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

 Blastx evalue: 9e-23
 Query name: gi|5107031|gb|AAD39929.1|AF133519_1 thioredoxin reductase 3 [Homo sapiens]
 Query range: 73-577  (total 577)

 Target: /data/www-rg/seblastian_results/131642767/tempfiles/temptarget.fasta
 Chromosome: gi|431909979|gb|KB030631.1|:subseq_680000,180000_ Strand: -
 Positions:
 -Exon 1  99896        100000
 -Exon 2  99583        99655
 -Exon 3  97575        97694
 -Exon 4  90799        90941
 -Exon 5  89203        89318
 -Exon 6  88151        88376
 -Exon 7  86846        86938
 -Exon 8  82253        82329
 -Exon 9  81499        81655
 -Exon 10 77783        77890
 -Exon 11 73901        73996
 -Exon 12 70141        70275
 -Exon 13 69873        69938

 Redox box: no

Query   AYQSGLLQKLLQEDLAYDYDLIIIGGGSGGLSCAK <---Intron---> EAAILGKKVMVLDFVVPSPQGTSWG <---Intron---> LGGTCVNV
        |/|||||||||||| |||||||/||||||||/||/ <   240bp    > ||||||||||||||||||||||||| <   1888bp   > ||||||||
Target  AHQSGLLQKLLQEDSAYDYDLIVIGGGSGGLACAQ                EAAILGKKVMVLDFVVPSPQGTSWG                LGGTCVNV
        gccagttcacccggtgtgtgcagagggtggcgtgc                gggatgaagagcgtggctccgattg                cggatgag
        caaggttaattaaaccaaaattttgggcggtcgca                accttgaattttatttcccagccg                gtggcgtat
        atgttaaggctgataatttcctcttttttctcttg                atctgagatgatctccaatgcacg                ttttttata
                                                                                                            

Query   GCIPKKLMHQAALLGQALCDSRKFGWEYNQQV <---Intron---> RHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIK <---
        ||/||||||||||||||| ||||||||||||| <   6633bp   > /|||||||/|||||| |||| |||||||||||||||||||||||||| <   
Target  GCVPKKLMHQAALLGQALSDSRKFGWEYNQQV                KHNWETMTEAIQNHIGSLNWSYRLSLREKAVAYVNSYGEFVEHHKIK     
        gtgcaataccggctgcgtagtaatgtgtaccg                acatgaaaggacacagtcatatacttagagggtgattggtggccaaa     
        ggtcaattaaccttgactgacgatggaaaaa                taaagactcactaaatgctaggagtctgaactcatacagattaaaata     
        ctttgaggtatctgggaatcaaatcggttaa                ggccggcgaagtacccctatgccggtggggtgctatctaactattaag     
                                                                                                            

Query   Intron---> ATNKKGQETYYTAAQFVIATGERPRYLGIQGDKEYCITS <---Intron---> DDLFSLPYCPGKPLVVGASYVALECAGFLAGFGL
        1480bp   > |||/||||| ||||/|||||||||||||||||||||||| <   826bp    > |||||||||||| |||||||||||||||||| ||
Target             ATNRKGQETCYTAAKFVIATGERPRYLGIQGDKEYCITS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGL
                   gaaaagcgattaggatgagaggaccttgacggagttaaa                ggcttccttcgaatggggttggcgtggtcggcgt
                   ccagagaacgacccatttccgagcgatgtagaaaagtcg                aattctcagcgactttgccatctagcgttcgtgt
                   actaaagatttttaatcaaatagggtaacaataacttt                ttctttgttctcaaaattattgtgataatttctca
                                                                                                            

Query   DVTVMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFIPVM <---Intron---> VQQLEKGSPGKLKVLAKSTEGTETIEGVYNT <---Intron-
        ||||||||/|||||||||||/|||||||||||||||||||| <   1212bp   > ||||||||||||||/|||||| ||/||/||| <   4516bp 
Target  DVTVMVRSVLLRGFDQEMAERVGSYMEQHGVKFLRKFIPVM                VQQLEKGSPGKLKVVAKSTEGPETVEGMYNT            
        ggagagctgcccgtgcgaggaggttagccggattaatacga                gcctgagtcgacagggataggcgagggataa            
        atctttgctttggtaaatcagtgcataaagtattgattctt                taataagccgatattcaccagcactagtaac            
        tcatggtattttcttaagagactccgaatttgcaaatatgg                tagggatataggaagtactaaaattaagtca            
                                                                                                            

Query   --> VLLAIGRDSCTRKIGLEKIGVKINEK <---Intron---> SGKIPVNDVEQTNVPYVYAVGDILEDKPELTPVAIQSGKLLAQRLFGASLEK <
          > ||||||||| |||||||||||||||| <   597bp    > /|||||||/||||||||||/||||| | ||||||||/|||||/||||  ||| <
Target      VLLAIGRDSSTRKIGLEKIGVKINEK                NGKIPVNDMEQTNVPYVYAIGDILEGKLELTPVAIQAGKLLARRLFGGRLEK  
            gttgagcgtaaaaagtgaaggaaaga                agaacgagagcaagctgtgaggacggacgcacggacggactgcactggctga  
            tttctggacgcgatgtaatgtataaa                agatctaataacatcatactgattagatatcctctacgattcggttgggtaa  
            tgaatttcctagaacgggttcactg                gtcgaaactgagccgcttctaattgatatgctcttagacgggtaactgttaag  
                                                                                                            

Query   ---Intron---> CDYINVPTTVFTPLEYGCCGLSEEKAIEVYKKENLE <---Intron---> IYHTLFWPLEWTVAGRENNTCYAKIICNKFDH <
           3608bp   > |||||||||||||||||||||||||||/ ||||||| <   3786bp   > /|||||||||||||||/|||||||||||| |/ <
Target                CDYINVPTTVFTPLEYGCCGLSEEKAIDEYKKENLE                VYHTLFWPLEWTVAGRDNNTCYAKIICNKLDN  
                      tgtaagcaagtaccgtgttgttggagaggtaagacg                gtcatttccgtagggagaaattgaaataacga  
                      gaatatcccttcctaaggggtcaaactaaaaaaata                taacttgctagctcggaaacgacattgaataa  
                      ttttttatagtttgatcttaatagatttataagtga                atttacgttggaaccaccttctagatctatct  
                                                                                                            

Query   ---Intron---> DRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGE <---Intron---> VFTTLEITKSSGLDITQKGCUG
           3625bp   > / |||||||||||||/||||||||||||||||||||||||||||| <   202bp    > / |||||||||||||/||||||
Target                NLVIGFHILGPNAGEITQGFAAAMKCGLTKQLLDDTIGIHPTCGE                ILTTLEITKSSGLDISQKGCUG
                      acgagtcacgcagggaacgtgggaatgcaacccggaagaccatgg                acaatgaaattgcgatcagttg
                      atttgtattgcacgatcagtccctaggtcaattaactgtaccgga                ttcctatcaccgtatcaagggg
                      tgaaattttagtctgtcaatatagatgcgggattcatattcattg                atcggacaaaaaacccgaccac
                                                                                                       * 
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 209 ; UGA-SECIS: 212

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|431909979|gb|KB030631.1|:subseq_680000,180000_ Strand = - Positions = 69663 - 69585
 Found by:  Infernal (score=27.73) Covels (score=23.81)
 Stem2 length = 11   Apical loop length = 15   Insertion in stem2 = 0, 0
 Free Energy = -13.95

         ..(((((((.......(((((((((((((((...............)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ..(({{(((.......{[[{(((((((((((...............)))))))))))}]]}......-...)))}}))..
 target  AGUUACACUGCUUCCUUGACGUCUUAGUUCGGAACCCUGUGUGAGGUGAGCUAAGACCGACACUCUU-CCAAGUCAGAAC
                         ****            ^^                       ****