------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ Strand = + Positions = 151085 - 151166
 Found by:  Infernal (score=32.3) Covels (score=32.52)
 Stem2 length = 11   Apical loop length = 15   Insertion in stem2 = 0, 1
 Free Energy = -16.45

         ..(((((((.........(((((((((((((((...............))))))))).))))))..........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccagg-cCuGAUGuu-u-uuucaugaccggc
         .(((((((((........{[[((((((((((((...............))))))))).)))]]}......-..))))))))).
 target  UACAAAGAUUCGCGUUUAUGAAGACUACACAGAAAACCUUUGUAAGGAUUUGUGUAGAUCUGAUGUUUGG-CAAAUUUUUGUU
                           ****           ^^^                        ****                   

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ Strand = - Positions = 187697 - 187624
 Found by:  Infernal (score=18.12) Covels (score=16.32)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -9.92

         ..(((((((.........((((((((((.(((((................))))).))))))))))........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccug-gcccuAAAcC-cuuuuuggggcgggc-caggcCuGAUGuuuuuucaugaccggc
         ...({(((((........([[{(((((({((((..........-----...))))}))))))}]])----...)))))})...
 target  CAAGCAACUCCUCCUGUGUGAUUAACUGCCUCUGAAAACCUAC-----UGGAGAGCCAGUUAUGAG----UUUGGGUUUUCAU
                           ****            ^^^                         ****                 

------- SECIS element -- id:3 -- grade:B ----
 Chromosome = gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ Strand = + Positions = 2502 - 2576
 Found by:  Infernal (score=17.86) Covels (score=11.97)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -15.01

         ..(((((((.......(((((((((((((((...............)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         (((((((((---....{[[{((((((((((......-..........))))))))))}]]}......-...)))))))))
 target  GUUAGAUGA---AUUUUGACAGAAAACAGAGAAUAC-CAGAGGGAUGUCUGUUUUCUUGAUUAUGCA-AAAUCAUUUGAC
                         ****           ^^                        ****                   

------- SECIS element -- id:4 -- grade:B ----
 Chromosome = gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ Strand = + Positions = 165846 - 165939
 Found by:  Infernal (score=13.92) Covels (score=6.87)
 Stem2 length = 11   Apical loop length = 30   Insertion in stem2 = 0, 0
 Free Energy = -15.15

         ..(((((((.......(((((((((((((((..............................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuugggg---------------cgggccaggcCuGAUGuu-u-uuucaugaccggc
         ...(((((((......{[[{(((((((((((..............................)))))))))))}]]}......-..)))))))...
 target  GAGAAGCUGGACUCUAUGAAAAAUAAUGUGGCAUUGGGAUGGAGAGAGACUCAUUAGUCACCUACAUUAUUUAGAUGACAUA-ACCUAGCUUACA
                         ****                                                    ****                   

------- SECIS element -- id:5 -- grade:B ----
 Chromosome = gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ Strand = - Positions = 74607 - 74540
 Found by:  Infernal (score=11.78)
 Stem2 length = 9   Apical loop length = 8   Insertion in stem2 = 0, 1
 Free Energy = -12.7

         ..(((((((.......(((((((((((((((.................))))))).))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggcca-ggcCuGAUGuu-u-uuucaugaccggc
         (((((((((---((..([[[(([((((({(------.....-----...)}))).))]))]]])......-.)))))))))))
 target  CAGAGGAAU---UUCAUGAAAUAACAUAUG------AGCAA-----GAGCUUAUGGUGAUGGAGGAAGUU-CAAGUUCCUCUG
                         ****                                        ****                   

------- SECIS element -- id:6 -- grade:B ----
 Chromosome = gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ Strand = + Positions = 237363 - 237431
 Found by:  Infernal (score=11.44) Covels (score=11.59)
 Stem2 length = 8   Apical loop length = 9   Insertion in stem2 = 0, 0
 Free Energy = -18.9

         ..(((((((...........(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg----UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..((((((((((........([[({(({((((((......--------...))))))}))})]])----))-))))))))..
 target  UGUUGUCCAGCUAAGUUGCAUGAAAAGUUCCAGAAACAUG--------CUGUCUGGAUUUCUGAG----AG-UUGGGCAGAC
                             ****          ^^                         ****                 
>SECIS.1 chromosome:gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ strand:+ positions:151085-151166
UACAAAGAUUCGCGUUUAUGAAGACUACACAGAAAACCUUUGUAAGGAUUUGUGUAGAUCUGAUGUUUGGCAAAUUUUUGUU
>SECIS.2 chromosome:gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ strand:- positions:187624-187697
CAAGCAACUCCUCCUGUGUGAUUAACUGCCUCUGAAAACCUACUGGAGAGCCAGUUAUGAGUUUGGGUUUUCAU
>SECIS.3 chromosome:gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ strand:+ positions:2502-2576
GUUAGAUGAAUUUUGACAGAAAACAGAGAAUACCAGAGGGAUGUCUGUUUUCUUGAUUAUGCAAAAUCAUUUGAC
>SECIS.4 chromosome:gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ strand:+ positions:165846-165939
GAGAAGCUGGACUCUAUGAAAAAUAAUGUGGCAUUGGGAUGGAGAGAGACUCAUUAGUCACCUACAUUAUUUAGAUGACAUAACCUAGCUUACA
>SECIS.5 chromosome:gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ strand:- positions:74540-74607
CAGAGGAAUUUCAUGAAAUAACAUAUGAGCAAGAGCUUAUGGUGAUGGAGGAAGUUCAAGUUCCUCUG
>SECIS.6 chromosome:gi|408541579|gb|JH947353.1|:subseq_4355463,250502_ strand:+ positions:237363-237431
UGUUGUCCAGCUAAGUUGCAUGAAAAGUUCCAGAAACAUGCUGUCUGGAUUUCUGAGAGUUGGGCAGAC

