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

 Blastx evalue: 1e-18
 Query name: gi|844287341|gb|AKN04700.1| thioredoxin reductase 2, partial [Meleagris gallopavo]
 Query range: 2-450  (total 450)

 Target: /data/www-rg/seblastian_results/848666714/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: -
 Positions:
 -Exon 1  77690        77838
 -Exon 2  77299        77373
 -Exon 3  76380        76458
 -Exon 4  75385        75447
 -Exon 5  74963        75033
 -Exon 6  71013        71124
 -Exon 7  69485        69659
 -Exon 8  60941        61077
 -Exon 9  55522        55617
 -Exon 10 55215        55307
 -Exon 11 54394        54465
 -Exon 12 52465        52562
 -Exon 13 50000        50126

 Redox box: no

Query   RGTKWGLGGTCVNVGCIPKKLMHQAALLGGALKDAQHYGWSMAHPVHHSW <---Intron---> SVMAQAVQNYVKSLNWGHRVQLQDK <---Intr
        /|| ||||||||||||||||||||||||| ||||||||||/// ||||/| <   316bp    > ||||| |||||||||||||||||/| <   840b
Target  QGTAWGLGGTCVNVGCIPKKLMHQAALLGSALKDAQHYGWNISQPVHHTW                SVMAQGVQNYVKSLNWGHRVQLQEK         
        cgagtgcggatgaggtacaacaccggctgagcaggcctgtaatccgccat                tgagcggcatgattatgcagcccga         
        agccggtggcgtatggtcaattaaccttggctaacaaaggatcactaacg                cttcagtaaatactaggagtataaa         
        aacagattattgttccttagtgtatctagtctatcgctcgtacattttc                gtggaattgttgacgcgacagaaaa          
                                                                                                            

Query   on---> KVKYFNMKGSFLDSHTVCGLAKGGKK <---Intron---> TTLTAEKIVIATGGRPKYPTH <---Intron---> ITGALEYGITSDDL
        p    > ||||||/|||| | ||| || | ||/ <   932bp    >   /||/ |||||||||||| | <   351bp    > / ||||||||||||
Target         KVKYFNIKGSFSDPHTVRGLTKAGKE                IVITADNIVIATGGRPKYPMH                VAGALEYGITSDDL
               agattaaagattgccagcgtaaggag                agaaggaagagaggacatcac                ggggcgtgaaaggc
               ataatataggtcacactggtcacgaa                tttccaatttccgggcaacta                tcgctaagtcgaat
              gggatccaaattttatacttaaagtag                ttttatttctttaaaaactgt                tataggtacatttc
                                                                                                            

Query   FWLKDSPGKT <---Intron---> LVVGASYVSLECAGFLTGVGLDTAVMMRSIPLRGFDQ <---Intron---> QMASLVTEHMESYGTKFLKKC
        |||| ||||| <   3838bp   > |   /  |||||||||||/|||| |||||/||||||| <   1353bp   > |||||||||||||||||||/|
Target  FWLKKSPGKT                LTGVSPDVSLECAGFLTGIGLDTTVMMRSVPLRGFDQ                QMASLVTEHMESYGTKFLKRC
        tttaatcgaa                taggtcggtcgtggtcagagtgaagaaaagcccgtgc                cagttgagcagttgaattaat
        tgtaaccgac                tcgtccatctagcgttcgtgtacctttggtctggtaa                atccttcaatacagcattagg
        cgagattaa                cattgaattctgttttaactagctacggatcattgttg                agttaatgcgattcaatagat
                                                                                                            

Query   VPMKVEKLESGRLQVTWKNTDLGTEEMDSFDTVMWAVG <---Intron---> RVPDSETLNLEIVGVKTNSETGKIIVDASEATSVPHIYAIGDITE 
        || ||||||  |||||||| || ||| |||/||||||| <   8407bp   > | ||//||||| |||||||||||||||||||||||||||/||||| 
Target  VPTKVEKLEGDRLQVTWKNADLDTEETDSFNTVMWAVG                RAPDTKTLNLETVGVKTNSETGKIIVDASEATSVPHIYAVGDITE 
        gcaaggatgggatcgataaggcgaggagttaagatggg                cgcgaaacatgagggaaatgagaaagggaggatgccatggggaag 
        tccataatagagtatcgaacatacaacactacttgct                ggccacactatactgtacacacgatttacgaccctcatactgatca 
        catataaggccagactgattcgcaaagttccctggaa                cactccatctggatagatctatagttttctatttttcttatacaag 
                                                                                                            

Query   <---Intron---> GRPELTPTAIAAGKLLARRLFGHSSELMDYDN <---Intron---> VPTTVFTPLEYGCVGLSEEKAVQCYGSDNVE <---I
        <   5323bp   > |||||||||||||||||/|||| ||||||||/ <   214bp    > ||||||||||||||||||| ||| /||||/| <   7
Target                 GRPELTPTAIAAGKLLAQRLFGQSSELMDYDS                VPTTVFTPLEYGCVGLSEEAAVQRHGSDNIE      
                       gccgtacagagggaccgccctgcttgcagtga                gcaagtactgtgtggctgggggcccgtgaag      
                       ggcatcccctccgattcagttgaccattaaag                tcccttcctaaggtgtcaacctagagcaata      
                       cttaaacaaataaaggtgtgccgtagggctct                gtcacctcgattttcgaaaatgattaacttg      
                                                                                                            

Query   ntron---> VFHAYYKPLEFTAAERDAAQCYMK <---Intron---> MVCLREREQRILGLHFIGPNAGEVIQGFALGIK <---Intron---> C
        49bp    > |/|||||||||| ||||| ||||| <   1831bp   > ||||||||||||||||||||||||||||||||| <   2338bp   > |
Target            VYHAYYKPLEFTVAERDATQCYMK                MVCLREREQRILGLHFIGPNAGEVIQGFALGIK                C
                  gtcgttactgtagggaggacttaa                agttcgagccacgcctagcaggggacgtgcgaa                t
                  taacaaactatctcagaccagata                ttgtgagaagttgtattgcacgattagtctgta                g
                  actattatagcagtagtatactga                ggcaagggaaatcttctaatacattaatttac                gt
                                                                                                            

Query   GATYPQLMKTIGIHPTCAEEITKLHITKRSGLDATVTGCUG
        ||||||/|||/|||||||||/||||||||||||||||||||
Target  GATYPQMMKTVGIHPTCAEEVTKLHITKRSGLDATVTGCUG
        ggatccaaaaggaccatggggaatcaaactgcggagagttg
        gccacattactgtaccgcaatcatatcagcgtacctcgggg
        ttgttggggatctcccttaatcggctagttcgtaacaccat
                                               * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 2916 ; UGA-SECIS: 2919

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = - Positions = 47083 - 47006
 Found by:  Infernal (score=30.44) Covels (score=29.61)
 Stem2 length = 11   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -16.53

         ..(((((((.......((((((((((.(((((...............))))).)))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggc-caggcCuGAUGuuu-uuucaugaccggc
         ..((((({(.......([[((((((((((((......-..........))))))))))))]]).....-.-.)})))))..
 target  UUAGGAUGCCAGCUGAUGAGGAUUUGUUUGUCAAACC-ACACCAUGGUGCAAACAAGUCUGAGCUUUU-C-UGGGUCCUUC
                         ****            ^^^                        ****