_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:1     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 1e-04
 Query name: gi|33519426|ref|NP_877393.1| thioredoxin reductase 1, cytoplasmic isoform 2 [Homo sapiens] >gi|33519428|ref|NP_877419.1| thioredoxin reductase 1, cytoplasmic isoform 2 [Homo sapiens] >gi|33519430|ref|NP_877420.1| thioredoxin reductase 1, cytoplasmic isoform 2 [Homo sapiens] >gi|34782844|gb|AAH18122.2| Thioredoxin reductase 1 [Homo sapiens]
 Query range: 364-499  (total 499)

 Target: /var/www/seblastian_output/357440974/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: -
 Positions:
 -Exon 1  44867        44977
 -Exon 2  41908        42003
 -Exon 3  36902        37036
 -Exon 4  18422        18487

 Redox box: no

Query   KCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIE <---Intron---> VYHSYFWPLEWTIPSRDNNKCYAKIICNTKDN <---Intron--->
        /|||||||||||||||||||||||||||||||||||| <   2863bp   > |||||||||||||||||||||||||||||||| <   4871bp   >
Target  QCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIE                VYHSYFWPLEWTIPSRDNNKCYAKIICNTKDN               
        ctgtgagcaagtactgtggtgctggagggatgggaag                gtcatttctgtaactagaaattgaaataaaga               
        agaaaatcccttcctaagcggtcaaactaatgaaata                taagatgctagctccgaaaagacattgacaaa               
        gtctattactatttgattttcttggatgggtgaattg                tcttctgagaggtaaatccattaaactttact               
                                                                                                            

Query    ERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAE <---Intron---> VFTTLSVTKRSGASILQAGCUG
         ||||||||||||||||||||||||||||||||||||||||||||| <  18414bp   > ||||||||||||||||||||||
Target   ERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAE                VFTTLSVTKRSGASILQAGCUG
         gcgggtcgcgcaggggacgtgggcatgcaaaccgaaagaccgtgg                gtaattgaactggaaccggttg
         agttgtattgcacgatcagtccctaggtcaaatagctgtactgca                ttcctctcagcgcgttacgggg
         attgctcagtattaataaccatagatagcagggccatacctctag                acaagtgcgctgacccgtccat
                                                                                          * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 217 ; UGA-SECIS: 220

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = - Positions = 18204 - 18118
 Found by:  Infernal (score=27.14) Covels (score=23.03)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 1, 0
 Free Energy = -14.3

         ..(((((((......................((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg---------------UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .(((((((((.....................([[[((((((.((((......---........))))))))))]]])----...))))))))).
 target  CAUUUGGCAGGGCAUCAAAGGGAUGCAUCCAUGAAGUCACCAGUCUCAAGCC---CAUGGGGUAGGCGGUGAUGGAA----CAACUGUCAAAUC
                                        ****            ^^                        ****