Alignments: v NC
:::<<<<<_______>>>>>,{{{{.{{{{{{,{{{{{{{{{{-----{{{-{{{,,<<<--<<~~~~~~>>>>>,,,,,,[[ CS
RF01959 1 AuUCcGguUGAUCCUgcCgGAggcc.accgCuAucGGgguccGauUaAGCCAuGcuAGucgagc*[14]*gcggCguAcaGCu 90
+ ::G UUGAUC UG C::AG::: A:CGCU :CGG:: ::: +UAA::CAUGC+AGUCGA:C G:GGCG AC+G:U
gi_545778205_gb_U000 223776 GAAGAGUUUGAUCAUGGCUCAGAUUgAACGCUGGCGGCA-GGC-CUAACACAUGCAAGUCGAAC*[34]*GUGGCGGACGGGU 223884
************************9789***********.555.699***************98...9..89*********** PP
v v v v v NC
[,,,,,,((((((((--((---(((((((,<<<<----<<<<<<<____>>>>>>>----->>>>,,,,<<<<<<<<-<<___ CS
RF01959 91 cAGUAACgCGcgGccAAccUAcCCucggGacggggAUAccCcCgGGAAACuGgGggUAAUacccgAUAggggggggcugCUGG 173
:AGUAA :::GG: AA:CU CC :::GGA: GGGAUA C::C GGAAAC G::G UAAUACC :AUA G: G
gi_545778205_gb_U000 223885 GAGUAAUGUCUGGG-AAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAA--------CGUCGC 223958
**************.689**************************************************9........588888 PP
v NC
___>>>>>>>>>>,,,,,,<<.......____.........>>,)))))))--))))))))))<<<--<-<<<--<<<<<<<< CS
RF01959 174 AAuGcgcccccccugAAAuGc.......uccg.........gCGCccgaGGAUggggCcgCGcCcgAUcAGGcaGucGGcgGg 240
AA :C + AA + GCC::: GAUG:G:CC::: ::GAU:AG::AGU:GG:G G
gi_545778205_gb_U000 223959 AAGAC--------CAAAGAGGgggaccu----ucgggccucUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGG 224029
88887........555444446776653....23467777799************9*************************** PP
NC
_______>>>>>>>>>>>----->>>>,,<<<<<<<<____>>>>--->>>>]]],<<<<<<__________>>>>>>,<<<< CS
RF01959 241 GUAAcGGcCcgCCgagCCuauaAgcgGUAcGGGccguGAGAgcgggAGCCCggaGAcGGgcuCUGAGACAaGagcCCgGGCCC 323
GUAACGGC C:CC:A::C+A +A:C::UA:::G ::UGAGAG:: GA C::::A:AC:GG::CUGAGACA G::CC:G ::CC
gi_545778205_gb_U000 224030 GUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCC 224112
*********************************************************************************** PP
v v NC
____>>>>,,,}}}}}}-},,,,,<-<<<---<<<<<____>>>>>->>>>,}}}}}}}}},,<<<~~~~~~>>>,,,<<<<< CS
RF01959 324 UACGGGGCGCAgCaGGCgCGAAAacUccgCAaugCgcGaaAgcGcgAcgggGggaccCCgaGUGcc*[15]*ggCUuUccccc 415
UACGGG::GCAGCAG::G:GAA A:U:C:CAAU::GCG AAGC::GA:G::G::A::CCG:GUG:: ::CUUUC :C:
gi_545778205_gb_U000 224113 UACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUA*[25]*UACUUUCAGCG 224214
****************************************************************98...9..78888888888 PP
v v v NC
<<~~~~~~>>>>>>--->,,<<<<<<-------<<<<-----<<____>>------->>>>>>>>>>,}}}}}}}}}},,,,, CS
RF01959 416 gg*[ 9]*ccggggGAAgAAGgGgcGGGcAAGaCcGGUGuCAGCCGCCGCGGUAAuACCgGCgcCcCgaGcgguggccauuaU 501
GG CC:G: GAAGAAG:::C GGC A :C:GUG+CAGC GCCGCGGUAAUAC:G: G:::C+AGCG:U:::C+ AU
gi_545778205_gb_U000 224215 GG*[41]*CCCGCAGAAGAAGCACC-GGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAU 224331
87...9..899999*********97.7888889************************************************** PP
v v v NC
,,,,,{{{-----{,[[[[-[-[[[,<<<<<<<-<<<<<<<<<<<----<<<<<<<_____>>>>>>>--->>>>>>>>>--> CS
RF01959 502 UAuUGGGCcUAAAGcGucCGcAgCcGGcccggcAaGucccccgggAAAuCcgcggGCUcAACccgcgGacgcccgggggauAC 584
UA UGGGC UAAAGCG::CG AG:CGG:::G :AAGUC::::G::AAAU C:C GGCUCAACC G:G AC ::C::::GAUAC
gi_545778205_gb_U000 224332 UACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAAC-UGCAUCUGAUAC 224413
****************************************************************999888.************ PP
v v v NC
>>>>>>>>,,,(((((((((--(((((((<<--<<<<<<<<---<<<______>>>------>>>>>>>>-->>,,,,<--<< CS
RF01959 585 ugccgggCUuGGGgccGgccGAggccggggGUAcucccgGGGUAGggGugAAAccCuaUaAUCCcgggagGACcACCacUGGC 667
U: C:::CUUG:G: ::G::GA:G::GG : A:UCC:G :GUAG::GUGAAA::C + A : C:GGA:GA :ACC :UGGC
gi_545778205_gb_U000 224414 UGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGC 224496
*********************************************************************************** PP
v v NC
____>>>)))))))-))))))-))),,,]]]]--]]]],,,,<<<<<<---<<---<<<<_________>>>>--->>>>>>> CS
RF01959 668 GAAaGCgcccggccaggcCggacCCGACgGugAGGgaCGAAAGCcgGGGgagCgAAccGGAUUAGAUACCCggGUAGcCCcgG 750
GAA+GC: CC::C: ::C:: +:C:GACG:U AGG::CGAAAGC::GGGGA:C+AAC:GGAUUAGAUACCC:GGUAG:CC::G
gi_545778205_gb_U000 224497 GAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACG 224579
*********************************************************************************** PP
NC
>,,,,,,,,,,((((((,,<<<<<<<<<<<<<<_____>>>>>>>>>>>>>>,,,<<____>>,,,,,))))))}}}},<<<- CS
RF01959 751 CuGUAAACgaUGcggGcUaggugccgggcgggcuucGagcccgcccggcgccGuAGgGAAGcCGuuAAgCccgCCGCCUggGg 833
C GUAAACGAUG::G:CU+GG::: G:C U+GAG:C :::CCG AG: AA :CGUUAAG:C::CCGCCU:GGG
gi_545778205_gb_U000 224580 CCGUAAACGAUGUCGACUUGGAGGU--UGUGCCCUUGAGGCGUG--GCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGG 224658
********************98865..56788999999988765..56889******************************** PP
NC
-----<<<<____>>>>---->>>,,,,,,,,{{{{{-{{{{{{{--{{,,{{{{{{{{{{{{{{{{{,,,,<<<<_______ CS
RF01959 834 AGUACggcCGCAAGgcuGAAACuuAAAGGAAUuGGCgGgGGaGCaCcaCAAcggguGcaGccuGCGGuUUAAccgGAuUCAAC 916
AGUACG CCGCAAGG U AAACU:AAA GAAUUG:CGGGGG::C:C ACAA::GGUG:AGC:UG:GGUUUAA:::GAU CAAC
gi_545778205_gb_U000 224659 AGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAC 224740
*********************************************8.************************************ PP
v v v NC
_>>>>,,,,,,,,{{{{{{{.,,,<<<<<<--~~~~~~>>->>>>,,,[[-[[[[--[[[[[[[[[,,,((((((<<<____> CS
RF01959 917 GCcggaaAuCUcACCgGggg.cGACaGccgaA*[28]*cgagCuGAGAGGaGGugCAuggCCgcCGuCAGcuCGugCcGUGAg 1020
GC:::+AA CU+ACC:GG:: GACA:CC: A :G+G: GA AGG+G:UGCAUGGC:G CGUCAGCUCGU:::GUGA:
gi_545778205_gb_U000 224741 GCGAAGAACCUUACCUGGUCuUGACAUCCACA*[35]*UGUGA-GACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAA 224851
********************558887665544...7..55555.9************************************** PP
NC
>>,,<<<<______>>>>,,)))))),,,,,((((,<<<<<<<---<<--<<<<<<<____>>>>>>>>>---->>>>>>>,, CS
RF01959 1021 GcGUCCuGUUAAGUCaGGcAaCGagCGAGACCCccacccccagUUGCcAucgcggccuuugggccgcggGcAcacugggggGA 1103
::GU ::GUUAAGUC:: CAACGAGCG ACCC :A:C::::GUUGCCA CG: ++G :CGGG AC+C::::G:GA
gi_545778205_gb_U000 224852 AUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCUUUUGUUGCCAGCGGU----CCG---GCCGGGAACUCAAAGGAGA 224927
*****************************************************7....455...7****************** PP
v NC
<<<<<<<<_____>>>>>>>>,,,,,)))),,,,]]]]-]]]---]]]]]]]],,,,}}}}}}},,,}}-}}}}}}}}}},,, CS
RF01959 1104 CcgCcggcGcuAAgccgGagGAAGGAggGGGCaACGgcAGGuCAGcaugCCCCGAAucccCcGGGCuaCACGCgggCugCAAU 1186
C:GCC:G:G+UAA:C:GGA:GAAGG : GG ACG CA:GUCA CAUG:CCC A ::CC:GGGCUACAC:CG:GCU:CAAU
gi_545778205_gb_U000 224928 CUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAU 225010
*********************************************************************************** PP
v v NC
<<<<<<<-----<<<--<<--<<<<____>>>>-->>---->>>----->>>>>>>,,,,,,<---<<<<<<<<________> CS
RF01959 1187 GgccgggACAauGgGuucCgAcccCGAaAGgggaaGguAAUCcCuuAAAcccggcCuuAGUugGGAccGaGGgCUGuAACUCG 1269
G:C::: ACAA G:G++:CGA C:CG AG:G AAG: A C:C UAAA :::G:C+UAGU :GGA::G::G:CUG+AACUCG
gi_545778205_gb_U000 225011 GGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCG 225093
*********************************************************************************** PP
v v NC
>>>>>>>--->,,,,,}}}}},,,,,<<<<<<<<_______>>>>>>>>,,,,,,}}---}}}}}}}}}}-}},,<-<<-<<- CS
RF01959 1270 cCCuCggGAAccuGGAauccgUAGUAacCGCgcgUCAacAucgcGCGguGAAUAcGuCCCuGCuCCuuGCACaCACcGcCCGU 1352
:C::C::GAA: GGAAUC::UAGUAA:CG:G: UCA +AU :C:CG:UGAAUACGU CC:G::CCUUG:ACACACCG:CCGU
gi_545778205_gb_U000 225094 ACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGU 225176
*********************************************************************************** PP
v v v v NC
<-<<<<<<<<--<<<<<<<<<<<<<<<.<<<<<~~~~~~>>>>>>>>>>>>>>>>>>>>-->>>>>>>>-->->>-->>-->, CS
RF01959 1353 CacgcCacccgAGcggggcccgggcgc.Ggccc*[14]*gggcCgagcccgggccccgCaAggggGgcgAAGUCGUAgCAAGG 1442
CAC:CCA :GA::G:::: C::: G G:: : : ::C A :::G ::::C::+A: GGG:GAAGUCGUA:CAAGG
gi_545778205_gb_U000 225177 CACACCAUGGGAGUGGGUUGCAAAAGAaGUAGG*[22]*CUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGG 225275
*********************987654144444...6..44444566899********************************* PP
NC
<<<<<<<<<<____>>>>>>>>>>::::::::::: CS
RF01959 1443 cggCCGcaggGGAAccugCGGccgGAUCACCUCcu 1477
:::CCG:AGGGGAACCU:CGG:::GAUCACCUCCU
gi_545778205_gb_U000 225276 UAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU 225310
*********************************** PP
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