------- SECIS element -- id:1 -- grade:B ----
 Chromosome = gi|408541726|gb|JH947206.1|:subseq_13264141,100905_ Strand = - Positions = 44381 - 44304
 Found by:  Covels (score=9.78)
 Stem2 length = 12   Apical loop length = 12   Insertion in stem2 = 0, 0
 Free Energy = -22.39

         ..(((((((........(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ....(({((........([[[((((((((((((....-........))))))))))))]]]).....-...))}))....
 target  GGCUCCACCAGCuGGGGUGAGGGGGUGGUGGUCAGUG-CCAAGCUGGGCUGCCAUCCCAGAGGCCGg-CUGGGAGGCCCA
                          ****                                     ****                  

------- SECIS element -- id:2 -- grade:B ----
 Chromosome = gi|408541726|gb|JH947206.1|:subseq_13264141,100905_ Strand = - Positions = 88437 - 88360
 Found by:  Covels (score=11.78)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -9.03

         ..(((((((........(((((((((((((((...............)))))))))))))))...........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu--u-uuucaugaccggc
         ....(({({(.......[[[{(((({(({(((.....-.........)))}))}))))}]]].......-..)})}))--..
 target  CACAGCAGGCAUcCCAAGGAUGGGUCAGCCCUCCACG-CAGCCCCCAGGGCCUCACCUUGAAGAGgcGg-AAGGCAGC--CA
                          ****           ^^                        ****         


------- SECIS element -- id:3 -- grade:B ----
 Chromosome = gi|408541726|gb|JH947206.1|:subseq_13264141,100905_ Strand = + Positions = 8360 - 8433
 Found by:  Infernal (score=11.06) Covels (score=0.41)
 Stem2 length = 7   Apical loop length = 24   Insertion in stem2 = 0, 0
 Free Energy = -14.06

         ..(((((((.......(((((((((((........................)))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccgAAAcCcuuuuugggguggg-ccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((.......([[((((((((........................))))))))]])----..-.)))))))..
 target  UUCUUUUCUCUGCUAGUGAAGUCUGGGGAAGGGAUAGUCUCCCCAGAGCUGCCCAGGCUGAG----GG-CAGAAGGGCU
                         ****        ^^                            ****         

>SECIS.1 chromosome:gi|408541726|gb|JH947206.1|:subseq_13264141,100905_ strand:- positions:44304-44381
GGCUCCACCAGCUGGGGUGAGGGGGUGGUGGUCAGUGCCAAGCUGGGCUGCCAUCCCAGAGGCCGGCUGGGAGGCCCA
>SECIS.2 chromosome:gi|408541726|gb|JH947206.1|:subseq_13264141,100905_ strand:- positions:88360-88437
CACAGCAGGCAUCCCAAGGAUGGGUCAGCCCUCCACGCAGCCCCCAGGGCCUCACCUUGAAGAGGCGGAAGGCAGCCA
>SECIS.3 chromosome:gi|408541726|gb|JH947206.1|:subseq_13264141,100905_ strand:+ positions:8360-8433
UUCUUUUCUCUGCUAGUGAAGUCUGGGGAAGGGAUAGUCUCCCCAGAGCUGCCCAGGCUGAGGGCAGAAGGGCU