------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JXSJ01000020.1:subseq_4028401,101980_ Strand = + Positions = 55005 - 55077
 Found by:  Infernal (score=31.09) Covels (score=29.56)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -16.49

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .(({(((((---(...{[[[((((((((({(................)})))))))))]]]}..--..-))))))})).
 target  CUUCUUCCA---UUAAUGAAGUCUAUGGUGUAAAACCUGCCUGCAGGAGGCUAUAGAUGGAUGU--GU-GUGGAGAGAA
                         ****           ^^^                        ****                 

------- SECIS element -- id:2 -- grade:C ----
 Chromosome = JXSJ01000020.1:subseq_4028401,101980_ Strand = + Positions = 43157 - 43240
 Found by:  Infernal (score=15.3)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 2, 0
 Free Energy = -20.37

         ..(((((((.........((((((((((((..(((................)))))))))))))))..........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggc--ccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .((((((((.........([[((({({(((..(((((............))))))))})})))]])......-...)))))))).
 target  CGUGUCCAGUGCAAUGAAUGAAGACGUCUUCAUGGCCAGCACCAUAGCAGGCCAAAGCUCUUUGAAAUUAUU-AUUCUGGACAUC
                           ****                                        ****                   

------- SECIS element -- id:3 -- grade:C ----
 Chromosome = JXSJ01000020.1:subseq_4028401,101980_ Strand = + Positions = 20691 - 20774
 Found by:  Infernal (score=15.3)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 2, 0
 Free Energy = -20.37

         ..(((((((.........((((((((((((..(((................)))))))))))))))..........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggc--ccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .((((((((.........([[((({({(((..(((((............))))))))})})))]])......-...)))))))).
 target  CGUGUCCAGUGCAAUGAAUGAAGACGUCUUCAUGGCCAGCACCAUAGCAGGCCAAAGCUCUUUGAAAUUAUU-AUUCUGGACAUC
                           ****                                        ****                   

------- SECIS element -- id:4 -- grade:B ----
 Chromosome = JXSJ01000020.1:subseq_4028401,101980_ Strand = + Positions = 56177 - 56268
 Found by:  Infernal (score=11.37)
 Stem2 length = 8   Apical loop length = 25   Insertion in stem2 = 0, 0
 Free Energy = -9.61

         ..(((((((..............(((((((((((((.........................)))))))))))))..........)))))))..
 model   uucggucaugcg-------UuaAUGAcGgccuggcccgAAAcCcuuuuuggggug------ggccaggcCuGAUGuu-u-uuucaugaccggc
         .((((((((..............{[[(((((({(((.........................)))}))))))]]}......-...)))))))).
 target  CCAGUUACACCUUCUGGUAUUUAUGAGGGUUCAGGUCAGCUAAGUAAGGUCCUUUAAAUAAACUCGAACUUGACAUUUUC-AUUUGUAAUUGA
                                ****                                           ****                   

------- SECIS element -- id:5 -- grade:C ----
 Chromosome = JXSJ01000020.1:subseq_4028401,101980_ Strand = - Positions = 16418 - 16345
 Found by:  Infernal (score=10.24) Covels (score=5.82)
 Stem2 length = 7   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -11.97

         ..(((((((.......(((((((((((((((...............)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .((((({(((--(...{[[{{(((((((........---..........)))))))}}]]}......-.))))}))))).
 target  UUUGCUCAGG--AUAUUGAAAGAGAGGCCAUCAACU---UCAUUGAUCAGUCUUUCAAGACACUGCG-CUCUUCAGCGGC
                         ****                                     ****                   

------- SECIS element -- id:6 -- grade:B ----
 Chromosome = JXSJ01000020.1:subseq_4028401,101980_ Strand = - Positions = 10185 - 10111
 Found by:  Infernal (score=10.17) Covels (score=8.78)
 Stem2 length = 10   Apical loop length = 18   Insertion in stem2 = 1, 0
 Free Energy = -10.67

         ..(((((((.......((((((((((((.(((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggc-ccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(({({((---((((([[{((([(([((.(..................)))]))])))}]])..--))))))})}))..
 target  CUGUACCAG---GGCAUGAUGGUGCUAGCUGCAAAUCAAGUGUGGUGGACGUGGGAGCUUGAGGA--UGCCUUUGAAUCC
                         ****            ^^^                        ****