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

 Blastx evalue: 1e-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/326076717/tempfiles/temptarget.fasta
 Chromosome: CM003725.1:subseq_7291820,130149_ Strand: +
 Positions:
 -Exon 1  52445        52593
 -Exon 2  52908        52982
 -Exon 3  53802        53880
 -Exon 4  54834        54896
 -Exon 5  55237        55307
 -Exon 6  59121        59235
 -Exon 7  60644        60818
 -Exon 8  69212        69348
 -Exon 9  74634        74729
 -Exon 10 74939        75031
 -Exon 11 75807        75878
 -Exon 12 77667        77764
 -Exon 13 80023        80149

 Redox box: no

Query   RGTKWGLGGTCVNVGCIPKKLMHQAALLGGALKDAQHYGWSMAHPVHHSW <---Intron---> SVMAQAVQNYVKSLNWGHRVQLQDK <---Intr
        /|| ||||||||||||||||||||||||| ||||||||||/// ||||/| <   314bp    > ||||| |||/|||||||||||||/| <   819b
Target  QGTTWGLGGTCVNVGCIPKKLMHQAALLGSALKDAQHYGWNISQPVHHTW                SVMAQGVQNHVKSLNWGHRVQLQEK         
        cgaatgcggatgaggtacaacaccggctgagcaggcctgtaatccgccat                tgagcggcacgattatgcagcccga         
        agccggtggcgtatggtcaattaaccttggctaacaaaggatcactaacg                cttcagtaaatactaggagtataaa         
        aacagattattgttccttagtgtaactagtctatcactcgtacattttc                gtggaattgttgacacgatacaaaa          
                                                                                                            

Query   on---> KVKYFNMKGSFLDSHTVCGLAKGGKK <---Intron---> TTLTAEKIVIATGGRPKYPTH <---Intron---> ITGALEYGITSDDL
        p    > ||||||/|||| | ||| || | ||/ <   953bp    > | /||/ ||||||||||||   <   340bp    > / ||||||||||||
Target         KVKYFNIKGSFSDPHTVRGLTKAGKE                TVVTADNIVIATGGRPKYPLQ                VAGALEYGITSDDL
               agattaaagattgccagcgtaaggag                aggaggaagagaggacatccc                ggggcgtgaaaggc
               ataatataggtcacactggtcacgaa                cttccaatttccgggcaacta                tcgctaagtcgaat
              gggatccaaactttatacttaaaatag                ttttatttttttaaaaactgg                tataggtacattta
                                                                                                            

Query   FWLKDSPGKT <---Intron---> LVVGAS-YVSLECAGFLTGVGLDTAVMMRSIPLRGFDQ <---Intron---> QMASLVTEHMESYGTKFLKK
        ||||/||||| <   3813bp   >  / |||  |||||||||||/|||| |||||/||||||| <   1408bp   > |||||||||||||||||||/
Target  FWLKESPGKT                CLTGASPDVSLECAGFLTGIGLDTTVMMRSVPLRGFDQ                QMASLVTEHMESYGTKFLKR
        tttagtcgaa                ttaggtcggtcgtggtcagagtgaagaaaagcccgtgc                cagttgagcagttgaattaa
        tgtaaccgac                gtcgcccatctagcgttcgtgtacctttggtctggtaa                atccttcaatacagcattag
        cgagattga                tcattaaattctgttttatctagctacggatcattgttg                agttaatgcgattaaataga
                                                                                                            

Query   CVPMKVEKLESGRLQVTWKNTDLGTEEMDSFDTVMWAVG <---Intron---> RVPDSETLNLEIVGVKTNSETGKIIVDASEATSVPHIYAIGDITE
        | | |||||/| |||||||| || ||| |||/||||||| <   8393bp   > | ||//||||| |||||||||||||||||||||||||||/|||||
Target  CFPTKVEKLKSNRLQVTWKNADLDTEETDSFNTVMWAVG                RAPDTKTLNLETVGVKTNSETGKIIVDASEATSVPHIYAVGDITE
        ttcaaggataaaatcgataaggcgaggagttaagatggg                cgcgaaacatgagggaaatgagaaagggaggatgccatggggaag
        gtccataatagagtatcgaacatacaacactacttgct                ggccacactatactgtacacacgatttacgaccctcatactgatca
        tcatataaggccagactgattcgcaaacttccctggaa                cactccatctggatagatttatagttttctatttttcttatacaag
                                                                                                            

Query    <---Intron---> GRPELTPTAIAAGKLLARRLFGHSSELMDYDN <---Intron---> VPTTVFTPLEYGCVGLSEEKAVQCYGSDNVE <---
         <   5285bp   > |||||||||||||||||/|||| ||||||||/ <   209bp    > ||||||||||||||||||| ||| /||||/| <   
Target                  GRPELTPTAIAAGKLLAQRLFGQSSELMDYDS                VPTTVFTPLEYGCVGLSEEAAVQRHGSDNIE     
                        gccgtacagagggaccgccctgcttgcagtga                gcaagtactgtgtggctgggggcccgtgaag     
                        ggcatcccctccgattcagttgaccattaaag                tcccttcctaaggtgtcaacctagagcaata     
                        cttaaacaaataaaggtgatccgtagggctct                gtcacctcggctttcgaaaatgattaatttg     
                                                                                                            

Query   Intron---> VFHAYYKPLEFTAAERDAAQCYMK <---Intron---> MVCLREREQRILGLHFIGPNAGEVIQGFALGIK <---Intron---> 
        775bp    > |/|||||||||| ||||| |||/| <   1788bp   > ||||||||||||||||||||||||||||||||| <   2258bp   > 
Target             VYHAYYKPLEFTVAERDATQCYIK                MVCLREREQRILGLHFIGPNAGEVIQGFALGIK                
                   gtcgttactgtagggaggacttaa                agttcgagccacgcctagcaggggacgtgcgaa                
                   taacaaactatctcagaccagata                ttgtgagaagttgtattgcacgattagtctgta                
                   actatcacagtagtaatatactaa                ggcaagggaaatcttctaatacattaatttac                a
                                                                                                            

Query   CGATYPQLMKTIGIHPTCAEEITKLHITKRSGLDATVTGCUG
        |||||||/|||/|||||||||/||| ||||||||||||||||
Target  CGATYPQMMKTVGIHPTCAEEVTKLRITKRSGLDATVTGCUG
        tggatccaaaaggaccatggggaatcaaactgcggagagttg
        ggccacattactgtaccgcaatcatgtcagcgtacctcgggg
        tttgttgggggtctcccttaatcggctagttcgtaacaccat
                                                * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 2873 ; UGA-SECIS: 2876

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM003725.1:subseq_7291820,130149_ Strand = + Positions = 83023 - 83100
 Found by:  Infernal (score=29.13) Covels (score=25.98)
 Stem2 length = 11   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -15.63

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