------- SECIS element -- id:1 -- grade:B ----
 Chromosome = your_sequence Strand = - Positions = 48269 - 48196
 Found by:  Covels (score=7.38)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -13.0   Free energy of apical portion = -0.4
 Type = 2

         ..(((((((........(((((((((((((((..................)))))))))))))))........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcC---cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .....({(((.......([[([({(((((((------((((......)))))))))))})])]])..--...)))}).....
 target  AAUGAUAAUGUUcAUAAUGAUAAUGAUAAUG------uucAAUAUCAUGAAUAUUAUCCUGAGAAUU--AUUUAUAAAACAA
                          ****                   ^^                   ****                 

------- SECIS element -- id:2 -- grade:C ----
 Chromosome = your_sequence Strand = - Positions = 59652 - 59576
 Found by:  Covels (score=7.39)
 Stem2 length = 7   Apical loop length = 15   Insertion in stem2 = 0, 0
 Free Energy = -7.3
 Type = 1

         ..(((((((........(((((((((((((((...............)))))))))))))))...........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu--u-uuucaugaccggc
         ...({((((((((....([[(({{[({((((......--.........))))})]}}))]]).....))-)-)))))})-..
 target  GCAAUGCUUUGCaGCAAUGAGGACGUCAGUAGAAAGC--UGUGCAGUAUGUUAGAUCCUGAGGACagUg-C-GGAGCCU-AA
                          ****           ^^^                       ****                    

------- SECIS element -- id:3 -- grade:B ----
 Chromosome = your_sequence Strand = - Positions = 184815 - 184735
 Found by:  Covels (score=8.48)
 Stem2 length = 11   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -4.7
 Type = 1

         ..(((((((........(((((((((((((((.................)))))))))))))))........)))))))....
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccg--gc
         .((({((((........([[[[(((([(((((.................)))))]))))]]]])..--....))))})))...
 target  UGAUAGGGCAUGcUCGUUGAAAUAUUAAGAUUAACUUaaUUAAGAUUAAGGUCUGGAUGGGGAGAA--ACAGGCUUCGUcuCA
                          ****           ^^                          ****                   

------- SECIS element -- id:4 -- grade:B ----
 Chromosome = your_sequence Strand = - Positions = 204008 - 203925
 Found by:  Covels (score=8.59)
 Stem2 length = 10   Apical loop length = 20   Insertion in stem2 = 0, 0
 Free Energy = -8.5   Free energy of apical portion = -0.9
 Type = 2

         ..(((((((........(((((((((((((((....................))))))))))))))).........)))))))...
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcC-----cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccg-gc
         .({(({{(((.......([[((({((((((((...(((((...)))))....))))))))})))]]).....-.-)))}}))})..
 target  GGUUUUCUGAAUgUUUUUGAGGUUAUUUUCAACAUUGaauugUAUUCAUUUUUUGAAAAUUGCUGAAAGAAa-A-UUAAUGACuAA
                          ****                                          ****                   

------- SECIS element -- id:5 -- grade:C ----
 Chromosome = your_sequence Strand = - Positions = 224994 - 224915
 Found by:  Covels (score=6.3)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -9.0   Free energy of apical portion = -0.7
 Type = 2

         ..(((((((........(((((((((((((((................))))))))))))))).........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuu-uuuucaugaccggc
         .((({{{{(........([[{{(({{(((((((((((......)))))))))))}}))}}]]).....-...)}}}}))).
 target  UUGGUUCGGAGUgGAGAUGAAAAGCUGGGUAUCAUCAgCAUAUUGAUGAUACCUCACUCCGAAACCaC-GUAUGAUCUCAC
                          ****                                      ****                  

------- SECIS element -- id:6 -- grade:B ----
 Chromosome = your_sequence Strand = + Positions = 251360 - 251433
 Found by:  Covels (score=7.55)
 Stem2 length = 9   Apical loop length = 12   Insertion in stem2 = 0, 0
 Free Energy = -8.7
 Type = 1

         ..(((((((........(((((((((((((((...............))))))))))))))).........)))))))...
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccg-gc
         ...(({((((((.....{[[({(((((((((.........-----...)))))))))})]]}....)-)-))))}))....
 target  CAAUUCUUUUUAgUGGAUGAUCAGGUGAGAUGAACAGACA-----UGAAUCUUAUUUAAGAUACAGu-A-GGAAUAACcAA
                          ****           ^^                        ****                   

------- SECIS element -- id:7 -- grade:C ----
 Chromosome = your_sequence Strand = + Positions = 90689 - 90766
 Found by:  Covels (score=6.65)
 Stem2 length = 7   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -10.6   Free energy of apical portion = -2.4
 Type = 2

         ..(((((((........((((((((((.(((((...............))))).))))))))))........)))))))....
 model   uucggucaugcg-UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggc-caggcCuGAUGuuuuuucaugaccg--gc
         .(((({({(........{[[{({({({(-{(((..(((-(....)))))))}-)})})})}]]}..--....)})}))))...
 target  UCUAGCCAUAUUaAUAAUGAAUACUACa-AUUUCCACU-GAUUUCAGUGGAC-uUUUGAAAGAUUU--UGUGAAGCCUGguCU
                          ****            ^^                         ****                   

------- SECIS element -- id:8 -- grade:B ----
 Chromosome = your_sequence Strand = + Positions = 59658 - 59730
 Found by:  Covels (score=7.52)
 Stem2 length = 9   Apical loop length = 11   Insertion in stem2 = 0, 2
 Free Energy = -4.8
 Type = 1

         ..(((((((........(((((((((((((((...............)))))))..))))))))...........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggcca--ggcCuGAUGuu--u-uuucaugaccggc
         ..(((..((((......([[((((((((((.......--------....)))))..)))))]]).......-.))))--)))..
 target  GGAAGUUACGGCuGGAAUGAAGGAACGAAUAAAAAUA--------AGGGAUUCGucUUCUUGAACGAgaAg-UUCGU--CUUAU
                          ****         ^^^                           ****                    

------- SECIS element -- id:9 -- grade:B ----
 Chromosome = your_sequence Strand = + Positions = 21762 - 21841
 Found by:  Covels (score=8.65)
 Stem2 length = 8   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -5.0   Free energy of apical portion = -2.0
 Type = 2

         ..(((((((.........(((((((((((((((................))))))))))))))).........)))))))...
 model   uucggucaugcg--UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccg-gc
         .(-{({(((.........([[{({({((((((.....(((......))).))))))})})}]]).....-.-.)))})})...
 target  AU-AUCACUUUGuuAUUUUGAUGAAAGCAAUCAAAAUUgGAGAUGCCCAGGAUUGUCUCUUGAGCCUAg-A-UAGUAAAAaGC
                           ****          ^^^                         ****                   

------- SECIS element -- id:10 -- grade:B ----
 Chromosome = your_sequence Strand = + Positions = 49036 - 49117
 Found by:  Infernal (score=11.24)
 Stem2 length = 7   Apical loop length = 25   Insertion in stem2 = 0, 0
 Free Energy = -4.2
 Type = 1

         ..(((((((.......(((((((((((((((.....................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC------cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...((((((.......{[[{{((((({((.........................))})))))}}]]}..--....))))))...
 target  UUUAUUUCUUCAACAGUGACAGUGGAGUCCCAAGCAUUUACCACUUUCCCAUCUGAGUCUACCAGAUAU--UUCCAGAAAUUCC
                         ****           ^^                              ****                 

------- SECIS element -- id:11 -- grade:B ----
 Chromosome = your_sequence Strand = - Positions = 420 - 334
 Found by:  Infernal (score=13.25) Covels (score=1.25)
 Stem2 length = 9   Apical loop length = 24   Insertion in stem2 = 0, 0
 Free Energy = -10.4   Free energy of apical portion = -0.4
 Type = 2

         ..(((((((..........(((((((((((((((......................))))))))))))))).........)))))))..
 model   uucggucaugcg---UuaAUGAcGgccuggcccuAAAcC-------cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ..(({(((((.........{[[[(((((((({(.........((.......))....)}))))))))]]]}.....-.-)))))}))..
 target  CAUAAAUCUGUCUAUGUAGUGAAGGCUUUCUUUGAAGGACAAGCAGGACAAGCAGAGACAGAAAGUCGGAUAUAGA-C-CAGGUCUAGA
                            ****           ^^                               ****                  

------- SECIS element -- id:12 -- grade:C ----
 Chromosome = your_sequence Strand = + Positions = 12174 - 12251
 Found by:  Infernal (score=13.48) Covels (score=9.7)
 Stem2 length = 8   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -6.3
 Type = 1

         ..(((((((.......(((((((((((((((...............)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ...((([(((......{[[((({(({{((((.....-.........))))}}))})))]]}......-..)))])))...
 target  CCAGGCAUUGUCAGAAUGAAAGCUUUAGCUAGAAGC-UACCUCUGGUGGCCUGGCCUUGAUAAGGCC-AUUGAGGCUCAA
                         ****            ^^                       ****