10        20        30        40        50        60        70        80        90       100       110       120                    
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                                                  CR1                P2a.1                                           
structure                                                                     ----------           ---------                                         
Homo sapiens                GGGUUGCGGAGGGUGGGCCUGGGAG--GGGUGGUGGCCA-UUUUUU--GUCUAACCCUAACUGAGAAG--GGCG-UAGGC-GCCGU--GCUUU-UGCUCCC------------------- 
Tupaia glis belangeri       GGG-AGUGGAGGGUGGGCCCGGGAC--GGGCGCGGACCC-GGUA----AUCUAACCCUGACUCACAAGA-GGCG-UAGGC-GCCGU--GCUUU-UGCUCCC------------------- 
Oryctolagus cuniculus       GGGCUGAGGAGGGUGGGCUCGGGAG--GGGCCC-GGUCA-UUUCUC--AUCUAACCCUAACUGAGCAG--GGCG-UAGGC-GCCGC--GCUUU-UGUUUCCC------------------ 
Cavia porcellus             --------------------GGGAG--GGGUGGUGGUCU-UCCCU---GUCUAACCCUAAG-GUGAAGAGGACG-UGGGU-GCCGU--GUUUU-UCGCUCC------------------- 
Chinchilla brevicaudata     GGGUUGAGAAUGGUGGGCC-GGGAG--GGGAGGUGGGCA-UGUUUU--GUCUAACCCUAACUAGGAGGAGGACG-UAGGC-GCCGU--GCUUU-UGUUCCC------------------- 
Geomys breviceps            -----------GGCGUGCCUGGGAG--GGGGGGCUGGUC-CCACUC--UUCUAACCCUAAGGGUGUC---GGCUGUAGGC-GCCGU--GCUUUUUACUUCCC------------------ 
Microtus ochrogaster        -------------------------------GA-CGCGC-GCCUC---UUCUAACCCUAAAAACUG-G--AGCUGUAGGU-GUUGC--UCUUU--CAGCGU------------------- 
Cricetulus griseus          ------------------------------------------------GUCUAACCCUGAAUUCUGAG--AGCUGUGGGU-ACUGU--GCUUU--CGUCUC------------------- 
Mus musculus                ------------------------------------------------ACCUAACCCUGAUUUUCAUU--AGCUGUGGGU-UCUGG--UCUUU-UGUUCUC------------------- 
Mus spretus                 ------------------------------------------------ACCUAACCCUGAUUUUCAUU--AGCUGUGGGU-UCUGG--UCUUU-UGUUCUU------------------- 
Mus musculus castaneus      ------------------------------------------------ACCUAACCCUGAUUUUCAUU--AGCUGUGGGU-UCUGG--UCUUU-UGUUCUC------------------- 
Rattus norvegicus           ------------------------------------------------GUCUAACCCUAUUGUU-AU---AGCUGUGGGU-UCUGU--UCUUU-UGUUCUC------------------- 
Mustela putorius furo       GGGUUGCGGAGGGUGGGCUCGGGAG--GGGUGGCGGUCA-UUUUCU--GUCUAACCCUAACUGAAACG--GGCG-UAGGC-GCUGC--GCUUU-UGUUCCC------------------- 
Procyon lotor               GGGUUGCGGAGGGUGGGCCUGGGAG--GGGUGGCGGUCG-UUUUAU--GUCUAACCCUAACUGAGAAG--GGCA-UAGGC-GCUGC--GCUUU-UGUUCCC------------------- 
Felis catus                 GGGUUGUGGAGGGUGGGCCUGGGAG--GGGAAGCGGUCA-GUUUUU--GUCUAACCCUAACUGAGAAG--GGCG-UAGGC-GCCGC--GCUUU-UGUUUCC------------------- 
Bos taurus                  GGGUUGCGGAGGGUGGGCCCCGGGU--UGGUGGCAGCCA-UUUCUC--AUCUAACCCUAAUUGAGACA--GGCG-UAGGC-GCUGU--GCUUU-UGGUUAC------------------- 
Sus scrofa                  GGGUUGCGGAGGGUGGGCCCAGGAG--CGGUGGCGGCCA-UUUUUUAAGUCUAACCCUAACUGAAAGA--GGCG-UAGGC-GCUGC--GCUUU-UGCUUCA------------------- 
Suncus murinus              -------------GGGUUGCGGGAGCUGCGAGC-GGCCG-UCUC----GUCUAACCCUAAA-GAGAAA--GGCG-UAGGU-GCUUG--GCCUU-GGCGACU------------------- 
Equus caballus              GGGUGGGGGAGAGUGGGUCUGGGCG--GGGCGGCGGUCA-CGUUUU--GUCUAACCCUAACUGAGCUG--GGCG-GAGGC-GCCGC--GCUUU-UGCUCCC------------------- 
Dasypus novemcinctus        GGGUUGCGGAGGGAGGGCCCGGGAG--GGGUGAGCGUCC-AUUAUC--GUCUAACCCUAACUGAGAUG--GGCG-UAGGC-GCCGC--GCUUU-UGCUUCC------------------- 
Dasyurus hallucatus         ---GUGCGGACGGGCUGCGUGGGCGGGUCGGUCCGUCCU-GGCAC---AUCUAACCCUAAAUGCGCGC--UGGU-UGAAG-UGGCU--UCUCC-UGGGCGAU------------------ 
Elephas maximus             GGGUUGAGGAGGGUACGCCCGGGA---GGGCGGUGGUCU-GUUCUG--UUCUAACCCUAACUGAUAAG--GGCG-UAGGC-GCCGU--GCUUU-UGUUCCC------------------- 
Trichechus manatus          GGGUUGAGGAUGGCGCCCCCGGGUC--GGGCAGUGGUCU-UUUUUG--UUCUAACCCUAACUGGCAAG--GGCG-UAGGU-GCUGU--GCUUU-UGUUCCC------------------- 
Gallus gallus               ----------------GCGU-GGCGGGUGG--AAGGCUC-CGCUGU--GCCUAACCCUAAUCGGGGGAAUUGAUGGUGCUGUCGCCGCGCUCC-CUCCGCC------------------- 
Anodorhynchus hyacinthinus  ----------------GCGU-GGCGGAUGG-GGAGGCUC-CAGUCU--CACUAACCCUAAU---------------GGCUGCCGCCGUGCUCC-CCGCACC------------------- 
Chelydra serpentina         ----------------GCUGCGGCGGCAGGUGGGGGCUC--AGUCU--UUCUAACCCUAAGCG--AAAUGUGACC-------------CCUCC-CCGCUGCAGC---------------- 
Bombina japonica            -----------GUUUAAUUAGAGGGAUUGGAAG-GUUCC-GCUUA---UGCUAACCCUAAUAUUGGGGGUCUGUUGAAAA--------CCUCU-UUAAGAUA------------------ 
Xenopus laevis              GAAUCAGCGUUUAAAGCUCAAUGUGGAC-GGAGGUCUCU-GUUU----CGCUAACCCUAAUACACUGGCUUCAGGGCGAUG-------GCUCU-UCGCGGCGG----------------- 
Ceratophrys ornata          -----------------ACAGUGGGAAUAGGAG-GGAGU-CUAUAU--UUCUAACCCUAAUAUACCCGGU--UCAGG-----------GCUCU-UAUGUGG------------------- 
Pyxicephalus adspersus      -----------------CCAGCGGUAAUAGGAG-AGU-U-CUAUCC--UUCUAACCCUAAUGCACAGACCCCUCGCU-----------GCUCU-UCA----------------------- 
Dermophis mexicanus         ---------------CUCUCUCCGGAGAGGGGCGGUUUC-UCUGUC--UUCUAACCCUAAUGCGGUGCUUCGGCAGAA----------GCUCUCCACUGCGUA----------------- 
Herpele squalostoma         ---------------UUCUCUCUGGAGCGGGGCGAUUUC-UCUUCC--UUCUAACCCUAAUGCGGUGCUUAGGCGACA----------GUUCU---CCGGGUG----------------- 
Typhlonectes natans         ---------------GUCAUUCCGGAGAGGGGCGUUUUC-UUCUUU--CUCUAACCCUAAUGUAUUGCUUGGGCAGCA----------GCUCU---CUCGGUA----------------- 
Oryzias latipes             -------------------------------GCGGGGUG--UUCU---ACCUAACCCUAAUUAGAGGCU-------------------GCCUCGUGUACUUAA----------------- 
Gasterosteus aculeatus      -------------------------------ACGGAGUG--UCUC---UUCUAACCCUAAAUACGGAGG-------------------CCCUCCUGUACUCAA----------------- 
Takifugu rubripes           -------------------------------ACGGAGUG--UCUC---UUCUAACCCUAAAUUAUCUCG-------------------GCUCCCUGUACUCGG----------------- 
Tetraodon nigroviridis      -------------------------------GCGGAGUG--UCUC---UUCUAACCCUAAGUUAAACUA-------------------GCUCCCUGUACUCGG----------------- 
Danio rerio                 -------------------------------GCAGAGUA--CUUU---CUCUAACCCUAACGCUUCUUU-------------------GCUUCCUGUACGGCU----------------- 
Rhizoprionodon porosus      ---------------CUCACAUUGCUGCGGGGUGGAGGC-GUUUUU--AACUAACCCUAAUGCAGAGUAAGUGGCUGG----------GCCUUCCUCACACUGCCUCCCGCUG------- 
Mustelus canis              ---------------CUCACAUUGCUGCGGGGUGGAGGC-GAUUUU--AACUAACCCUAAUGCAGAGUAAGUGGCUGG----------GCCUUCCUCACACUGCCUCCCGCUG------- 
Dasyatis sabina             ----------------GUGUCCAGCUGCGGGG--GAGACAGUGUCGCUCUCUAACCCUAAUGUGGGGGCAA-CGCGGG----------CCCUU-UGUUUAAAG--UCCCGCUGU------ 
Rhinoptera bonasus          ----------------GCGUCCAGCUGCGGGG---AGAAAGUGUCGUUCUCUAACCCUAAUGCGAGGGCAA-UGCGGG----------CCCUU-UGUUUAAAG--UCCCGUUGUCGCGCG 
structure                                    ((((((((((((((((((((((           CUAACCCU                              (((((|-------------------------- 
                                                       P1                     Template                               P2a                J2a|2b       

                                    130       140       150       160       170       180       190       200       210       220       230       240           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                        CR2                                   P2a.1                                                  
structure                              --------------  ---------- -----                    ----------                                                
Homo sapiens                ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUG-CCGCC-UUCCACCGUUCAUUCU----------------------------- 
Tupaia glis belangeri       ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGUUCG--GA-AAAGCCCUGUGGCCUA-UCGCC-AUCCACCAUCCUUUCU----------------------------- 
Oryctolagus cuniculus       ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGCGUG-GGA-AAAGCCUUG--GCCUA-CCGCC-GUCCACCGUUCAUUUC----------------------------- 
Cavia porcellus             ---------CGCACGCUGUUUUUCU--CGCUGACUUU-CAGCGUGCA--GA-AAAGCCUUG--GCCUA-CCGUC-GGUUAUUGUCUAAUUA----------------------------- 
Chinchilla brevicaudata     ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGUGCG--GA-AAAGCCUUG--GCCUG-CCGUC-GACCACUGUCUAAUUA----------------------------- 
Geomys breviceps            ---------CGCGCGCUGUUUUUCU--GGCUGGCUUU-CAGCGAGCG-GAA-AAAGCUUUG--GUCUA-CAGGCCACUCACUUUGUAUCCC----------------------------- 
Microtus ochrogaster        ---------CGCCCGCUGUUUUUCU--CGCUGGCUUU-CAGCGGGCC--AG-AAAGUUCAG--ACCUCUCAGCA-GAUCGUCGCGUCGUUC----------------------------- 
Cricetulus griseus          ---------CGCCCGCUGUUUUUCU--CGCUGACUUC-CAGCGGGCG--GG-AAAGUCCAG--ACCUG-CAGCG-GGCCAUCGCGCGUUUU----------------------------- 
Mus musculus                ---------CGCCCGCUGUUUUUCU--CGCUGACUUC-CAGCGGGCC-AGG-AAAGUCCAG--ACCUG-CAGCG-GGCCACCGCGCGUUCC----------------------------- 
Mus spretus                 ---------CGCCCGCUGUUUUUCU--CGCUGACUUC-CAGCGGACC-AGU-AAAGUCCAG--ACCUG-CAGCG-GGCCACCGCGCGUUCC----------------------------- 
Mus musculus castaneus      ---------CGCCCGCUGUUUUUCU--CGCUGACUUC-CAGCGGGCC-AGG-AAAGUCCAG--ACCUG-CAGCG-GGCCACCGCGCGUUCC----------------------------- 
Rattus norvegicus           ---------CGCCCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCC-UGG-AAAGUUCAG--ACCUG-CAGCG-GGUCACCGCGCAUUCU----------------------------- 
Mustela putorius furo       ---------CGCACGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUUG--GCCUA-CUGCC-ACACACCAUCCAGUUU----------------------------- 
Procyon lotor               ---------CGCACGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUA-CUGCC-AUCCACCAUCCAGUUU----------------------------- 
Felis catus                 ---------CGCACGCUGUUUUUUU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUA-CCGCC-GUCCACCGUACAGUUU----------------------------- 
Bos taurus                  ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUA-CCGCC-AUCCACCAUCCAGUCU----------------------------- 
Sus scrofa                  ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUA-CCGCC-AUCCACCAUCCAGUCU----------------------------- 
Suncus murinus              ---------CGCCCGCUGUUUUU-U--GGCUGGCUUU-CAGCGGGUG--AA-GAGGCCCAAG-ACCUA-CCGCC-ACCCACCGUCUAGUGUCUUAAGGGCACAAAGUCCUGCCCGCCACC 
Equus caballus              ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GUCUA-CCGCC-ACUUACCAUCCAGUCU----------------------------- 
Dasypus novemcinctus        ---------CGCGCGCUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--GA-AAAGCCUCG--GCCUA-CUGCC-GUCUACUGUCGUAUCU----------------------------- 
Dasyurus hallucatus         ---------CGCUCGCUGUUUUUGU--GGCUGGCUUU-CAGCGGGCU-GGA-GGAGCCGGG--AGCGG--AGGCGGAGGACCGAG----------------------------------- 
Elephas maximus             ---------CGCGCGUUGUUUUUCU--CGCUGACUUU-CAGCGGGCG-GGA-AAAGCCUCG--GUCUA-CCGCC-GUCUACCG-AUAGCCU----------------------------- 
Trichechus manatus          ---------CGCGCGUUGUUUUUCU--CGCUGACUUU-CAGCGGGCG-GGA-AAAGCCCUG--GCCUA-CCGCC-GUCUACCG-AUAGUUU----------------------------- 
Gallus gallus               ---------CGCCCGCUGUUUUACU--CGCUGACUUU-CAGCGGGCG-AGA-GGAGCCGCCCCGGGGGGGAGGCGGGCGGCGGGAGGGGGCCGGGGCGCCGCGGCGGUGGGGGUCGGGGG 
Anodorhynchus hyacinthinus  ---------CGUCCGCUGUUUUAUU--CGCUGACUUU-CAGCGGACG-GGG-GGAGCCGCCUGGGGGGGA-------------------------------------------------- 
Chelydra serpentina         ---------CGUCCGCUGUUUUACU--CGCUGACUUU-CAGCGGACG-GGG-GGAGCGGGU----------------------------------------------------------- 
Bombina japonica            ---------UGCGUGUUGUUUUAUU--GGCUGACUUU-CAGCGCGCA-UUG-AGAGGAGUU----------------------------------------------------------- 
Xenopus laevis              ---------UGCCUGUUGUUUUACU--UGCUGACUUU-CAGCGGGCA-CGG-AGAGCAAGC----------------------------------------------------------- 
Ceratophrys ornata          ---------CGCUCGUUGUUUUGCC--GGUUGCCUUU-CAGCGGGCG--AA-AGAGCUCAG----------------------------------------------------------- 
Pyxicephalus adspersus      ---------UGCUCGUUGUUUUUCU--CGCUGACUUU-CAGCGGGCG--AA-AGAGCAAUG----------------------------------------------------------- 
Dermophis mexicanus         ---------CGCUCACUGUUUUUCU--AGCUAACUUU-CAGUGAGCA-GGG-AGAGCGAAGUC--------------------------------------------------------- 
Herpele squalostoma         ---------CGCUCGCUGUUUUUCU--GGCUAACUUU-CAGCGAGCG-GAG-AGAGCGAAGCC--------------------------------------------------------- 
Typhlonectes natans         ---------UGCUCGCUGUUUUGCU--GGCUAACUUU-CAGCGAGCA--G--AGGGCGAAGUC--------------------------------------------------------- 
Oryzias latipes             ---------CGUAUGCUGUUUUGUUGUUUCUGGCUUU-CAGCAGAC-UACAUGAGGCGUUG-GGCG------UGAAGCUUGAAAAUAUCCGUA--------------------------- 
Gasterosteus aculeatus      ---------CGUUUGCUGUUUU-UU---UCUGGCUUUUCAGUAAAC-UACGGGAGGGGCUGACGCGACGCUGGGAACGUUUCCGAACGACAAC--------------------------- 
Takifugu rubripes           ---------CGUUUGCUGUUUU--UG--UCUGGCUUU-CAGGAAAC-UACAGGGAGUCUUG-GACG------UCUCGGUUCACGGAU--------------------------------- 
Tetraodon nigroviridis      ---------CGUUUGCUGUUUU-UUG--UCUGGCUUU-CAGGAAAC-UACAGGGAGUCUUG-AGAG------UCUCGGUUCACGGAC--------------------------------- 
Danio rerio                 ---------UGUAUGCUGUUUUGUC---UUAAGCUUU-CAGCAUAU-UACAUGAAGCUUUC-CGC-----------GGUUUCGAUACUU------------------------------- 
Rhizoprionodon porosus      ---CGUGAAACCUCGCUGUUUUCUU--GGCUAACUUU-CAGCGAGGUGAGGCAAGGCGGCAAA----------------------------------------------------AAAAA 
Mustelus canis              ---CGCGAAACCUCGCUGUUUUCUU--GGCUAACUUU-CAGCGAGGUGAGGAGAGGCGGCAAA-------------------------------------------------AAAAAAAG 
Dasyatis sabina             ---CGGGAGCCCUCGCUGUUUUCUU--GGCUAACUUU-CAGCGAUGG-CGA-AAGGGCCCAGC-----------------------------------------------------AAAG 
Rhinoptera bonasus          AAGCGGGAGCCCUCGCUGUUUUCUU--GGCUAACUUU-CAGCGAUGG-UGA-AAGGGCCUAGC-----------------------------------------------------AAAG 
structure                   --------|(((((((((          ((((((((( )))))))))     ))))) |----------------------------------------------------------||- 
                                        P2b                 P3       P2b         P2a                                                          J2a|3  

                                    250       260       270       280       290       300       310       320       330       340       350       360           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                                         CR3                                                                         
structure                                                           --------------                                                                   
Homo sapiens                ---------------------AGAGCAAA----CA-----AAAAAUGUC--AGC-UGC---UGG-CC-CGUUCGCCCCUCCC-----GGGGA------------CCUGCGGCGGGUC--- 
Tupaia glis belangeri       ---------------------GGAACAAACAGACAAAAAAAAAAAUGUC--AGC-UGC---UGG-UC-CGUUCGCUCCUCCC-----GGG-C------------CCUGCGGUGGCCGCCA 
Oryctolagus cuniculus       ---------------------GCAGUAAA----CA-----AAAAAUGUC--AGC-CGC---UGG-CC-GGUUCGCCCUUCCC-----GGGGA------------CCUGCGGUGGCUC--- 
Cavia porcellus             ---------------------GAAGCAAA----CA-----AAAAAUGUC--AGC--G----UGG-CC-GGGCCGCCCCUCCC-----GGAUA------------CCUGCGGCGGCUC--- 
Chinchilla brevicaudata     ---------------------AAAGCAAA----CA-----AAAAAUGUC--AGC--G----UGG-CC-GGUCCGCCCCUCCC-----GGGUA------------CCUGCGGCAGCUC--- 
Geomys breviceps            ---------------------GAAACCAAAUU-GAAAAAAAAAAAUGCC--AGC-UCC---GGCCGGU---CCACCCCUCCC-----GGGGU------------CCUGCGGCCCGGCC-- 
Microtus ochrogaster        ---------------------UCAACCA-----CA-----AAAAAUGCC--AGCGCAAA--GCGCGUC---A---GCCU--------AGAAC------------CUUGCGGCCCCG---- 
Cricetulus griseus          ---------------------CCA-CCA-----CAA----AAAAAUGUC--AGCGCUGG--GCUC-AU---GU--GCCU--------GGAGC------------CUUGCGGCC------- 
Mus musculus                ---------------------CGAGCCU-----CAAAA--ACAAACGUC--AGCGCAGGA-GCUCCAG---GUUCGCCG--------GGAGC------------UCCGCGGCGCCG---- 
Mus spretus                 ---------------------CGAGCCU-----CAAAA--ACAAACGUC--AGCGCAGGA-GCUUCAG---GUUCGCCG--------GGAGC------------UCCGCGGCGUCG---- 
Mus musculus castaneus      ---------------------CGAGCCU-----CAAAA--ACAAACGUC--AGCGCAGGA-GCUCCAG---GUUCGCCG--------GGAGC------------UCCGCGGCGCCG---- 
Rattus norvegicus           ---------------------GGAACCU-----CA-----AAAAAUGUC--AGCGUAGGA-GCUC-UG---GU--GCC---------AGAGC------------UCCGCGGCGCUG---- 
Mustela putorius furo       ---------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-GGC---UGG-CC-UGCUCGCCCCUCCC-----GGGAG------------CCUGCGGCGACUC--- 
Procyon lotor               ---------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-CGC---CGG-CC-UGCUCGCCCCUCCC-----GGGAU------------CCUGCGGUGGCUC--- 
Felis catus                 ---------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-UGC---UGA-CU-UGCUCGCCCCUCCC-----AGGAC------------CCUGCGGUGGCUC--- 
Bos taurus                  ---------------------GCAACAAA----CA-----AAAAAUGUC--AGC-CGC---UGG-CU-CGCUCACCUCUCCC-----GGGAA------------CCUGCGGUGGUCC--- 
Sus scrofa                  ---------------------GAAACAAA----CA-----AAAAAUGUC--AGC-CUC---UGG-CU-CGCUCACUGCUCCC-----GGGAA------------CCUGCGGUGGUUC--- 
Suncus murinus              CUUCGA---------------GGAGCGAAA---CCC----AAAAAAGUC--AGC-CCC---UGGCCGCCUCUCGC-CCUCUC-----GC-AA------------CCCGCCU--------- 
Equus caballus              ---------------------GGAGUAAA----CA-----AAAAAUGUC--AGC-CGC---UGG-CU-CGCUCGCCCCUCCC-----GGGAC------------CCUGCGACGGCUC--- 
Dasypus novemcinctus        ---------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-CGC---UGG-UC-CGCUCGCCCCAUCC-----GGGAA------------CCUGCGGUGGCUC--- 
Dasyurus hallucatus         --------------------------------CC------AAAAACGUC--AGC-CG----AGGCCGG---GCGGCCC------------CG------------CUCGUGGC-CCGUCCG 
Elephas maximus             ---------------------GGAGCAAA----CAA----AAAAAUGUC--AGC-CGC---CGG-CC--GCUCGCCCCUCCC-----GGGAA------------CCUGCAGUGGCUC--- 
Trichechus manatus          ---------------------GGAGCAAA----CAA----AAAAAUGUC--AGC-CGC---UGG-CC--GCUCACCCCUCCC-----GGGAA------------CCUGUGGUGGCUC--- 
Gallus gallus               GGGGAGAGAAAGGGCCGAAAGGGGCUCCGCGGCCAA----AAAAACGUC--AGC-GAG---GGGUCCG---CUCGCCCCGAU-----CCGCC------------CUGGGGU--------- 
Anodorhynchus hyacinthinus  --------------------AGGGGUUUGCAAUCA-----AAAAACGUC--AGC-GAC---GGGUCUC---CCCAGCCCAGC-----CCGCC------------CUGGGGUCUCCGUCCC 
Chelydra serpentina         ----------------------GGAGACGCCAACCA----AAAAACGUC--AGC-GAG---GGGCCCU---CCCCUCCCACG-----CCGAC------------CUGGGCCUGUGG---- 
Bombina japonica            ----------------------GCUGCCCAGGACUA----AAAAAUGUC--AGC-UG----GGAGUCCU--UCCUC-UCCCU-----UAUU-------------UCUGCCUCACAACCU- 
Xenopus laevis              ----------------------GUAGACGACGACUA----AAAAACGUC--AGC-UG----GGAGA-CU--CCUCCGUUCGCACAGCCCGA-------------CCUGCUCCAUUGCCCA 
Ceratophrys ornata          ----------------------AGAAGCGAGGACCA----AAAAACGGC--AGC-CG----CGGGCCC---UCCUGUUCCCA-----CCAU-------------CCCAGCUUUUCCACAC 
Pyxicephalus adspersus      ----------------------GAAGCUCAGGACUA----AAAAACGUC--AGC-CG----UAGGCUU---UCCUAUAGCCG-----CAGG-------------CCUGCCUGU-CAGUG- 
Dermophis mexicanus         --------------CAGUUUC-ACGACAACGGAGA-----AAAAAUGUU--AGC-UG----GGGAACG---UCCCUUUCCCG-----AGAG-------------CCCGCGCCGUCCUUUU 
Herpele squalostoma         ------------GUGGUUUACGACGAUAGAGGAGA-----AAAAAUGUU--AGC-UG----GGGAACG---UCCCUUUCCCG-----AGAG-------------CCCGCGCCAUCCU--- 
Typhlonectes natans         --------------GAAUUUCG--GACAAGGGAGA-----AAAAAUGUU--AGC-CG----GGGAACG---CCCCUUUCCCG-----AAUG-------------CCCGUGCCGUCCUUCC 
Oryzias latipes             ---------------------------------CA-----AAAAAAGCC-AGAAAAGA-CUCCCCG----------------------------------UCGCGCUCAG---------- 
Gasterosteus aculeatus      ---------------------------------CAA----AAAAAAGCCAAGA--UGACCACUCCG----------------------------------UCGUGUUCAG---------- 
Takifugu rubripes           ---------------------------------C------AAAAAAGCCAAGA--AAAUCACUCCG----------------------------------UCGCGUUCAG---------- 
Tetraodon nigroviridis      ---------------------------------C------AAAAAAGCCACGA--UGAUCGCUCCG----------------------------------UCGUGUUCGG---------- 
Danio rerio                 ---------------------------------U------AAAAAAGCUAUAG----AGUACUCUG------------------------------------GCGCUCGG---------- 
Rhizoprionodon porosus      GUUGGGAG------------CAGCAACGGCAAGCAAA---AAAAAAGUUCCAGC-CGAG--GCCUCC--UCA-CCACGCGGCCUGGGUCUGAGGGUAACAUGGCCCUGCGGGAGAGAGCC 
Mustelus canis              GUUGGGAG------------CAGCAGCGGCAAACAAAA--AAAAAAGUUCCAGC-CGAG--GCCUCC--UCACCCCCGCGGCCUGGGUCUGAGGGUAACACGGCCCUGCGGGAGAGAGGC 
Dasyatis sabina             GUUGGGAAGCGUGAUUUAUUGUUGGUGGGCAGAGAG----AAAAAAGUUUAAGC-CGCG--GCCUCC--UC--CCCGGCGGCCCAGGACCC-------------CCUGUU-GCAACGUGC 
Rhinoptera bonasus          GUUGGGAAGCGUGAUUUAUUGUUGGUGGGCAGAGAG----AAAAAAGUUUCAGC-CGCG--GCCUCC--UC--CCCGGCGGCCCAGGACCC-------------CCUGUU-GCAACGUGC 
structure                   ---------------------------------------|  ))) )))  )))       )))))))))))))))))))))))))))))              ((((((|--------- 
                                                                          P3                           P1                             P4             

                                    370       380       390       400       410       420       430       440       450       460       470       480           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                                                                                                              CR4    
structure                                                                                                                                ----------- 
Homo sapiens                ---------------------------------------------------GCCUGCCC-----------AG-------CCCCCGAAC--CCCG--CCUGG-------AGGCCGCGGUCG 
Tupaia glis belangeri       GCCC-----------------------------------------------GCCCUCUC-----------AU-------CCCCCGCGU--CCCG--CCUAG-------AGGCCGCGGUCG 
Oryctolagus cuniculus       ---------------------------------------------------GCCCGCCC-----------GG-------CCCCCGUGC--CCCG--CCUG--------AGGCCGCGGUCG 
Cavia porcellus             ---------------------------------------------------GUCCA-CC-----------GG-------CCCCCGAGC--CCCG--CCU---------AGGCCGCGGCCG 
Chinchilla brevicaudata     ---------------------------------------------------GCCCGGCU-----------GG-------CCCCCGAGC--CCCG--CCCA--------GGGCCACGGCUG 
Geomys breviceps            ---------------------------------------------------GCCCGCCC---------GAAC-------CCCCCGCGA--CCCG--CCUG--------AGGCCACGGCCG 
Microtus ochrogaster        ---------------------------------------------------GGCCGCCC-----------AG--------CCCCG-CA--CCCG--CCUUG-------AGGCCGCGGUUG 
Cricetulus griseus          ---------------------------------------------------GGCCGCCC-----------AG--------CCCCG-CA--CCCG--CCUG--------AGGCCGCGGUCG 
Mus musculus                ---------------------------------------------------GGCCGCCC-----------AG--------UCCCG-UA--CCCG--CCUAC-------AGGCCGCGGCCG 
Mus spretus                 ---------------------------------------------------GGCCGCCC-----------AG--------UCCCG-UA--CCCG--CCUAC-------AGGCCGCGGCCG 
Mus musculus castaneus      ---------------------------------------------------GGCCGCCC-----------AG--------UCCCG-UA--CCCG--CCUAC-------AGGCCGCGGCCG 
Rattus norvegicus           ---------------------------------------------------GGCCGCCC-----------AG--------CCCGG-UA----CC--CGCCUGG-----AGGCCGCGGACG 
Mustela putorius furo       ---------------------------------------------------GCCCGCUU-----------AG-------CCCCCG-CA--UCCC--GCCUGG------AGGCCGCGGUCG 
Procyon lotor               ---------------------------------------------------GCCCGCUU-----------AG-------CCCCCGCGU--CCCG--CCUGG-------AGGCCGCGGUCG 
Felis catus                 ---------------------------------------------------GCCUCCUU-----------AG-------CCCCCGCGU--CCCG--CCUAG-------AGGCCGCGGUCG 
Bos taurus                  ---------------------------------------------------GCCCGCCC-----------AG-------CCCCAGUGC--CCCG--CCUG--------AGGCCGCAGUCG 
Sus scrofa                  ---------------------------------------------------GCCCGCCC-----------AG-------CCCCCGCGC--CCCG--CCUG--------AGGCCGCGGUCG 
Suncus murinus              ---------------------------------------------------CCG-UCCC-----------AG--------CCUCCAUC--CCCG--CCCC--------AGGCCGCGGUCG 
Equus caballus              ---------------------------------------------------GCCCGCCC-----------AG-------CCCCCGCGC--CCCG--CCUGG-------AGGCCGCGGUCG 
Dasypus novemcinctus        ---------------------------------------------------GUCCGCCC-----------UG-------CCCCCGCGC--UCCG--CCUAG-------AGGCCGCGGUCC 
Dasyurus hallucatus         CACUGUCCGGGCCAGGCCCCGGCCCGAACCCCCUGGAGACAACUCCCGCAGGGUCUGCGCUGCGCCGCGGAG--------CCCCG-GCUGCCCACGUAG---------AGGCGGCGG-CC 
Elephas maximus             ---------------------------------------------------GCCCGCCC-----------AG--------CCCCGCUC--CCCG--CCUGG-------AGGCCGCGGUCG 
Trichechus manatus          ---------------------------------------------------GCCCGCCC-----------AG--------CCCCGCGC--CCCG--CCUGG-------AGGCCGCGGUCG 
Gallus gallus               -----------------------------------------------------------------------------------------CCCCG--CUCGCG------UGGCCGCGGUCG 
Anodorhynchus hyacinthinus  CCCACGCAGCC-------------------------------------GGGGGCCUGCC---------GCGGAGG---CUCCCUC----CGCCG--CACUUCACGG--AGGCCGCGGUCG 
Chelydra serpentina         ------------------------------------------------UGGGGCCCGCC--------AGCGAAGU--CCCCGCCG----CCCCG--CCCCGGUG----AGGCCGCGGUCA 
Bombina japonica            GGA-------------------------------------------------CUCUUUA---------UUUA-------GCGGUG-----CCCC-AUUUGUCG-----AGGCCGCAGUCA 
Xenopus laevis              AGA--------------------------------------------GCCCCGGGUUUUCU----CUGUGGAAUGU---AUCAGGCGCU-CCCCGGUCUGUCUGUCUGGGGCCGCGGUCG 
Ceratophrys ornata          UGC------------------------------------------------GCCUGGGU----UCUCACUCAA-GUGUUCGGCAG-----CUUC-CACUUACG-----AGGCCGCGGUCU 
Pyxicephalus adspersus      UGC------------------------------------------------GCGGCCUC-------UGCUCGCAAUGU-CCGCAG-----CGCC-UUCCUAUG-----AGGCCGCAGUCU 
Dermophis mexicanus         UCUUCCU----------------------------------------CGGGCCCGUUGG-------C-AUAGCCCCU---GGCCU-----CCUC-GCUCUAU------AGGCCGCGGUCA 
Herpele squalostoma         -CUUCCU----------------------------------------CGGGCCCAUUGG-------CGAUAGCCCCC---GGCCU----CCCUC-GCUCACC------AGGCCGCGGUCA 
Typhlonectes natans         UCUCCUC----------------------------------------UGGGCCCGUUGG-------CGAUAGCCCCC---GGCCU----CCCUC-GCUCCUU------AGGCCGCGGUCA 
Oryzias latipes             ---------------------------------------------------------------------U-UCCCUGCU---------GGAAAC----------------GCCGCGGUCA 
Gasterosteus aculeatus      ---------------------------------------------------------------------UGUCCCGCCU-GAAACACCGCGAAU-----------UUCCUGCCGUGGUCG 
Takifugu rubripes           ----------------------------------------------------------------------GUCCCCCCCAGGAACACCGAGAGC-------------CCUGUUGUGGUCA 
Tetraodon nigroviridis      -----------------------------------------------------------------------UCCCCCCUCAAAGCACCGCGAGC-------------CCGGUUGCGGUCA 
Danio rerio                 ---------------------------------------------------------------------UCUCACAGGU---UUGGCUGUUUGU-----------------ACGCGGACA 
Rhizoprionodon porosus      AACACGG---------GGGGGCCCCGGUCCGGCUAACAGGGCAGGAG----GUCGGCCC------CAAUUGCCU--CA--GGCCC-----AGCC--ACUCC-------GGGCCGCGAUCA 
Mustelus canis              AACACG----------GGGGCCCCCGGUCCGGCGAACAGGGCAGGAG----GUCGGUCC------CAAUCGCCUCACA--GGCCC-----AGCC--ACUCC-------GGGCCGCGGUCA 
Dasyatis sabina             GGAAUGGCG----------------------------------------GCCUCGGCCC------CCCU--GCU-GCA--CGCCC-----AGCC--GUUU--------AGGCCGCGGUCA 
Rhinoptera bonasus          GAAAUGGCG----------------------------------------GCCUCGGCCC----CCACCUUUGCUCGCA--UGCCC-----AGCC--GAGU--------AGGCCGCGGUCA 
structure                   -----------------------------------------------------------------------------------------|((((                  ((((( (( 
                                                       Hypervariable paired region                                     P5                       P6   

                                    490       500       510       520       530       540       550       560       570       580       590       600           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                                                CR5                                                                  
structure                   -                                   -----------------------------------                                                  
Homo sapiens                GCCCG-GGGCUUC----UCCG---GAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UCUCUCGGGGG----C-GA-----GGGCG-AGGU------------ 
Tupaia glis belangeri       GCCCG-GGGCUUC----UCCG---GAGGUGCCCAUUGCCGCCGCGAAGAGUUAGGCUCUGUCAGCCG--CGGG-CUCUCGGGGGG----CCCA-----GGGCG-AGGU------------ 
Oryctolagus cuniculus       GCCCG-GGGCUUC----UCCG---GAGGUGCCCAAUGCCGCCGCGAAGAGUUAGGCUCUGUCAGCCG--CGGG-UCCCUCGGGGG----CCAA-----GGGCG-AGGC------------ 
Cavia porcellus             GCGCG-GGGCUUC----CCUG---GAGGCGCCCAUGGCCGCCGCGAAGAGUUCGUCUCUGUCAGCUG--CGGG-UCGCCCGGGGG----CCGC-----GGGAG-AGUC------------ 
Chinchilla brevicaudata     GCGCG-GGGCUUC----UCCG---GGAGCGCC-AUGGCCGCCGCGAAGAGUUCGUCUCUGUCAGCCG--CGGG-UCGCGCGGGGG----CCGC-----GGGGG-AGUC------------ 
Geomys breviceps            GCCCG-GGGCCUC----UGCG---GAGGUGCCCAUUGCCGCCGCGAAGAGUUAGGCUCUGUCAGCCG--CGGG-AUCCGCGCGGG----CC-------GGGCCGCGGC------------ 
Microtus ochrogaster        GCCU--GGAGUUC----UCCG---GA---CUCCGCUGCCGCCGCGAAGAGUUCGUCUCUGUCAGCCG--CGGA-GUAU-CAGGGG----CUG------GGGCCAGGCC------------ 
Cricetulus griseus          GCCU--GGAG-UC----CUCG---GG---CUCCGCUGCCGCCGCGAAGAGCUAGACUCUGUCAGCCG--CGGG-GCGU-CAGGGG----CUG------GGGCGAGCCC------------ 
Mus musculus                GCCU--GGGG-UC----UUAG---GA---CUCCGCUGCCGCCGCGAAGAGCUCGCCUCUGUCAGCCG--CGGG-GCGC-CGGGGG----CUG------GGGCCAGGCC------------ 
Mus spretus                 GCCU--GGGG-UC----UUAG---GA---CUCCGCUGCCGCCGCGAAGAGCUCGCCUCUGUCAGCCG--CGGG-GCGC-CGGGGG----CUG------GGGCCAGGCC------------ 
Mus musculus castaneus      GCCU--GGGG-UC----UUAG---GA---CUCCGCUGCCGCCGCGAAGAGCUCGCCUCUGUCAGCCG--CGGG-GCGC-CGGGGG----CUG------GGGCCAGGCC------------ 
Rattus norvegicus           GCCU--GGGG-UC----UUAG---AA---CUCCGCUGCCGCCGUGAAGAGCUAGUCUCUGUUAGCUA--CGGG-GCAC-CGGGCG----CUG------GGGUCAGGCC------------ 
Mustela putorius furo       GCCCG-GGGCUUC----UCCG---GAGGCACCCAUUGCCGUCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-ACCCUUGGGGG----CCAA-----GGGCG-AGGC------------ 
Procyon lotor               GCCCG-GGGCUUC----UCCG---GAGGCACCCAUUGCCGUCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-ACCUUUGGGGG----CCAA-----GGGCG-AGGC------------ 
Felis catus                 GCCCG-GGGCUUC----UCCG---GAGGCACCCAUUGCCGUCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UCCCUUGGGGG--GGCCGA-----GGGCG-AGGC------------ 
Bos taurus                  GCCCG-GUGCUUC----UCCG---GAGGUGUCCAUUGCCGCCGUGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UCGCUCGGUGG---GCCGA-----GG-CA-UGGC------------ 
Sus scrofa                  GCCCG-GGGCUUC----UCCG---GAGGCGCCCAUUGCCGCCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UCCCUCGGGGG----CCAA-----GG-CG-AGGC------------ 
Suncus murinus              GUCCG--GGCUUC----UUCG---GAAGUCCC-GUUGCCGUCGCGAAGAGUUCGCCUCUGUCAGCCG--CGGG-GCU--UGGGG-----CCAG-----GGA----CGG------------ 
Equus caballus              GCCCG-GGGCUUC----UCCG---GAGGCGCCCAAUGCCGCCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UGCCUCGGGGG----CCAG-----GGACG-AGGC------------ 
Dasypus novemcinctus        GCCCG-GGGCUUC----UCCG---GAGGCACCCAAUGCAGCCGCGAAGAGUUAGGCUCUGUCAGCCG--CGGA-UCCCGCGGGGG----CCAA-----GGGUG-AGGC------------ 
Dasyurus hallucatus         GUCUCGGGGCCCCUG--CGUG--CGGGGCGCCCACUGCGGCCGCCAAGAGCUCGUCUCUGUCAGCCU--CGGGUGCACGUGGGCC---CGCGGUCGAGCCCUAAGGCC------------ 
Elephas maximus             GCCUG-GGGCUUC----UCCG---GAGGUUCCCGCUGCCGCCGCGAAGAGUUGGGCUCUGUCAGCCG--CGGG-UCCCGCGGGAA----CCAA-----GGGCG-AGGC------------ 
Trichechus manatus          GCCUG-GGGCUUC----UCCG---GAGGUUCCCAUUGCCGCCGCGAAGAGUUAGGCUCUGUCAGCCG--CGGG-UCCUGCGGGAA----CCAA-----GGGCG-AGGC------------ 
Gallus gallus               GCC---GGC--------ACCC---------GCCAUUGCCGCCGCGAAGAGUUCGCCUCUGUCAGCCU--CGGCG----GCGCGCGGGA-GGUGCGG--CGCGC--GGCCCC--------- 
Anodorhynchus hyacinthinus  GCC---GGU--------GUCC---------GCCACUGCCGCCGCGAAGAGUUCGUCUCUGUCAGCCU--CGGCG----GCGGUGGGGA-GCGAGAG--GGCUC--GUCCCC--------- 
Chelydra serpentina         GCC---GGC--------UCGC---------GCCACUGCUGCCGCGAAGAGUUCGUCUCUGUCAGCCU--CGGGG----GCGGCCGGGG-UGGA-AG--GGCGG--GUCCC---------- 
Bombina japonica            GUC----------UUGUUCUUAUACG--------CUGCUGUUGCGAAGAGUUCGUCUCUGUCAGCCUCCGGGG------CAACGC---CUUGAAUU--UGGAG--AG------------- 
Xenopus laevis              GCA--------------UCAU-------------CUGCUGUCGCGAAGAGUUCGUCUCUGUUAGCCCUUGGGG----GCCCUGGU-----GCGGAG--UGGAG--AGUCCGGGUCU---- 
Ceratophrys ornata          ACC------------GCUGUCAC-----------UGGUAGUCGCGAAGAGUUCGUCUCUGUCAGCCUUGGGAG------CCGCGG--ACGGAGUAUGAGGUCC--AGU------------ 
Pyxicephalus adspersus      GCC------------AAUACCCC-----------GGGCAGCCGCGAAGAGCUCGUCUCUGUCAGCCUUUGGCG------CUGCGG---CGGAGUGGGGGAGGC--CGC------------ 
Dermophis mexicanus         GCUC--GGGCCCC--AGCUCCGGCAGGGGUUCCACUGCUGCCGCGAAGAGUUCGCCUCUGUCAGCCUU-GAGG------UGGCC----GGGAUAGAA-UAGGC--GGGCUCG-------- 
Herpele squalostoma         GCCC--GGGCCCU--GGCUCUGCUAGGGCGUCCAAUGCUGCCGCGAAGAGUUCGUCUCUGAUUGCCUU-GAGG------UAGCC----GGGCUCGAA-UAGGU--GGGCUCG-------- 
Typhlonectes natans         GUCC--GGGCCCU--UGCUCUGGCAUGAGGUCCAUUGCUGCCGCGAAGAGUUCGUCUCUGUCAGCCUU-GAGG------UGGCC----AGCAUGGAA-UUGGC--GGGCUUG-------- 
Oryzias latipes             GCUCG-------------------------------GCUGCUGCGAAGAGUUCGUCUCUGUU-------GUUUCG-------------GGGA---------------------------- 
Gasterosteus aculeatus      GCUUGU------------------------------GCUGCCGCGAAGAGUUCGUCUCUGUU-------GCUCCGGUGUUCUCAUGGCGGGA---------------------------- 
Takifugu rubripes           GUCCG-------------------------------GCUGCCGCAAAGAGUUGGUCUCUGCU-------GCUCCGGUGUCUUG---GCGGGA---------------------------- 
Tetraodon nigroviridis      GUCUG-------------------------------GCUGCCGCGAAGAGUUGGUCUCUGCC-------GCUCCGGUGUCUUCAUGUCGGGA---------------------------- 
Danio rerio                 GUUUG-------------------------------ACUGCCGCCAAGAGUUCGGCUCUGCU-------GCACAUUCGGCAGGUCUGU-GGA---------------------------- 
Rhizoprionodon porosus      GCCC--GGGCUUU---CCCUACUUU-GGGGCCCAAUGCUGUCGCGAAGAGUUCGGCUCUGUCAGCCC--GGCU------GGGUC------CGGGUGG-GGGCC--GGCACAGAGGGACAC 
Mustelus canis              GCCCG-GGGCUUUCCCCCCCACCAUGGGGGCCCAAUGCUGCCGCGAAGAGUUCGGCUCUGUCAGCCC--GGCU------GGGCC------AGGGUGG-GGGCC--GGCACAGAGGGACAC 
Dasyatis sabina             GCGC--CGGUUUC-CACGCCAGUGU-GGGGCUUGAUGCUGUCGCGAAGAGUUCGUCUCUGUUAGCCU--GGCA------GGGUG----UGCUACGCA-GGGUC--GGGGU---------- 
Rhinoptera bonasus          GCGC--CGGCUUC-CACGCCAGUGU-GGGGCUUGAUGCUGUCGCGAAGAGUUCGUCUCUGUCAGCCU--GGCA------GGGGG----UGCUACGCA-GGGUC--GGGGU---------- 
structure                   (( |------------------------------| ))))))))) ((((     ))))          ))))|---------------------------------------------- 
                                              L6                   P6     P6.1     P6.1           P5                   Hypervariable paired region   

                                    610       620       630       640       650       660       670       680       690       700       710       720           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                                     CR6                                                        CR7                  
structure                                                       -------------                                             ---------------            
Homo sapiens                ----------------UCAGGCCUUUCAGG---CCGCAGG-AAGAGGAA-CG-----GAGC-GA-GUCCC-------CGCGCGCGGCGCGAUUCCC-UGAG-CUGUGGGACGUGCAC--C 
Tupaia glis belangeri       ----------------UUAGGCC-UCGUGG---CCGCAGG-GACAGCAA-CG-----GAGC-GG-GUCCC------CGCGAGCCUGUGCGCGUCCC-UGAG-CCGUGGGACUUGCAC--C 
Oryctolagus cuniculus       ----------------GCAGGCC-GUCUGG---CCGCAGG-GAGAGGAA-CG-----GAGC-GG-GUCCC-------CCAGCGUGGUGCGCUUCCC-UGAG-CUGUGGGACUUGCAC--C 
Cavia porcellus             ----------------CCAGGCC---UUGG---CCGCAGG-GAGAGAAA-CG-----GAGC-AG-GUCCU---------CGCGCGGUGCACUCCCC-UGAG-CUGUGGGAAGUGCAC--C 
Chinchilla brevicaudata     ----------------CUAGGCC-GAGUGG---CCGCAGG-AAGAGAAA-CG-----GAGC-CU-GUCCC-------UGUGCACGGGGCGCUUCUC-UGAG-CUGUGGGAAGUGCCC--C 
Geomys breviceps            --------------------CGGACGCCGAU--CCGCAGG-GACAGCAA-CG-----GAAC-CG-GCCCC-------UUCGCCCUGUGCGCUUCCC-GGAG-CUGUGGGAUGAGCAC--C 
Microtus ochrogaster        --------------------CGGAC-AGCG---UCGCAAG-UACAGUAA-CG-----GAGC-UG-GUCCU---------UGUUCGGUGG-CUUCCC-UGAG-CUGUAGGAAGUACAC--C 
Cricetulus griseus          --------------------CGGC--AGCG---CCGCAAG-CAGAGAAA-CG-----GAGC-UG-GUCCC--------GUGAACGGUGA-CUUCCC-UGAG-UUGUGGGAAAUGCAC--C 
Mus musculus                ---------------------GGGCGAGCG---CCGCGAG-GACAGGAA-UG-----GAAC-UG-GUCCC-------CGUGUUCGGUGU-CUUACC-UGAG-CUGUGGGAAGUGCAC--C 
Mus spretus                 ---------------------GGGCGAGCG---CCGCGAG-GACAGGAA-UG-----GAAC-UG-GUCCC-------CGUGUUUGGUGU-CUUACC-UGAG-CUGUGGGAAGUGCAC--C 
Mus musculus castaneus      ---------------------GGGCGAGCG---CCGCGAG-GACAGGAA-UG-----GAAC-UG-GUCCC-------CGUGUUCGGUGU-CUUACC-UGAG-CUGUGGGAAGUGCAC--C 
Rattus norvegicus           ---------------------GGGAGAGCG---CCGCAAG-GACAGUAA-CG-----GAAC-UG-GUCCC-------UGAGUUCGGUGG-CUUUCC-UGAG-AUGUGGGAAGUGCAC--C 
Mustela putorius furo       -------------------------UCUGG---CCGCAGG-GAGAGAAA-CG-----GAGC-GG-GUCCC-------CUCGCGCGGUGCGCUUCCC-UGAG-CUGUGGGACUUGCAC--C 
Procyon lotor               -------------------------UCUGG---CCGCAGG-GAGAGAAAACG-----GAGC-GG-GUCCC-------CUUGCGCGGUGCGCUUCCC-UGAG-CUGUGGGACUUGCAC--C 
Felis catus                 -------------------------UCUGA---CCGCAGG-GAGAGAAA-CGG----GAGC-AG-GUCCC-------CGCGCGCGGUGCGCUUCCC-UGAG-CUGUGGGACUUGCAC--C 
Bos taurus                  -------------------------UGUAA---CCGCAGG-GAAAGGAA-CG-----GAGUGGG-GUCCC-------CGCGCGCGGUGCGCUUCCC-UGAG-CUGUGGGACUUGCAC--C 
Sus scrofa                  -------------------------UCUGA---CCGCAGG-GAAAGGAA-CG-----GAGU-UG-GUCCC-------CGCGCGCUGUGCGCUUCCC-UAAG-CUGUGGGCUGUGCAC--C 
Suncus murinus              ----------------------GACCCUGU---CCGCAGG-GAGAGAAACUG-----GAGC-CG-GGCCC---------UCCACGGUGC-C-UCCC-CGAG-CUGUGGGAUCUGCAC--C 
Equus caballus              -------------------------UCUGG---CCGCAGG-GAGAGGAA-CG-----GAGC-GG-GUCCC-------CGCGCGCGGUGCGCUUCCC-UGAG-CUGUGGGACGUGCAC--C 
Dasypus novemcinctus        ----------------UUAGGCC--GCGGG---CCGCAGG-AAGAAAAA-CC-----GAGC-GA-GUUCU-------CACGCGCGGUGCGCUUCCC-UGAG-CUGUGGGUCGUGCGC--C 
Dasyurus hallucatus         -----GGGCGUGGGG-CUG-----------GGGUCGCAGG-GAGAGUAACCGU----GAGCCGGCGCCC--------AGCCUUCAGGGCGC-UCCCUCGAG-CUAUGGGAGCUGCCC--C 
Elephas maximus             ----------------UGGGGCC-UCCUGA---ACGCAGG-GAGAGAAA-CG-----GAGC--G-GUUCC-------CCGCGUGCGUGCGCUUCCC-UGAG-UUGUGGGAUGUGCGC--U 
Trichechus manatus          ----------------UUAGGCC-UCCUGA---ACGCAGG-GAGAGAAA-UG-----GAGC--G-AUUCC-------CCGAGUACGUGUGCUUCCC-UGAG-UUGUGGGAUGUGCGU--C 
Gallus gallus               ----------------GCG--------------CCCCCAG-CAGAGCAAACGG----GAGC-GG-CGCC---CCCGGGGUAACCCCCGCGCUCCCC-UGCG-CCGUGGGGCGCGCGG--A 
Anodorhynchus hyacinthinus  ----------------GCGCCGGGG--------ACCCCAG-CAGAGCAAAACG----GAGC-GG-CGUC---CUCGGCACAGCCGCCGCGCUUCCC-UCAA-CCGUGGGAUGCGCGG--A 
Chelydra serpentina         ----------------GAGCCCGUC--------GGCC-GG-GAGAGCAAACGU----GAGCGGC-AGCCCC-------UGCGCCACCGCCCUCCCC-UAAG-CUGUGGGGCCCGCGG--U 
Bombina japonica            ----------------CCUGGGAAUGUAACAAGGGGUAGG-GAAAAUAACGA-----GAGCUGA-GUUG-------GCUUCUCCUGUGCUG-UUCC-UGAG-CUGUGGAACUUGCAA--U 
Xenopus laevis              ----------------GGG--------------GGGUCGG-GAGAACAAAAG-----GGGGCGC-GCUGGUGCUCAGGCUCAGUCAUGCUU-UCCC-UUAG-UUGUGGGAUAUGCGU--G 
Ceratophrys ornata          ----------------AAUGAG------------AGCAGGGAAGAGUAAAGC-----GAGCCGC-GCUA------CUUGUCCUAUCUGCCG-CUCC-UAAG-CUGUGGGGCGUGUAG-GG 
Pyxicephalus adspersus      ----------------UGAU--------------GGCAGCUGAGAAUAAAGC-----GAGCCCA-GCUG----CCCCGCUCUGUUCCACUG-CCCC-UGAG-CUGUGGGGUUGGUGA-AU 
Dermophis mexicanus         ----------------CGGCAGC----------GCGCGGGAAAGAGCAAAU-G--GUGAACUGG-GUGC-------CUGUUGGGGUCGC-G-UCCC-UGAA-GAGUGGGAAGUGCGA--U 
Herpele squalostoma         ----------------CGGCGAU----------GCGCAGGAAAGAGCAAAACA--GUGAACUGG-GCGU-------GUGCUGGGGUCGC-G-UCCC-UGAA-GUGUGGGAUGUGCGA--U 
Typhlonectes natans         ----------------UGGCGGC----------GCGCGGGAAAAAGCAAAU-G--GUGAACUAG-GUGC-------GUGUUGUGGUCGU-G-UUCC-UGAAGC-GUGGAAUGUGCGA--U 
Oryzias latipes             ------------------------UUGUCAACAGCUGAGC--AGAUAAAAA-----UGAGCA--AGGCGAU-----------CCUGCCG---AACC-UCA---UGUGGUC---CGGUUCG 
Gasterosteus aculeatus      ------------------------CUUGUGAUAACUGAGC--AGAGUAAAAC----UGAGCA--GGGCGAC-----------UCUCCCA---GAUCGUUC--CAGUGAUC---CGGUCAG 
Takifugu rubripes           ------------------------UCACCAAGGACUGAAC--AGAGAAACAG----UGAGCG--UGGUGAC-----------UCUACCG---GUUC-UUC--CAAUGUCC---CGGUUAG 
Tetraodon nigroviridis      ------------------------UCACCGAGGACCGAAC--AGAGCAAAAC----UGAGCC--UGGUGAC-----------UCUACCG---GUUC-UCC--CAGUGUUC---UGGUAGG 
Danio rerio                 ------------------------CUGCACAACACUGAGC--AGAUUAACU-----UGAGCA--UGGCGAA---------GGUUUGC-G---GACC-UCAAACACUGAUC---CUGCAAA 
Rhizoprionodon porosus      ACCGGGCCGGGGCGCCGAGGAUAGCUACCGC--CCGCAGG-GAUAGUAAAUAUCCGUGACCAGU-GGC--------CUCGGUGGCUGCGUC-UCCC-GGAG-CAAUGGGACC-CGCAAGG 
Mustelus canis              ACCGGGCCGGGGCGCCGGGGAUAGCUACCGC--CCGCAGG-GAUAGCAAAUAUCCGUGACCAGU-GGU--------CUCGGUGGCUGCGUC-UCCC-GGAG-CAAUGGGACC-CGCAAGG 
Dasyatis sabina             ----------------GCGGAG------------GGCAGG-GAGAUUAAAUAG-CUUGACCAGA-CGC-----UAUGGCCUGUACUGCAUU-UCCC-AGAG-CUGUGGGACC-UGCAAAU 
Rhinoptera bonasus          ----------------ACGGGG------------GACAGG-GAGAUUAAAUAG-CUUGACCAGA-CGC-----UAUAACCUGUACUGCAUC-UCCC-AGAG-CUGUGGGACC-UGCAAAU 
structure                   --------------------------------| ))))))  ANANNAA        ((((    (((                 ((((   ((((          ))))   ))))    
                                                                P4      BoxH         P7a     P7b                  P8a    P8b           P8b    P8a    

                                    730       740 
                            ....|....|....|....|...
                                          CR8       
structure                              ---------    
Homo sapiens                C-AGGACUCG-GCUCACACAUGC 
Tupaia glis belangeri       G-GGGACUUU-GCUCGGACAAUC 
Oryctolagus cuniculus       C-GGGACUCG-GCUCAAACACGC 
Cavia porcellus             --GGGAC-GG-GCUCCUACAAGC 
Chinchilla brevicaudata     --GAGACUCG-GCUCCUACAAGC 
Geomys breviceps            C-GGGGU-CG-GCUCCUACAGUU 
Microtus ochrogaster        C-AGAGCUCG-GCUCCUACAACC 
Cricetulus griseus          A-GGAACUCG-GUUCCCACAACC 
Mus musculus                C-GGAACUCG-GUUCUCACAACC 
Mus spretus                 C-GGAACUCG-GUUCUCACAACC 
Mus musculus castaneus      C-GGAACUCG-GUUCUCACAACC 
Rattus norvegicus           U-GGAACUCA-GUUCCUACAACC 
Mustela putorius furo       C-GGGACUAG-GCUCACACACAC 
Procyon lotor               C-GGGACUAG-GCUCACACACAU 
Felis catus                 C-GGGACUGG-GCUCAGACACAU 
Bos taurus                  C-GGGACUCG-GCUCAGACAUCU 
Sus scrofa                  U-GGGACUCG-GCUCAGACACUU 
Suncus murinus              C-GGGACUCG-AACCCUACACUU 
Equus caballus              C-GGGACUCG-GCUCAAACACGU 
Dasypus novemcinctus        U-GGGACUCG-GCUCAGACACGU 
Dasyurus hallucatus         C--GGGCACG-GCUCGGACACCC 
Elephas maximus             C-GGGGCUCA-GCUCCGACAGGU 
Trichechus manatus          C-GGGACUCA-GCUCCGACAGGU 
Gallus gallus               C--GGCGUC--GCUCCCACACGC 
Anodorhynchus hyacinthinus  C--GGCGCC--GCUUCGACACCC 
Chelydra serpentina         CGGGGCUGC--GCUCAGACACGC 
Bombina japonica            CG-CAGUC-G-GCUCUGACACUU 
Xenopus laevis              UU-CAGCCAG-UCCCCGACAUGU 
Ceratophrys ornata          UA-CACAA-G-GCUCCGACAUUC 
Pyxicephalus adspersus      UG-CAGCAUG-GCUCCGACAACU 
Dermophis mexicanus         CU-GUGUUCCUGUUCAGACACAC 
Herpele squalostoma         CU-GUCCGCUUGUUCAGACAUUG 
Typhlonectes natans         CU-GUGCGCUAGUUCAUACACAC 
Oryzias latipes             GUA-UCCUAC-GCUCAGACAAAU 
Gasterosteus aculeatus      AAA-GCCCCC-GCUCAAACACCC 
Takifugu rubripes           GAU-ACCCAA-GCUCAAACACUC 
Tetraodon nigroviridis      AAU-GUCCAA-GCUCAAACACCC 
Danio rerio                 UAC-GCCACC-GCUCAGACAUGC 
Rhizoprionodon porosus      CU--GCCCU--GGUCAUACACGC 
Mustelus canis              CU--GCCCU--GGUCAUACACAU 
Dasyatis sabina             CU--GCGCU--GGUCAUACAUUU 
Rhinoptera bonasus          CU--GCGCU--GGUCAUACAUUU 
structure                       )))    ))))  ACA    
                                P7b     P7a BoxACA