....((((((..(((((....)))))..))))))...)))))))))))...(((((.((((((.....)))))).)))))....))))).....))))))))))...)))).))))))))))...................(((((((...(((......)))....).))))))........)))))))))).))......
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=82 c
--------------------------ACGCGCAACUUCUCUUUCCUUUGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=36 c*
--------------------------ACGCGCAACUUCUCUUUCCUUUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=85 ma
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=0 ma*

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGAAgUGUCGUCU----------------------------------------------------------------------------------------------------------------------------------------- l=15 a=1 
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUUGAAgUGUCGUCU----------------------------------------------------------------------------------------------------------------------------------------- l=16 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUGACAUCUcUUUC--------------------------------------------------------------------------------------------------------------------------------------------------------- l=15 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAAAGGGUGUU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=12 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGGUGAUUUCGGgUA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=16 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACGUCAACGgGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=14 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGCUUGCACuUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=14 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCGAGAGCUUGCACGUC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=17 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUCGAGAGCUUGCACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=16 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=20 a=1 
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGAUCGAGAGCUUGCACGUCAACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=13 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=15 a=6 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=19 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=22 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=23 a=4 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=82 (c)
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CaAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGGAUCGAGAGCUUGCACGUCAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAAGCCGAGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=11 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cGAAAGCCGAGGAUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=15 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAAAGCCGAGGAUCGAGAGCUUGCACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=28 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUGAAAGCCGAGGAUCGAGAGCUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=1 
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAAGAAUCAUGAAAGCCGAGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=22 a=1 
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGAAAAAGAAUCAUGAAAGCCGAGGAUCGAGAGCUUGCACGUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=45 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAGCAAGAAAAAGAAUCAUGAAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGGCAGCUGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=10 a=1 
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGaGGCAGCUG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=12 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAACCGCGGCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=12 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGGGCcGCUUUUG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=13 a=1 
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUUAUGCGGGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=11 a=1 
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAGgUAUGCGGGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=14 a=1 
----------------------------------------------------------------------------------------------------------------------------------------------------------------AUGGUGGUUUUG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=12 a=1 
-------------------------------------------------------------------------------------------------------------------------------------------------------------GGUcUGGUGGUUUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=14 a=1 
----------------------------------------------------------------------UUUUUUUUCUCGUUCCUAAGACC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=1 
--------------------------------------------------UUUCAUCUUUUUUCU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=15 a=1 
-------------------------------------------CCUUUGCUUUCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=12 a=1 
-------------------------------------CUCUUUCCUUUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=12 a=2 
------------------------------------UCUCUUUCCUUUGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=14 a=1 
---------------------------------ACUUuUCUUUCCUUUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=16 a=1 
---------------------------------gCUUCUCUUUCCUUUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=16 a=1 
-----------------------------CGCAACUUCUCU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=12 a=1 
--------------------------ACGCGCAACUUCU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=13 a=1 
--------------------------ACGCGCAACUUCUCU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=15 a=1 
--------------------------ACGCGCAACUUCUCUU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=16 a=1 
--------------------------ACGCGCAACUUCUCUUUCCUUU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=22 a=4 
--------------------------ACGCGCAACUUCUCUUUCCUUUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=85 (ma)
--------------------------AaGCGCAACUUCUCUUUCCUUUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=23 a=1 
--------------------------ACGCGCAACUUCUCUUUCCUUUGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=24 a=36 (c*)
--------------------------ACGCGCAACUUCUCUUUCCUUUGCU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 
--------------------------ACGCGCAACUUCUCUUUCCUUUGCUUUCAU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=30 a=1 
--------------------------ACGCGCAACUUCUCUUUCCUUUGCUUUCAUC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=31 a=1 
-------------------CGCGUUGACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=10 a=1 
------------------UCGCGUUGAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=10 a=1 
GAAACCUUUCCUUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=14 a=1 
GAAACCUUUCCUUUCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ l=16 a=1 
GAAACCUUUCCUUUCCUUUCGCGUU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- l=25 a=1 

mb-01111
ax-1010011
ku-01
ss-101101111110
fn-111
