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

 Blastx evalue: 6e-49
 Query name: gi|908549945|ref|XP_003458718.2| PREDICTED: selenoprotein T2-like [Oreochromis niloticus]
 Query range: 2-222  (total 223)

 Target: /data/www-rg/seblastian_results/381602060/tempfiles/temptarget.fasta
 Chromosome: OMLM01010512.1:subseq_1,12408_ Strand: +
 Positions:
 -Exon 1  7463         7683
 -Exon 2  10878        10988
 -Exon 3  11079        11205
 -Exon 4  11286        11373
 -Exon 5  11455        11570

 Redox box: YES

Query   KKTTAIMAEYSQTGLLAALLLFTALTLRDIYVGRSSSQSGHQPPDNSAVFPDTEPRKPAKAAIYSGPVLRFQYC <---Intron---> ISUGYSKVFQ
        ////| |||/||| ||||||||/|||/||||/| |||| |/|| ||  | || /  ||||///|/||||/|||| <   3194bp   > ||||||||||
Target  RRSSANMAEFSQTSLLAALLLFSALTVRDIYLGSSSSQRGYQPSDNPNVSPDIKTGKPAKSSLYTGPVLKFQYC                ISUGYSKVFQ
        acttgaaggtacaactggcccttgcagcgatcgatatccgtccagacagtcgaaagacgattctagcgcatctt                attgtaagtc
        ggcccatcatgacgttccttttcctctgatatggcgcaggaacgaacatccatacgaccacctacgcttataag                tcggagatta
        agcaacgggccggccggtgcgtggcgcgcttcccgtggcacagcctccccgcagtaagcggtgtagcgggcgc                ttcaaccagcg
                                                                                                    *       

Query   DYSQAISQVYPDIRIQGENYPPTAFNR <---Intron---> CVAQLISYLKLLSILVIVSGQNPFLLLHLQTPPAWTWSQNNK <---Intron--->
        /|//||||/|||/ |/||||||| ||| <    90bp    > |   ||||||||/||/||||||||/|| | || ||||/|/|| <    80bp    >
Target  EYARAISQLYPDLHIEGENYPPTPFNR                CAGNLISYLKLLAILLIVSGQNPFVLLGLHTPRAWTWTQDNK               
        gtgcgaacctcgccagggatccactaa                tggacattcaccgaccagagcactgccgccacagtatacgaa               
        aacgctgatacatatagaaacccctag                gcgattcatattctttttggaacttttgtaccgcgcgcaaaa               
        gctacccggcgccctgggcccccccc                gtatcacccggccccgccttggtcccctctctcacgcgcgccg               
                                                                                                            

Query    IFSCLMAFFLCNMMETHFLSTGAFEVTLND <---Intron---> VPLWSKLQSGYVPNIQEMFQILDNHMKMNQVDHMTFTS
         |||||||||||||||||||||||||/|||/ <    81bp    > |||||||||||||||||/|||||/|||/|||||/||//
Target   IFSCLMAFFLCNMMETHFLSTGAFEITLNE                VPLWSKLQSGYVPNIQEIFQILDSHMKLNQVDHVTFSA
         atttcagttctaaagactctaggtgaacag                gctttacctgtgcaacgatcacgacaacacggcgattg
         ttcgttctttgattacattccgctatcta                atctgcatacgatcataattattagatataataatctcc
         ctctcgccccccgggttcgctaccgctac                actggcgtattttgccggttgctcccgggcggccgccct
                                                                                             
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 156 ; UGA-SECIS: 588

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = OMLM01010512.1:subseq_1,12408_ Strand = + Positions = 11727 - 11798
 Found by:  Infernal (score=32.99) Covels (score=32.54)
 Stem2 length = 11   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -21.04

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ....(((((---....{[[[(((((((((((.....-.........)))))))))))]]]}..--....)))))....
 target  CUGCUGGCG---UUCAUGAAGGUUGGGUCCUAAAGC-AGACUCUGCAGGGCCUGGCUGGAUGU--CCCCCGCCACAAA
                         ****           ^^^                       ****