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

 Blastx evalue: 9e-17
 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/410011353/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: +
 Positions:
 -Exon 1  49997        50145
 -Exon 2  50469        50543
 -Exon 3  51373        51451
 -Exon 4  52375        52437
 -Exon 5  52789        52859
 -Exon 6  56657        56768
 -Exon 7  58073        58247
 -Exon 8  65800        65936
 -Exon 9  71213        71308
 -Exon 10 71497        71589
 -Exon 11 72379        72450
 -Exon 12 74541        74638
 -Exon 13 76874        77000

 Redox box: no

Query   RGTKWGLGGTCVNVGCIPKKLMHQAALLGGALKDAQHYGWSMAHPVHHSW <---Intron---> SVMAQAVQNYVKSLNWGHRVQLQDK <---Intr
        /|| ||||||||||||||||||||||||| ||||||||||/// ||||/| <   323bp    > ||||| |||||||||||||||||/| <   829b
Target  QGTSWGLGGTCVNVGCIPKKLMHQAALLGSALKDAQHYGWNISQPVHHTW                SVMAQGVQNYVKSLNWGHRVQLQEK         
        cgattgcggatgaggtacaacaccggctgagcaggcctgtaatccgccat                tgagcggcatgattatgcagcccga         
        agccggtggcgtatggtcaattaaccttggctaacaaaggatcactaacg                cttcagtaaatactaggagtataaa         
        agcagattattgttccttagtgtaactagtttatcactcgtacattttc                gtggaattgttgacgcgacagaaaa          
                                                                                                            

Query   on---> KVKYFNMKGSFLDSHTVCGLAKGGKK <---Intron---> TTLTAEKIVIATGGRPKYPTH <---Intron---> ITGALEYGITSDDL
        p    > ||||||/|||| | ||| |/ | ||/ <   923bp    >   /||/ |||||||||||||| <   351bp    > / |||||||||||/
Target         KVKYFNIKGSFSDPHTVRGVTKAGKE                IVVTADNIVIATGGRPKYPTH                VAGALEYGITSDDI
               agattaaagattgccagcggaaggag                aggaggaagagaggacatcac                ggggcgtgaaagga
               ataatataggtcacactggtcacgaa                tttccaatttccgggcaacca                tcgctaagtcgaat
              gggatccaaattttatacctaaaatag                ttttatttctttaaaaactat                tataggtacatttc
                                                                                                            

Query   FWLKDSPGKT <---Intron---> LVVGASYVSLECAGFLTGVGLDTAVMMRSIPLRGFDQ <---Intron---> QMASLVTEHMESYGTKFLKKC
        |||/ ||||| <   3797bp   > |   /  |||||||||||/|||| |||||/||||||| <   1304bp   > |||||||||||||||||||/|
Target  FWLQKSPGKT                LTGVSPDVSLECAGFLTGIGLDTTVMMRSVPLRGFDQ                QMASLVTEHMESYGTKFLKRC
        tttcatcgaa                taggtcggtcgtggtcagagtgaagaaaagcccgtgc                cagttgagcagttgaattaat
        tgtaaccgac                tcgtccatctagcgttcgtgtacctttggtctggtaa                atccttcaatacagcattagg
        cgagattaa                cattgaatgctgttttgactagctacggatcattgttg                agttaatgcgattcaatagat
                                                                                                            

Query   VPMKVEKLESGRLQVTWKNTDLGTEEMDSFDTVMWAVG <---Intron---> RVPDSETLNLEIVGVKTNSETGKIIVDASEATSVPHIYAIGDITE 
         | ||||||| |||||||| || ||| |||/||||||| <   7552bp   > | ||//||||| |||||||||||||||||||||||||||/||||| 
Target  FPTKVEKLESDRLQVTWKNADLDTEETDSFNTVMWAVG                RAPDTKTLNLEAVGVKTNSETGKIIVDASEATSVPHIYAVGDITE 
        tcaaggatgagatcgataaggcgaggagttaagatggg                cgcgaaacatgggggaaatgagaaagggaggatgccatggggaag 
        tccataatagagtatcgaacatacaacactacttgct                ggccacactatactgtacacacgatttacgaccctcatactgatca 
        catataaggccagactgattcgcaaacttcccgggaa                cactccatctggatagatctatagttttctatttttcttatacaag 
                                                                                                            

Query   <---Intron---> GRPELTPTAIAAGKLLARRLFGHSSELMDYDN <---Intron---> VPTTVFTPLEYGCVGLSEEKAVQCYGSDNVE <---I
        <   5276bp   > |||||||||||||||||/|||| ||||||||| <   188bp    > ||||||||||||||||||| ||| /||||/| <   7
Target                 GRPELTPTAIAAGKLLAQRLFGQSSELMDYDN                VPTTVFTPLEYGCVGLSEEAAVQRHGSDNIE      
                       gccgtacagagggaccgccctgcttgcagtga                gcaagtactgtgtggctgggggcccgtgaag      
                       ggcatcccctccgattcagttgaccattaaaa                tcccttcctaaggtgtcaacctagagcaata      
                       cttaaacaaataaaggtgctccgtagggctct                gtcacctcggttttcgaaaatgattaacttg      
                                                                                                            

Query   ntron---> VFHAYYKPLEFTAAERDAAQCYMK <---Intron---> MVCLREREQRILGLHFIGPNAGEVIQGFALGIK <---Intron---> C
        89bp    > |/|||||||||| ||||| ||||| <   2090bp   > ||||||||||||||||||||||||||||||||| <   2235bp   > |
Target            VYHAYYKPLEFTVAERDATQCYMK                MVCLREREQRILGLHFIGPNAGEVIQGFALGIK                C
                  gtcgttactgtagggaggacttaa                agttcgagccacgcctagcaggggacgtgcgaa                t
                  taacaaactatctcagaccagata                ttgtgagaagttgtattgcacgattagtctgta                g
                  actattatagcagtaatatactga                ggcaagggaaatcttctaatacattaatttac                gt
                                                                                                            

Query   GATYPQLMKTIGIHPTCAEEITKLHITKRSGLDATVTGCUG
        |||| |/|||/|||||||||/|||/||||||||||||||||
Target  GATYAQMMKTVGIHPTCAEEVTKLNITKRSGLDATVTGCUG
        ggatgcaaaaggaccatggggaataaaactgcggagagttg
        gccacattactgtaccgcaatcatatcagcgtacctcgggg
        ttgttggggatctcccttaatcggctagttcgtaacaccat
                                               * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 2153 ; UGA-SECIS: 2156

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = + Positions = 79154 - 79231
 Found by:  Infernal (score=29.53) Covels (score=30.99)
 Stem2 length = 11   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -15.63

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