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

 Blastx evalue: 2e-22
 Query name: gi|5764543|gb|AAD51325.1|AF171055_1 thioredoxin reductase TR2 [Homo sapiens]
 Query range: 169-579  (total 579)

 Target: /var/www/seblastian_output/213632899/tempfiles/temptarget.fasta
 Chromosome: gi|511782571|gb|CM001963.1| Strand: +
 Positions:
 -Exon 1  75429        75587
 -Exon 2  78664        78779
 -Exon 3  79764        79989
 -Exon 4  81533        81625
 -Exon 5  89551        89627
 -Exon 6  90188        90344
 -Exon 7  97191        97298
 -Exon 8  102081       102176
 -Exon 9  104967       105101
 -Exon 10 105968       106033

 Redox box: no

Query   EYNQQVRHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIK <---Intron---> ATNKKGQETYYTAAQFVIATGERPRYLGIQG
        /|   |/|||||||||||||||||||||||||||||||||||||||||||||| <   3076bp   >  ||||||||||||||||||||||||||||||
Target  DYFFLVKHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIK                VTNKKGQETYYTAAQFVIATGERPRYLGIQG
        gttttgacatgaaaagacacaatcatgtattcagagggtgattggtggccaaa                gaaaagcgattaggctgagaggaccttgacg
        aattttaaagactcactaaatgctaggagtctgaactcatacagattaaaata                tcaaagaacaacccatttccgagcgatgtag
        ttccaggccggggaaatgcccctacgccggtggagtgctctctagttattaag                gctaaaggtttttagtcaagtagagcaacaa
                                                                                                            

Query   DKEYCITS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGFGLDVTVMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFIPVMV
        |||||||| <   984bp    > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/
Target  DKEYCITS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGFGLDVTVMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFIPVMI
        gagttaaa                ggcttccttcgaatggggttggcgtggtcggtgcggagagctacccgtgcgaggaggttagccggatccatacgaa
        aaaagtcg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgcataaagtattgattctt 
        taacttt                ttctttgtcctcaaaggtcttccggtagtgtctcatcatgacactctctcaagaaagtccgggttggcagacatgg 
                                                                                                            

Query    <---Intron---> QQLEKGSPGKLKVLAKSTEGTETIEGVYNTV <---Intron---> LLAIGRDSCTRKIGLEKIGVKINEKS <---Intron
         <   1543bp   > ||||||||||||||||||||||||||||||| <   7925bp   > ||||||||||||/||||||||||||| <   560bp 
Target                  QQLEKGSPGKLKVLAKSTEGTETIEGVYNTV                LLAIGRDSCTRKMGLEKIGVKINEKS           
                        cctgagtcgacagtgataggagaagggtaag                ttgagcgttaaaagtgaaggaaagaa           
                       taataagccgatattcaccagcactagtaact                ttctggacgcgatgtaatgtataaag           
                       tagggatataggaagtaccaaaaataactcat                gattttcctagagcgggtccattgg            
                                                                                                            

Query   ---> GKIPVNDVEQTNVPYVYAVGDILEDKPELTPVAIQSGKLLAQRLFGASLEKCD <---Intron---> YINVPTTVFTPLEYGCCGLSEEKAIE
           > |||||||||||/|||||||||| | ||||||||||||||||/||||||||||| <   6846bp   > |/|||||||||||||||||/||||||
Target       GKIPVNDVEQTSVPYVYAVGDISEGKPELTPVAIQSGKLLARRLFGASLEKCD                YVNVPTTVFTPLEYGCCGLAEEKAIE
             gaacgagggcaagctgtggggatggacgcacggactgaccgcactggttgatg                tgagcaagtaccgtgttgtgggagag
             gatctaataacgtcatactgatcagacatcctctacgattcggttgcctaag                aatatcccttcctaaggggtcaaacta
            taaatattgagctgatctttgttggtgagcttccagacggatgattgctaagt                tttttgtggtttggttccaataaatta
                                                                                                            

Query   VYKKENLEIY <---Intron---> HTLFWPLEWTVAGRENNTCYAKIICNKFDHDR <---Intron---> VIGFHILGPNAGEVTQGFAAAMKCGL
        |||||||||| <   4782bp   > ||||||||||||||||||||||||||| |||| <   2790bp   > ||||||||||||||||||||||||||
Target  VYKKENLEIY                HTLFWPLEWTVAGRENNTCYAKIICNKLDHDR                VIGFHILGPNAGEVTQGFAAAMKCGL
        gtaagacgat                catttccgtagggagaaattgaaataatgcgc                gagtcacgcaggggacgtgggaatgc
        taaaaatata                acttgctagctcggaaacgacattgaataaag                ttgtattgcacgatcagtccctaggt
        ataagtaaat                ttgcgttagaatcagccttcagacctaacttg                gaattttaacctgtcaatatagatgc
                                                                                                            

Query   TKQLLDDTIGIHPTCGEVF <---Intron---> TTLEITKSSGLDITQKGCUG
        ||||||||||||||||||| <   866bp    > ||||||||||||||||||||
Target  TKQLLDDTIGIHPTCGEVF                TTLEITKSSGLDITQKGCUG
        aacccggaagaccatgggt                aatgaaattgcgaacagttg
        caattaactgtaccggatt                cctatcaccgtatcaagggg
        aagattcctatccatgggc                gtaacagggaatctgaccac
                                                             * 
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 213 ; UGA-SECIS: 216

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|511782571|gb|CM001963.1| Strand = + Positions = 106247 - 106319
 Found by:  Infernal (score=18.86) Covels (score=17.86)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -16.89

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(([{(((.--....{[[{((((({(((((................)))))})))))}]]}----....)))}]))..
 target  UGGGACUGCU--UCCUUGACGCCUUAGCUUGGAGCCCUGUUGUGAGGUGAGCCAAGGCCGAC----UCUCGCAAGCCAG
                         ****              ^^                      ****