9 2016 helix x~~~~~~~~~ ~~|_____(~ ~~)___|~|_ ____|~|___ ________|~ E.coli -|--AAAUUG AA|GAGUU(U GA)UCA|U|G GCUC|A|GAU UGAACGCU|G chl.Z.mays -|--CUCAUG GA|GAGUU(C GA)UCC|U|G GCUC|A|GGA UGAACGCU|G chl.Chlamy.humicola -|nnnnnnnn nn|nnnnn(n nn)nnn|n|n GCUC|A|GGA UGAACGCU|G chl.Polytoma.62-27 -|nnnnnnnn nn|nnnnn(n nn)nnn|n|n nnnn|n|nnA UGAACGCU|A chl.Poly.obtusum -|nnnnnnnn nn|nnnnn(n nn)nnn|n|n nnnn|n|AGG UGAUCGCU|A chl.Poly.uvella.964 -|ACUUCGAA AA|GAGUU(- GA)UCC|U|G GCUC|A|AGG UGAUCGCU|G Con.chlor.95% -|++++++++ ++|GAGUU(+ GA)UCC|U|G GCUC|A|GGA UGAACGCU|G diff.95% x......... .......... .......... .......$.$ ...$.....o |________| _|~~~~|___ ____|~~|__ _|~~|_____ |~~|______ ____(~~~~~ |GCGGCAGG| C|CUAA|CAC AUGC|AA|GU C|GA|ACGGU |AA|CAGGAA GAAG(CUUG- |GCGGCAUG| C|UUAA|CAC AUGC|AA|GU C|GA|ACGGG |--|------ aagu(ggu-- |GCGGCAUG| C|UUAA|CAC AUGC|AA|GU C|GU|ACGGG |--|--uaau ggcu(uuac- |GCGGCAUG| C|UUAA|CAC AUGC|AA|GU C|GA|ACGAG |--|-----a cuua(guaa- |GCnGCAUG| C|UUAA|CAC AUGC|AA|GU C|GU|ACGAG |ua|uaauau uggu(cguaa |GCUGCAUG| C|UUAA|CAC AUGC|AA|GU C|GG|ACGAA |ua|uggugu aagg(aucga |GCGG+AUG| C|+U+A|CAC AUGC|AA|GU +|G+|ACG++ |++|++++++ ++++(+++++ ...?.....| .......... .......... .......... .......... .......... ~~~)______ __________ _____|~~~~ ~~|___|~~~ ~~~|______ __|~|__|~~ ---)CUUCUU UGCUG-ACGA GUGGC|GGAC GG|GUG|AGU AAU|GUCUGG GA|A|AC|UG ---)guuu-- ------CC-A GUGGC|GAAC GG|GUG|AGU AAC|GCGUAA GA|A|CC|UG ---)ggcuau ua----uuuA GUGGC|GGAC GG|GUG|CGU AAC|ACGUAA GA|A|CC|UA ---)uaagu- ------uauA GUGGC|GGAC GG|GUG|CGU AAC|GCGUAA GA|A|CC|UA aaa)accgag auuauacu-A GUGGC|GGAC GG|GUG|CGU AAC|ACGUGA GA|A|UC|UA ---)ccuucu ugua--ua-A GUGGC|GGAC GG|GUG|AGU AAC|ACGUGA GA|A|UC|UA +--)++++++ +++++++++A GUGGC|G+AC GG|GUG|+GU AA+|+CGU+A GA|A|++|++ .......... .......... .......... .......... .......... .......... ~|____|~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ C|CUGA|--- ---------- ---------- ---------- ---------- ---------- C|CCUU|--- ---------- ---------- ---------- ---------- ---------- C|CUUU|--- ---------- ---------- ---------- ---------- ---------- C|CUUU|--- ---------- ---------- ---------- ---------- ---------- C|CUUU|--- ---------- ---------- ---------- ---------- ---------- C|CUUu|uau auauuuaauu aaaaacaaau gaaguuuugu uauuuuugau gugauuaauu C|++++|--- ---------- ---------- ---------- ---------- ---------- .......... .......... .......... .......... .......... .......... ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~|___|~|_ ____|~~~|_ ______(~~~ ---------- ---------- ---------- --|UGG|A|G GGGG|AUA|A CUACUG(GAA ---------- ---------- ---------- --|GGG|A|G GGGA|ACA|A CAACUG(GAA ---------- ---------- ---------- --|UGG|A|G GGGG|AAA|A CAUCGG(GAA ---------- ---------- ---------- --|CAG|A|G GGGG|AUA|A CAUCGG(GAA ---------- ---------- ---------- --|UGU|A|G AGGG|AUA|A CAUCGG(GAA aaauauaaga guuuaacuua auaauuaaau uu|uGU|A|G AGGG|AUA|A CAUCGG(GAA ---------- ---------- ---------- --|+GG|+|+ ++G+|A+A|A C+++++(GAA .......... .......... .......... ....$$.... .......... .......... ~)________ |~~~~|____ _|~~~~~|__ _(~~~~)___ |~~~~|____ __|~~|__(~ A)CGG-UAGC |UAAU|ACCG C|AUAAC|GU C(GCAA)GAC |CAAA|GAGG GG|GA|CC(- A)CGG-UUGC |UAAU|ACCC C|GUAG-|GC U(GAGG)AGC |AAAA|gga- --|--|--(- A)CCGACGCU |AAUU|CCCC A|UGAUA|GC U(gagg)AGU |GAAA|agcg g-|--|--(- A)CUGUUGAU |AAUA|CCCC A|UAAUG|AC U(gagg)AGU |UAAA|acca ug|u-|--(- A)CCGUAUAU |UAAU|ACCU C|GUAUA|AC U(gaag)AGU |AAAA|gcgg --|--|--(- A)CCGCUUAU |UAAU|ACCU C|GUAUA|GC U(gaag)AGU |UAUA|gcgg u-|--|--(c A)+++-++G+ |UAA+|+C++ +|+UA++|+C +(++++)+G+ |+AAA|++++ ++|+-|--(- ........?. .o.o...... ...o...... .......... ...o...... .......... ~~~~~~~)__ |______|~| _______|~~ |__|______ __|___|~~| _|~|___|~~ ---UUCG)GG |CCUCUU|G| CCAUCGG|AU |GU|GCCCAG AU|GGG|AU| U|A|GCU|AG ---GAAA)-- |---ucc|G| CCCAAGG|AG |GG|GCUCGC GU|CUG|AU| U|A|GCU|AG --gaaa-)-- |--ccgc|G| CCAAAAG|AG |GG|GCUUGC GG|CUG|AU| U|A|GCU|AG --aaaa-)-- |gcaugg|G| CUGAAAG|AG |GG|GCUUGC GU|CUG|AU| U|A|GCU|AG --gaaa-)-- |-ccgcg|A| CUAAAAG|AG |GA|GCUUGC GG|CUG|AU| U|A|GCU|AG uauaaaa)-- |-acggc|G| ACUUGAG|AU |GA|GCUUGC GG|CUG|AU| U|A|GCU|AG +++++++)-+ |++++++|G| CC+++++|A+ |++|GCU+++ G+|CUG|AU| U|A|GCU|+G .......... ........o. $$........ .......... .......... .......... |________( ~~~~~~~~)_ _______|__ _|~~~~~|_| ___|~~|___ _|____(~~~ |UAGGUGGG( G-UAACGG)C UCACCUA|GG C|GACGA|U| CCC|UA|GCU G|GUCU(GAG |UUGGUGAG( G-CAAUAG)C UUACCAA|GG C|GAUGA|U| CAG|UA|GCU G|GUCC(GAG |UUGGUGGG( GGUAAAAG)C CUCCCAA|GG C|CACGA|U| CAG|UA|GCU G|GUCU(GAG |UUGGAGGG( GGUAAAAG)C CUCCCAA|GG C|CAUGA|U| CAG|UA|GCU G|GUCU(GAG |UUGGUGAG( G-UAAUGG)C UUACCAA|GG U|CACGA|U| CAG|UA|UCU G|GUUU(GAG |UUGGUGAG( G-UAAAGG)C UUACCAA|GG C|CACGA|U| CAG|UA|UCU G|GUUU(GAG |UUGGU++G( +-+AA++G)C ++ACCAA|GG C|+A+GA|U| CAG|UA|+CU G|+U++(GAG .....?.... .......... ..?....... *......... .......... .......... ~)____|~~~ |____|___| ~|______(~ ~~~~~~~~~) ______|~|_ ___(~~~~)_ A)GGAU|GAC |CAGC|CAC| A|CUGGAA(C UGAGACACG) GUCCAG|A|C UCC(UACG)G A)GGAU|GAU |CAGC|CAC| A|CUGGGA(C UGAGACACG) GCCCAG|A|C UCC(UACG)G A)GGAU|GAU |CAGC|CAC| A|CUGGGA(C UGAGACACG) GCCCAG|A|C UCC(UACG)G A)GGAU|GAU |CAGC|CAC| A|CUGGGA(C UGAGACACG) GCCCAG|A|C UCC(UACG)G A)GAAU|GAU |CAGA|CAC| A|CUGGGA(C UGAGACACG) GCCCAG|A|C UCC(UACG)G A)GAAU|GAC |CAGA|CAC| A|CUGGGA(C UGAGAUACG) GCCCAG|A|C UCC(UACG)G A)G+A+|GA+ |CAG+|CAC| A|CUGG+A(C UGAGA+ACG) G+CCAG|A|C U+C(UACG)G .......... .......... .......... .......... .......... .......... ___|~~~|__ ____|~|_|~ ~~~~|_|~|_ __|~~~|___ __(~~~~)__ ___|~|____ GAG|GCA|GC AGUG|G|G|G AAUA|U|U|G CA|CAA|UGG GC(GCAA)GC CUG|A|UGCA GAG|GCA|GC AGUG|G|G|G AAUU|U|U|C CG|CAA|UGG GC(GAAA)GC CUG|A|CGGA GAG|GCA|GC AGUG|A|G|G AAUU|U|U|C CA|CAA|UGG GC(GAAA)GC CUG|A|UGGA GAG|GCA|GC AGUG|A|G|G AAUU|U|U|C CG|CAA|UGG GC(GAAA)GC CUG|A|CGGA GAG|ACA|GC AGUG|G|C|U AAUA|U|U|U CA|CAA|UGG GC(GAAA)GC CUG|A|UGGA GAG|ACA|GC AGUG|G|C|U AAUA|U|U|U CA|CAA|UGG GC(GAAA)GC CUG|A|UGAA +AG|GCA|GC AGUG|+|G|G AAU+|U|U|+ CG|CAA|UGG GC(G+AA)G+ ++G|A|CGGA ....o..... .......?.o .......... .$........ .......... ......$.*. |_________ _|~~|____| ~~~~~~|___ _(~~~~)___ _|~~~~~~|_ ___|_|_|~~ |GCCAUGCCG C|GU|GUAU| GAAGAA|GGC C(UUCG)GGU U|-GUAAA|G UAC|U|U|UC |GCAAUGCCG C|GU|GGAG| GUGGAA|GGC C(UACG)GGU C|-GUCAA|C UUC|U|U|UU |GCAAUGCCG C|GU|GGAG| GAAGAA|GGU C(uauu)GAU U|-GUAAA|C UCC|U|U|UU |GCAAUGCCG C|GU|GGAG| GAAGAA|GGU C(ugug)GAU U|#GUAAA|C UCC|U|U|UU |GCAAUGCCG C|GU|GGAG| GAUGAA|GGU C(uauu)GAU U|-GUAAA|C UCC|U|U|UU |GCAAUGCCG C|GU|GGAG| GAUUAA|GAU C(uauu)GAU U|-GUAAA|C UCC|U|U|UU |GCAAU+CCG C|GU|G++G| G++GA+|+G+ +(++++)G+U +|-+U+AA|C ++C|U|U|UU .......... .......... ...o....*. .......... .......... .......... ~|_____|~~ ~|_|~~~~|_ _______(~~ ~~~~~)____ ____|~~~~~ |_|~~~~|__ A|GCGGG|GA G|G|AAGG|G AGUAAAG(UU AAUAC)CUUU GCUC|AUUGA |C|GUUA|CC C|UCGGA|GA A|G|AAAC|- -------(-- -----)---- ----|AAUGA |C|GGUA|UC C|UUAGA|GA A|G|aaga|u c------(-- -----)---- ----|--uga |C|GGUA|UC U|UCAGA|GA A|G|aaua|a g------(-- -----)---- ----|--uga |C|GGUA|UC A|CCGGG|GA A|G|aaaa|a -------(-- -----)---- ----|--uga |C|GUUA|CC A|UCGGG|GA A|G|aaaa|a c------(-- -----)---- ----|--uga |C|GUUA|CC +|+++++|+A +|G|AA++|+ +------(-- -----)---- ---+|++UGA |C|G++A|++ .......... .......... .......... .......... .......... .......... ___|~~~|__ |~~|_____| ___|~~~|__ ___(~~~~~| __|~|___|_ _|~~~~~~~) CGC|AGA|AG |AA|GCACC| GGC|UAA|CU CCG(UGCCA| GC|A|GCC|G C|GGUAAUA) UGA|GGA|AU |AA|GCAUC| GGC|UAA|CU CUG(UGCCA| GC|A|GCC|G C|GGUAAGA) UAA|GGA|AU |AA|GCUCC| GGC|UAA|CU CUG(UGCCA| GC|A|GUC|n C|GGUAAUA) UGA|AGA|AU |AA|GCUCC| GGC|UAA|CU AUG(UGCCA| GC|A|GCC|n C|GGUAAUA) CGG|GGA|AU |AA|GAAUC| GUC|UAA|CU UUG(UGCCA| GC|A|GAC|G C|GGUAAUA) UGA|GGA|AU |AA|GAAUC| GUC|UAA|CU UUG(UGCCA| CG|A|GAC|A C|GGUAAUA) +++|+GA|AU |AA|GC++C| GGC|UAA|CU C+G(UGCCA| GC|A|GCC|G C|GGUAA+A) .......... .....$.... .$........ $........| ?$....$..$ .......... _____|____ _|~|______ ____|~~~~~ ~~~~~|___| __|~~~|_|~ |____|~_~| CGGAG|GGUG C|A|AGCGUU AAUC|GGAAU UACUG|GGC| GU|AAA|G|C |GCAC|GCA| CAGAG|GAUG C|A|AGCGUU AUCC|GGAAU GAUUG|GGC| GU|AAA|G|C |GUCU|GUA| CAGAG|GGAG C|A|AGCGUU AUCC|GGAAU GAUUG|GGC| GU|AAA|G|C |GUCU|GUA| CAUAG|GGAG C|A|AGCGUU AUCC|GGGAU GAUUG|GGC| GU|AAA|G|C |GUCU|GUA| CAGGG|GAUU C|A|AGCGAU ACCU|CGUAU GAUUG|GGC| GU|AAA|G|C |GUCU|GUA| CAGGG|GAUU C|A|AGCGAU ACCU|GGUAU GAUUG|GGC| GU|AAA|G|G |GUCU|GUA| C+G+G|G++G C|A|AG+GUU AUCC|GGAAU +A+UG|GGC| GU|AAA|G|+ |GU++|GUA| ..$......$ ........$. .$.$.o.o.. .......... .......... .......... ___|~|____ ______|___ ______|~~~ ~~|_______ (~~~)_____ __|~~~|___ GGC|G|GUUU GUUAAG|UCA GAUGUG|AAA UC|CCCGGGC (UCA)ACCUG GG|AAC|UGC GGU|G|GCUU UUCAAG|UCC GCCGUC|AAA UC|CCAGGGC (UCA)ACCCU GG|ACA|GGC GGU|G|GUCC GAAAAG|UCU AAUGUC|AAA UC|CAUUGGC (UCA)ACCAA AG|GCA|GGC GGU|G|GUUU AAAAAG|UCU ACUGUC|AAA UA|UCAAGGC (UCA)ACCUU GG|ACA|GGC GGC|G|GUUU UACAAG|UUU AAUGUA|AAA GA|CUUAGGC (UCA)ACCAA AG|GAA|AGC GGC|G|GUUA CACAAG|UUU AAUGUA|AAA GA|CUUAGGC (UUA)ACCAA AG|GGU|UGC GGU|+|G+++ +++++G|U++ +++GU+|AAA ++|+++++GC (U+A)AC+++ ++|+++|+G+ ..$....... .......... .......... .......... .......... .......... ______|~~~ |_________ |~~~|_____ __________ ___|__|~~| ________|~ AUCUGA|-UA |CUGGCAAGC |UUG|AGUCU CGUAGAGGGG GGU|AG|AA| UUCCAGGU|G GGUGGA|-AA |CUACCAAGC |UGG|AGUAC GGUAGGGGCA GAG|GG|AA| UUUCCGGU|G AUUGGA|gUA |CUAUCGGAC |UAG|AGUGC GGAAGAGGUA GAG|GG|AA| UCCCUAGC|G GGUAGA|gUA |CUUUUAGAC |UAG|AGUGC GGUAGAGGUA GAG|GG|AA| UCCCUAGC|G AUUAAA|-AA |CUAUAAAAC |UAG|AGUUC GGAAGAGGUA GAG|GG|AA| UUCCUAAA|G AUUAAA|-AA |CUAUGUUAC |UAG|AGUUC GGAAGAAGUA GAG|GG|AA| UUCCUAAA|G +++++A|++A |CU++++++C |U+G|AGU++ +G+AG+GG+A +AG|GG|AA| +U++++GU|G .......... .......... .......... ......*... .......... .$....*?.. ~~|___(~~~ ~~~)___|~~ ~~~~|_____ ___|~~|__| ~~~~|_|~~| __(~~~~)__ UA|GCG(GUG AAA)UGC|GU AGAG|AUCUG GAG|GA|AU| ACCG|G|UG| GC(GAAG)GC GA|GCG(GUG AAA)UGC|AU UGAG|AUCGG AAA|GA|AC| ACCA|A|CG| GC(GAAA)GC UA|ACA(GUG AAA)UGU|GU AGAU|UUUAG GGA|GA|AC| ACCA|G|CG| GC(GAAG)GC UA|ACG(GUG AAA)UGU|GU AGAU|UUUAG GGA|GA|AC| ACCA|G|CG| GC(GAAG)GC GA|ACA(GUG AAA)UGU|GU AGAU|AUUAG GAG|GA|AC| ACCA|G|AG| GC(GAAG)GC GA|ACA(GUG AAA)UGU|GU AGAU|AUUAG GAG|GA|AC| ACCA|G|AG| GC(GAAA)GC +A|GCG(GUG AAA)UG+|+U +GA+|AU++G +A+|GA|AC| ACC+|+|++| GC(GAA+)GC ...$.*.... ......$... .....?.... .$........ .......... .......... |_|_______ __________ __|~~~|___ |_|~~|____ |~~~~|____ ___|~~~|_| |G|GCCCCCU GGACGA-AGA CU|GAC|GCU |C|AG|GUGC |GAAA|GCGU GGG|GAG|C| |A|CUCUGCU GGGCCG-ACA CU|GAC|ACU |G|AG|AGAC |GAAA|GCUA GGG|GAG|C| |G|CUCUACU GGGCCG-aGA CU|GAC|ACU |G|AG|AGAC |GAAA|GCUA CGG|GAG|C| |G|CUCUACU GGGCCG-uAA CU|GAC|ACU |G|AG|AGAC |GAAA|GCUA AAG|GAG|U| |G|CUCUACU GGGACG#aAA CU|GAC|GCC |G|AG|AGAC |GAAA|GCUA UGG|UAG|C| |G|CUCUACU AGGACG#aAA CU|GAC|GCU |G|AG|AGAC |GAAA|GCUA UGG|UAG|C| |+|CU+U+CU +G+C++-++A CU|GAC|ACU |+|AG|++AC |GAAA|GC+A +GG|+AG|C| .......... ...?...... .......$.* .......... .......... .$......$. ~~~|____(~ ~~~~~~~~)_ ___|~~~|_| _______|~~ ~~~~~~~~|_ _____|~~|_ AAA|CAGG(A UUAGAUAC)C CUG|GUA|G| UCCACGC|CG UAAACGAU|G UCGAC|UU|G AAA|UGGG(A UUAGAGAC)C CCA|GUA|G| UCCUAGC|CG UAAACGAU|G GAUAC|UA|G GAA|AAGG(A UUAGAUAC)C CUU|GUA|G| UCGUAGC|UG UAAACGAU|G GAAAC|UA|A GAA|AAGG(A UUAGAUAC)C CUU|GUA|A| UUUUAGC|UG UAAACGAU|G GAAAC|UA|A GAA|CAAG(A UUAGAUAC)C UUG|GUA|G| UCAUAGC|CG UAAACGAU|G GAAAC|UA|A GAA|CAAG(A UUAGAUAC)C UUG|GUA|G| UCAUAGC|UG UAnnCGAU|G GAAAC|UA|A +AA|++GG(A UUAGA+AC)C C++|GUA|G| UC+U+GC|+G UAAAC+AU|G GA+AC|UA|+ ......$... .......... $.......$. .$........ .......... .......... __________ _(~~~~~~~~ )_________ ___|~~~|__ (~~__)__|~ ~~~~|_____ GAGGUUGUGC C(-cuuga-- )GGCGUGGCU UCC|GGA|GC (UAAC)GC|G UUAA|GUCGA GUGCUGUGCG -(acucgacc )-CGUGCAGU GCU|GUA|GC (UAAC)GC|G UUAA|GUAUC GUGGGGG--- -(-cuaac-- )----CCCCU GCU|GUA|GC (UAAC)GC|G UUAA|GUUUC GUGCUGC--- -(-cgaau-- )----GCAGU GCU|GUA|GC (UAAC)GC|G UUAA|GUUUC GUGGGG---- -(-gauac-- )-----CUCU GCU|GUA|CG (UAAC)GC|G UUAA|GUUUC GUAGGGG--- -(--gaca-- )----CCUCU GCU|GUA|CG (UAAC)GC|G UUAA|GUUUC ++++UG++++ +(++++++++ )++++++A+U +++|++A|++ (UAAC)GC|G U+AA|GU+UC ....$..... .......... .......$.. .......... .......... .......... _|_|___|~| ___|~~~~~~ |____(~~~~ )____|~~~~ |___|~~~|_ __|~~|____ C|C|GCC|U| GGG|GAGUAC |GGCC(GCAA )GGUU|AAAA |CUC|AAA|U GA|AU|UGAC C|C|GCC|U| GGG|GAGUAC |GUUC(GCAA )GAAU|GAAA |CUC|AAA|G GA|AU|UGAC C|C|GCC|U| GGG|GAGUnU |GCUC(GCAA )GAGU|GAAA |CUC|AAA|G GA|AU|UGAC C|C|GCC|U| GGG|GAGUAU |GCUC(GCAA )GAGU|GAAA |CUC|AAA|G GA|AU|UGAC C|C|GCC|U| GGG|GAGUAC |GUUC(GCAA )GAAU|GAAA |CUC|AAA|G GA|AU|UGAC C|C|GCC|U| GGG|GAGUAC |GUUC(GCAA )GAAU|GAAA |CUC|AAA|G GA|AU|UGAC C|C|GCC|U| GGG|+AGUA+ |G+UC(GCAA )G++U|GAAA |CUC|AAA|G GA|AU|UGAC .......... .......... .......... .......... .......... .......... _________| ~~~~|_____ _|~|______ _____|~~~~ |____(~~~~ ~~~~)____| GGGGGCCCG| CACA|AGCGG U|G|GAGCAU GUGGU|UUAA |UUCG(AUGC AACG)CGAA| GGGGGCCCG| CACA|AGCGG U|G|GAGCAU GUGGU|UUAA |UUCG(AUGC AAGG)CGAA| GGGAAn-nn| nACA|AGCGG U|G|GAUUAU GUGGU|UUAA |UUCG(AUGC AACG)CGAA| GGGAGUCUA| CACA|AGAGG U|G|GAUUAU GUGGU|UUAA |UUCG(AUGC AACA)CGAA| GGGAACCUG| CACA|AUCAG U|G|GAUCAU GUGGU|UUAA |UCUG(AUGC AACA)CGAA| GGGAACCUG| CACA|AUCGG U|G|GAUCAU GUGGU|UUAA |UCUG(AUGC AACA)CGAA| GGGG+CCCG| CACA|A+CG+ U|G|GA++AU GUGGU|UUAA |UUCG(AUGC AA++)CGAA| ...$.$.$$. .......$$. .......... .......... ..?*...... .......... ~~~~~~~~|_ ______|~~~ ~~|_______ _|~~|_____ __(~~~~)__ _____|~|__ GAACCUUA|C CUGGUC|UUG AC|AUCCACG G|AA|GUUUU CA(GAGA)UG AGAAU|G|UG GAACCUUA|C CAGGGC|UUG AC|AUGCCGC G|AA|UCCUC UU(GAAA)GA GAGGG|G|UG GAACCUUA|C CAGGGU|UUG AC|AUGUCCA G|AA|UCCUC CA(GAAA)UG GGGGA|G|ug GAACCUUA|C CAGGGU|UUG AC|AUGCUCA G|AA|UUUUU CA(GAAA)UG GAAAA|G|ug GAACCUUA|C CAGGUU|UUG AC|AUGCCCA G|AA|UAUCU UA(GAAA)UA AGAUA|G|ug GAACCUUA|C CAGGUU|UUG AC|AUACCCA G|AA|UGCCC UA(GAAA)UA GGGUA|G|ug GAACCUUA|C CA+G++|UUG AC|A++++++ +|++|+++++ ++(+A+A)++ +++++|+|++ .......... .......... .......... .......... .......... .......... ________(~ ~~~~)_____ _____|____ _____|___| _|____|~~_ _|________ CC------(U UCG-)----- -GGAA|CCGU GAGAC|AGG| U|GCUG|CAU G|GCUGUCGU CC------(C UCG-)----- -GGAA|CGCG GACAC|AGG| U|GGUG|CAU G|GCUGUCGU uuugaaag(u ucuu)Cuuuc auaaa|CUGG AACAC|AGG| U|GGUG|CAU G|GCUGUCGU cca-----(g aaa-)----- uggaa|CUGG GACAC|AGG| U|GGUG|CAU G|GCUGUCGU uuaauaua(c uaag)Ucuau uaaaa|CUGG GACAC|AGG| U|GGUG|CAU G|GCUGUCGU uuuauaga(u uaag)Ucuau aaaaa|CUGG GCUAC|AGG| U|GGUG|CAU G|GCUGUCGU ++++++++(+ ++++)+++++ +++++|++++ +++AC|AGG| U|GGUG|CAU G|GCUGUCGU .......... .......... .......... .......... .......... .......... |~~|______ |___(~~~~) ___|~~|___ _(~~~~~~)_ ___|~~|___ ___|~~~~~| |CA|GCUCGU |GUU(GUGA) AAU|GU|UGG G(UUAAGU)C CCG|CA|ACG AGC|GCAAC| |CA|GCUCGU |GCC(GUAA) GGU|GU|UGG G(UUAAGU)C UCG|CA|ACG AGC|GCAAC| |CA|GCUCGU |GCG(UUGA) CGU|GU|ACG G(UUAAGU)C CUG|CA|ACG AGC|GCAAC| |CA|GCUCGU |GCG(UUGA) CGU|GU|AUG G(UUAAGU)C CUG|CA|ACG AGC|GCAAC| |CA|GCUCGU |GCG(UUGA) CGU|GU|AUG G(UUAAGU)C CUG|CA|ACG AGC|GCAAC| |CA|GCUCGU |GCG(UUGA) CGU|GU|ACG G(UUAAGU)C CUU|CA|ACG AGC|GCAAC| |CA|GCUCGU |G++(+U+A) ++U|GU|++G G(UUAAGU)C +++|+A|ACG AGC|G+AAC| .......... .......... .......... .......... .......... .......... _____|____ ___|~~|___ |~~|___(~~ ~~~~~~~)__ _|___|~~~| _______|~~ CCUUA|UCCU UUG|UU|GCC |AG|CGG(-u ccgg---)CC G|GGA|ACU| CAAAGGA|GA CCUCG|UGUU UAG|UU|GCC |a-|---(cu augaguu)-- u|GGA|ACC| CUGAACA|GA CCUCG|UCUU UAG|UU|--- |--|---(-a au-----)-- -|---|ACU| CUAAAGA|GA CCUCG|UCUU UAG|UU|--- |--|---(-a aua----)-- -|---|ACU| CUAAAGA|GA CCUCG|UCUU UAG|UU|--- |--|---(-a uuu----)-- -|---|ACU| CUAAAGA|GA CCUCG|UCUU UAG|UU|--- |--|---(-a uuu----)-- -|---|ACU| CUAAAGA|GA CCU++|U+++ +A+|U+|+++ |++|++-(++ +++++++)-+ +|+++|+++| +U++++A|+A .......... .......... .......... .......... .......... .......... ~~~|_____( ~~~~~)____ _|~~~~~~~| _____|~~~| _________| ~~~|__|___ CUG|CCAGU( GAUAA)ACUG G|AGGAAGG| UGGGG|AUG| ACGUCAAGU| CAU|CA|UGG CCG|CCGGU( GUUAA)GCCG G|AGGAAGG| AGAGG|AUG| AGGCCAAGU| CAU|CA|UGC CUG|CUCGC( GCAA-)GCUU G|AGGAAGG| UGAGG|AUG| ACGUCAAGU| CAG|CA|UGC CUG|CCAGU( GUAA-)ACUG G|AGGAAGG| UGAGG|AUG| ACGUCAAGU| CAG|CA|UGC CUG|CUUAC( GUAA-)GUUU G|AGGAAGG| UGGGG|AUU| ACGUCAAGU| CAU|CA|UGC CUG|CAAAC( GUAA-)GUUU G|AGGAAGG| UGGGG|AUU| ACGUCAAGU| CAU|CA|UGC C+G|C++++( +++++)+++G G|AGGAAGG| +++GG|AUG| A+GUCAAGU| CA+|CA|UGC .......... .........? .......... ........o. .......... .......... ____|~~~|_ ______|~~~ |_________ ___|~~~~|_ ______|~~~ ~~|___|~~| CCCU|UAC|G ACCAGG|GCU |ACACACGUG CUA|CAAU|G GCGCAU|ACA AA|GAG|AA| CCCU|UAU|G CCCUGG|GCG |ACACACGUG CUA|CAAU|G GGCGGG|ACA AA|GGG|UC| CCCU|UAC|A CCCUGG|GCC |ACACACGUA AUA|CAAU|G GUUGGG|ACA AU|CAG|AA| CCCU|UAC|A CCCUGG|GCU |ACACACGUA AUA|CAAU|G GUUGAU|ACA AU|CAG|AA| CCCU|UAU|A ACCUGG|GCU |ACACACGUG AUA|CAAU|G GUUGGG|ACA AU|GAG|AA| CCCU|UAU|A ACCUGG|GCU |ACACACGUG AUA|CAAU|G GUUGGG|ACA AU|GAG|AA| CCCU|UA+|+ ++CUGG|GC+ |ACACACGU+ +UA|CA++|G G+++++|ACA A+|+++|++| .......... .......... .......... .......... .......... .......... __|~~~|___ (~~~~)___| ~~~~|__|~~ ~~|___|~~~ ~~|_______ |~~~~~~|__ GC|GAC|CUC (GCGA)GAG| C-AA|GC|GG AC|CUC|AUA AA|GUGCGUC |GUAGUC|CG GC|GAU|CUC (GCGA)GGG| U-GA|GC|UA AC|UCC|AAA AA|CCCGUCC |UCAGUU|CG GC|UAA|CCC (GCGA)GGG| CAAU|GC|GA AU|CUG|CUA AA|CUCAACC |UCAGUU|CG GC|AAC|CCU (GCGA)AGG| C-UA|GC|AA AU|CUG|CUA AA|AUCAGCC |UCAGUU|CG GC|AAC|UCC (GCGA)GGA| C-UA|GC|GA AU|CUA|CA- AA|CCCAGCC |CCAGUU|CG GC|AAC|UCC (GCGA)GGA| U-UA|GC|GA AU|CUA|CA- AA|CCCAGCC |CCAGUU|CG GC|+A+|+++ (G++A)+++| +-++|GC|+A A+|+++|++A AA|++++++C |U+AGUU|C+ .......... .......... .......... .........o .......... .o........ __________ (~~~~~~~~) __________ __|~~~~~|_ _____|~~~~ |________( GAUUGGAGUC (UGCAACUC) GACUCCAUGA AG|UCGGA|A UCGCU|AGUA |AUCGUGGA( GAUUGCAGGC (UGCAACUC) GCCUGCAUGA AG|CAGGA|A UCGCU|AGUA |AUCGCCGG( GAUUGCAGGC (UGCAACUC) GCCUGCAUGA AG|CCGGA|A UCGCU|AGUA |AUCGCCAG( GAUUGCAGGC (UGCAACUC) GCCUGCAUGA AG|CCGGA|A UCUCU|AGUA |AUCGCCGG( GAUUGCAGGC (UGCAACUC) GCCUGCAUGA AG|AUGGA|A UUGAU|AGUA |AUCGCCAG( GAUUGCAGGC (UGCAACUC) GCCUGCAUGA AG|GUGGA|- UCGAU|AGUA |AUCGCCAG( +AUUG+AGGC (UG+AACUC) GCCU+CAUGA AG|++GGA|A UCG+U|AGUA |AUCGC+++( .......... .......... .......... .........? .$$....... .......... ~~~~~~~~)_ _______|~~ ~~~~~~~~~| __________ ___|~~|_|~ |__|~|__|~ UCAGA-AU)G CCACGGU|GA AUACGUUCC| CGGGCCUUGU ACA|CA|C|C |GC|C|CG|U UCAGCcAU)A CGGCGGC|GA AUCCGUUCC| CGGGCCUUGU ACA|CA|C|C |GC|C|CG|U UCAGCUAU)A UGGCGGU|GA AUACGUUCU| CGGGUUUUGU ACA|CA|C|n |nn|n|nn|n UCAGCUAU)A CGGCGGU|GA AUACGUUCC| UAGACUUUGU ACA|CA|C|n |nn|n|nn|n UCAGCUAU)A UGGCGGU|GA AUAUGUCAC| UAGGUUUUGU ACA|Cn|n|n |nn|n|nn|n UCAGCUAU)A UGGCGGU|GA AUACGUAAC| CAGGUUUUGU ACA|CA|C|C |GC|C|CG|U UCAGC+A+)A ++GCGGU|GA AU++GUUC+| CGGG+CUUGU ACA|CA|C|C |GC|C|CG|U .......... .......... ......oo.. $$.$.$.... .......... .......... |_|~|_____ __________ _______|~~ ~~|_______ ____|~~~|_ _~~~~~~~__ |C|A|CACCA UGGGAGUGGG UUGCAAA|AG AA|GUAGGUA GCUU|-AA|C C(uucg)-GG |C|A|CACUA UAGGAGCUGG CCAGGUU|UG AA|GUCAUUA CCCU|uAA|C C(guaa)-GG |n|n|nnnnn nnnnnnnnnn nnnnnnn|nn nn|nnnnnnn nnnn|-nn|n n(nnnn)nnn |n|n|nnnnn nnnnnnnnnn nnnnnnn|nn nn|nnnnnnn nnnn|-nn|n n(nnnn)nnn |n|n|nnnnn nnnnnnnnnn nnnnnnn|nn nn|nnnnnnn nnnn|-nn|n n(nnnn)nnn |C|A|CACUC CGAAAGGAAA GGGGGUC|UA AG|UACCUU- UAUU|-AA|C C(gaaa)-GG |C|A|CAC+A ++++A+++++ +++++++|++ AA|++++U++ ++++|+AA|C C(++++)++G .........* .......... .......... .o........ .......... .......... |~|_______ ___|~~~~|_ __________ __________ _|~~|_|~|_ _|~~|__|~~ |A|GGGCGCU UAC|C-AC|U UUGUGAUUCA UGACUGGGGU G|AA|G|U|C G|UA|AC|AA |A|GGGGGAU GCC|U-AA|G GCUAGGCUUG CGACUGGAGU G|AA|G|U|C G|UA|AC|AA |n|nnnnnnn nnn|n-nn|n nnnnnnnnnn nnnnnnnnnn n|nn|n|n|n n|nn|nn|nn |n|nnnnnnn nnn|n-nn|n nnnnnnnnnn nnnnnnnnnn n|nn|n|n|n n|nn|nn|nn |n|nnnnnnn nnn|n-nn|n nnnnnnnnnn nnnnnnnnnn n|nn|n|n|n n|nn|nn|nn |A|GGUAAUG GUA|CaAA|G CCUCUAUCUC UGAUUGGAGU G|AA|G|U|C G|UA|AC|AA |+|+++++++ +++|+-A+|+ ++++++++++ U+A+++++GU G|AA|G|U|C G|UA|AC|AA .......... .......... .......... .......... .......... .......... |_|~|_____ _____(~~~~ )_________ _|~~~~~~~~ ~~~~~| |G|G|UAACC GUAGG(GGAA )CCUGCGGUU G|GAUCACCU CCUUA| |G|G|UAGCC GUACU(GGAA )GGUGCGGCU G|GAUCACCU CCUUU| |n|n|nnnnn nnnnn(nnnn )nnnnnnnnn n|nnnnnnnn nnnnn| |n|n|nnnnn nnnnn(nnnn )nnnnnnnnn n|nnnnnnnn nnnnn| |n|n|nnnnn nnnnn(nnnn )nnnnnnnnn n|nnnnnnnn nnnnn| |G|G|UAAUG GUUCC(AGAA )GGAGCUGUU G|GAUAACAU ACAAA| |G|G|UA+++ GUACU(GGAA )GGUG++++U G|GA++ACCU CCUU+| .......... ..$.*.o... ...$...... ........o. o.oo..