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

 Blastx evalue: 9e-42
 Query name: gi|992178883|ref|XP_007234102.2| PREDICTED: selenoprotein T2-like [Astyanax mexicanus]
 Query range: 1-223  (total 226)

 Target: /data/www-rg/seblastian_results/610542656/tempfiles/temptarget.fasta
 Chromosome: CM007959.1:subseq_15652970,101553_ Strand: -
 Positions:
 -Exon 1  51336        51553
 -Exon 2  50625        50735
 -Exon 3  50407        50533
 -Exon 4  50258        50345
 -Exon 5  50006        50115

 Redox box: YES

Query   MAEYSQAGILTALLLFTVVTVRDIYLGRSAVEQQPEHQQQQAAAESSGPGGFLNPDPLTQRQSKAKFYTGPLLKFQYC <---Intron---> ISUGYS
        |||||| ||||||||||||||/|||/||| / |   |  | / / / |     / ||  || ||   ||||/||||/| <   600bp    > ||||||
Target  MAEYSQTGILTALLLFTVVTVKDIYVGRSMMTQ---HPAQASDSLNMGADSLRDADP--QRFSKQALYTGPVLKFQFC                ISUGYS
        aggtacagatagccctaggagagatggataaac---ccgcgtgacaagggatcgggc--cataacgctagcgcatctt                attgta
        tcaagacgttccttttcttctaatatggcttca---accaccagtatgcagtgacac--agtgaactacgcttatatg                tcggag
        gaatcagtcgggtggcatctaactccggcggta---caggctccgtggtttggtcca--ggccggccctgaggacgt                cccagtc
                                                                                                        *   

Query   KVFQEYSRSISQLYPDIRIEGENYPPKPLNK <---Intron---> YAANFISYFKLLAIALVVTGQNPFQMLGMETPRIWSWGQENK <---Intron
        ||||||||||||||||||||||||||  /|| <    91bp    > |  || ||||||||||||/||||| |||/|||| |/| |||| <    61bp 
Target  KVFQEYSRSISQLYPDIRIEGENYPPTTINK                YLGNFFSYFKLLAIALVVSGQNPFAMLGLETPRAWTWTQENK           
        agtcgttctaacttcgacagggatccaaaaa                tcgatttttaccgagcggagcactgacgcgacagtatacgaa           
        attaaacgctgatacatgtagaaacccctaa                atgattcatattctctttggaactcttgtaccgcgcgcaaaa           
        ggcggccgtccggcgcccaagatctcaccc                atcatctcccattctcgtctaatcctgtaggtcaagggtaatg           
                                                                                                            

Query   ---> IFSCLMAFFLSNMLETHFLSTGAFEITLND <---Intron---> VPIWSKLQSGYVPNIQELFNILDNHLKMNQVDKLKF
           > |||||| |||||||||||||| |||||||| <   142bp    > |||||||||||||||||/| |||||/|||||||/ |
Target       IFSCLMTFFLSNMLETHFLSTSAFEITLND                VPIWSKLQSGYVPNIQEIFQILDNHIKMNQVDKISF
             atttcaattcaaatgactttaagtgaacag                gcattacctgtgcaacgatcacgacaaaacggaatt
             ttcgttctttgattacattccgctatcta                atctgcatacgatcataattattaaatataataatct
             acgcggaccctcgggcccgcctatacaat                taacgcgggaacacctggccactttctggtatcgcct
                                                                                               
 Sequence until next stop: 
CCATCTCTGTAG
 P  S  L  * 

 Distance CDS-SECIS: 196 ; UGA-SECIS: 622

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007959.1:subseq_15652970,101553_ Strand = - Positions = 49809 - 49726
 Found by:  Infernal (score=28.53) Covels (score=30.03)
 Stem2 length = 10   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -20.23

         ..(((((((................(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg---------UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ((((((({(................{[[[((((((((((.................))))))))))]]]}..--..-.)})))))))
 target  UCAGUGGGACUGCAUUGUGGUGUAAUGAAGGCUUGGUCUGCAAACAGCUAGCUGUGAGGCCAGGCUGGAUGU--CC-CUGCCACUGA
                                  ****            ^^^                      ****