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

 Blastx evalue: 5e-26
 Query name: gi|950942516|ref|XP_014450858.1| PREDICTED: selenoprotein M, partial [Alligator mississippiensis]
 Query range: 1-147  (total 147)

 Target: /data/www-rg/seblastian_results/190015676/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: +
 Positions:
 -Exon 1  46810        46863
 -Exon 2  48902        48937
 -Exon 3  49246        49280
 -Exon 4  50008        50086
 -Exon 5  60800        61036

 Redox box: YES

Query   APRPDPRQLQGLARGKVE <---Intron---> TCGGURLNRMKE <---Intron---> VKAFVTEDIPLY <---Intron---> HNLVMKHLPG
        |  ||  /|||||||||| <   2038bp   > ||||| |||/|| <   308bp    > |||||||||||| <   727bp    > ||||||||||
Target  AYEPDWGKLQGLARGKVE                TCGGUWLNRLKE                VKAFVTEDIPLY                HNLVMKHLPG
        gtgcgtgaccgcgcgagg                atggttcaccag                gagtgaggacct                cacgaacccg
        caacaggatagtcggata                cgggggtagtaa                tacttcaatcta                aatttaatcg
        ccggcgggggggcgcggg                ccaaaggtcggg                ggttccgcctg                cccggggtcta
                                              *                                                             

Query   ADPELVLLNIRYEELE <---Intron---> RIPLSDMTREEINQMVQELGFYRKESQDAPVPEEFQLAPAKPPLPLQTKEENSEVSPSEASAAKNESP
        ||||||||| |||||| <  10713bp   > |||||||/||||||/||||||||||/ || ||||||||||/|   || ||/ /      | |||/| |
Target  ADPELVLLNFRYEELE                RIPLSDMSREEINQLVQELGFYRKEAPDALVPEEFQLAPARPLPILQAKEQGAGPPFPPAPAAKSEHP
        ggcgcgccatatggcg                aaccagaacggaaccgcgcgttcaggcggcgcggtccgcgacccaccgagcgggcctccgcggaagcc
        cacattttatgaaata                gtctgatggaataattaatgtagaaccacttcaatatcccgctcttacaaagcgcctccccccagaac
        tctgtggcccacgggg                atcgtcgcgagtcggggggatccggattcggtggcgccacgtgccgaggggctaacccattatgcgtc
                                                                                                            

Query   TEPNNQEHPDL
          | |||||||
Target  RMPGNQEHPDL
        aacgacgccgc
        gtcgaaaacat
        ggtccgacata
                   
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 263 ; UGA-SECIS: 635

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = + Positions = 61300 - 61368
 Found by:  Infernal (score=34.13) Covels (score=25.0)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -24.94

         ..(((((((.......(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ..({(((((---....{[[[(((((((((..........-----....)))))))))]]]}.....-.-.)))))})..
 target  UGCAGGGAC---AGAAUGAAGCCCUCAGCUGAAAGCUCU-----GGGUGCUGAGGGUGGAUGAGCU-G-AGUCCCAGAG
                         ****           ^^^                       ****