------- SECIS element -- id:1 -- grade:B ----
 Chromosome = your_sequence Strand = - Positions = 3517 - 3433
 Found by:  Covels (score=10.12)
 Stem2 length = 10   Apical loop length = 21   Insertion in stem2 = 0, 0
 Free Energy = -6.4
 Type = 1

         ..(((((((........(((((((((((((((.....................)))))))))))))))..........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcC------cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .......({(.......{[[{{((((((((((.....................))))))))))}}]]}....-.-..)}).......
 target  GGCAGCGUUGCCuUUUAUGAACCUCAGGGAGGAACACuugcuuCUCCUCUGUCCUUCCCUGGGCAGAUGCGu-c-UAUUGGCAGAGU
                          ****           ^^                              ****                   

------- SECIS element -- id:2 -- grade:B ----
 Chromosome = your_sequence Strand = - Positions = 71982 - 71908
 Found by:  Covels (score=5.12)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -11.2
 Type = 1

         ..(((((((........(((((((((((((((.................)))))))))))))))........)))))))....
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccg--gc
         .(({([{((((......([[[(((([(((((------(...........))))))]))))]]])..--..))))}])}))...
 target  UUGCGGAUCUUAaUUAAUGAAUUCCAUCCAU------uuCCAUCAGACCGGUGGGGGGGGGGAGGG--GAGAGAAACACacGG
                          ****                  ^^                   ****                   

------- SECIS element -- id:3 -- grade:C ----
 Chromosome = your_sequence Strand = + Positions = 210264 - 210340
 Found by:  Covels (score=5.0)
 Stem2 length = 8   Apical loop length = 15   Insertion in stem2 = 0, 0
 Free Energy = -9.5
 Type = 1

         ..(((((((........((((((((((.(((((.................))))).))))))))))..........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccug-gcccuAAAcC--cuuuuuggggcgggc-caggcCuGAUGuu-u-uuucaugaccggc
         ..(({(({(........([[[{(((((({((.------..............))}))))))}]]])......-...)}))})-).
 target  CUCUCAUGUCCUgCUUAUGAGUUUCCCaGAGG------uaUCCCCUUGGCCACUGuGGGAACAGAAUGCuGg-GCUAGAUAG-GC
                          ****                                         ****                   

------- SECIS element -- id:4 -- grade:C ----
 Chromosome = your_sequence Strand = + Positions = 161546 - 161630
 Found by:  Covels (score=5.42)
 Stem2 length = 9   Apical loop length = 21   Insertion in stem2 = 0, 0
 Free Energy = -8.9   Free energy of apical portion = -6.4
 Type = 2

         ..(((((((........((((((((((.(((((...................))))).)))))))))).........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccug-gcccuAAAcC----cuuuuuggggcgggc-caggcCuGAUGuuu-uuucaugaccggc
         ....(({(.........([[{{({(((([(((..((((((....))))))...)))]))))})}}]]).....-....)}))....
 target  CCAUCAUUAAGUaACCAUGAUUUACAGcAUGGAUAGCCaaccUUUUGGCUUCCUUGGgCUGCACUGAGUGAAg-AGGAAUUGUCUU
                          ****                                           ****                  

------- SECIS element -- id:5 -- grade:C ----
 Chromosome = your_sequence Strand = + Positions = 123513 - 123586
 Found by:  Covels (score=13.12)
 Stem2 length = 8   Apical loop length = 10   Insertion in stem2 = 0, 0
 Free Energy = -8.7
 Type = 1

         ..(((((((........(((((((((((((((...............))))))))))))))).........)))))))...
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccg-gc
         .(({(([{(........([[(((({{{(((((........-----..)))))}}}))))]]).....-.-.)}]))}))..
 target  AGCUGCACAGAGaAACAGGAAGGACCAACCUGAAAUCUCC-----UCUGGGUCUUUCUUGAUUCCCu-C-AUCGGUUGcCA
                          ****           ^^^                       ****                   

------- SECIS element -- id:6 -- grade:B ----
 Chromosome = your_sequence Strand = + Positions = 88543 - 88618
 Found by:  Covels (score=6.85)
 Stem2 length = 8   Apical loop length = 10   Insertion in stem2 = 0, 0
 Free Energy = -10.6
 Type = 1

         ..(((((((........((((((((((.(((((...............))))).)))))))))).........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggc-caggcCuGAUGuuu-uuucaugaccggc
         ..(([({(((((.....{[[[([{({({((({(........-----..)})))})})}])]]]}.....-)))))})]))..
 target  CAUGAAAUGGCCaGGUUUGAAGACCCCuGCUCUAAACCUAA-----GGGCAGCcGAGAGUGGAUAGAAa-GGCCACUGUAAC
                          ****            ^^^                        ****                  

------- SECIS element -- id:7 -- grade:B ----
 Chromosome = your_sequence Strand = + Positions = 71940 - 72021
 Found by:  Covels (score=9.14)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 1, 0
 Free Energy = -4.5   Free energy of apical portion = -2.4
 Type = 2

         ..(((((((........((((((((((.((.(((...............))))).))))))))))............)))))))..
 model   uucggucaugcg-UuaAUGAcGgccug-gc-ccuAAAcCcuuuuuggggcgggc-caggcCuGAUGuu---u-uuucaugaccggc
         ..({{(({(........{[{([((((((-(.((......-(((....))))))-))))))])}]}........-...)}))}})..
 target  GGUCUGAUGGAAaUGGAUGGAAUUCAUu-AaUUAAGAUC-CGCAAUCGCGGAU-gAUGAAGUGAUGAGgacGu-UUGCCUCUUGGC
                          ****            ^^                          ****                     

------- SECIS element -- id:8 -- grade:B ----
 Chromosome = your_sequence Strand = - Positions = 193572 - 193491
 Found by:  Infernal (score=12.28) Covels (score=0.32)
 Stem2 length = 10   Apical loop length = 27   Insertion in stem2 = 0, 0
 Free Energy = -24.9   Free energy of apical portion = -4.2
 Type = 2

         ..(((((((.......((((((((((.(((((.........................))))).))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuugggg----------cgggc-caggcCuGAUGuuuuuucaugaccggc
         ((((((((((--(...([[{([([((({(((...........((.(((....))).)))))})))])])}]])----)--))))))))))
 target  CUCUGCCUUG--UCUAUGAUGACACAUUUUCUAAUGGUGACAGCUGGAUGAAUCCUGCGGAUAUGGGGCUGAG----A--UGAGGCAGGG
                         ****            ^^                                   ****                 

------- SECIS element -- id:9 -- grade:B ----
 Chromosome = your_sequence Strand = + Positions = 116098 - 116159
 Found by:  Infernal (score=13.89) Covels (score=1.06)
 Stem2 length = 8   Apical loop length = 8   Insertion in stem2 = 0, 0
 Free Energy = -11.6
 Type = 1

         ..(((((((........((((((((((((.....................))))))))))))........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccgAAAcCcuuuuuggggugggccaggcCuGAUGuuuuuucaugaccggc
         ....(((((........{[[{((((((((........-------------))))))))}]]}----....)))))....
 target  UCCAGUGUGCUUGUGAUUGAUGGCAGACUUGAAUCUU-------------GGUCUGUCUGAU----CCUACACACCUUC
                          ****          ^^                         ****