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

 Blastx evalue: 6e-22
 Query name: gi|296010807|ref|NP_001171531.1| thioredoxin reductase 3 isoform 4 [Mus musculus]
 Query range: 1-501  (total 501)

 Target: /data/www-rg/seblastian_results/304687285/tempfiles/temptarget.fasta
 Chromosome: CM004099.1:subseq_88703410,229586_ Strand: +
 Positions:
 -Exon 1  100138       100296
 -Exon 2  106462       106522
 -Exon 3  107435       107544
 -Exon 4  109911       110015
 -Exon 5  110206       110278
 -Exon 6  111839       111958
 -Exon 7  116915       117057
 -Exon 8  121148       121240
 -Exon 9  124738       124814
 -Exon 10 125251       125407
 -Exon 11 127548       127655
 -Exon 12 128351       128446
 -Exon 13 129449       129583
 -Exon 14 130084       130149

 Redox box: no

Query   MSSPPGRRARLASPGTSRPSSEAREELRRRLRDLIEGNRVMIFSKSYCPHSTR <---Intron---> VKELFSSLGVVYNILELDQVD <---Intro
        ||||||||||||||||||||||||||||||||||||||||||||||||||||| <   6165bp   > ||||||||||||||||||||| <   912bp
Target  MSSPPGRRARLASPGTSRPSSEAREELRRRLRDLIEGNRVMIFSKSYCPHSTR                VKELFSSLGVVYNILELDQVD          
        attccgccgccgtcgaaccttggcggccccccgcaggaagaataaattccaac                gagcttttgggtaacgcgcgg          
        tccccgggcgtcccgcggcccacgaatgggtgattagagttttgagagcagcg                taattcctgttaattataat           
        gggaccccccgcctgcccgttgccggggccggcccgccgggcccgtctaccgg                tgactacgagctccgattat           
                                                                                                            

Query   n---> DGASVQEVLTEISNQKTVPNIFVNKVHVGGCDRTFQ <---Intron---> AHQNGLLQKLLQDDSAHDYDLIIIGGGSGGLSCAK <---In
            > |||||||||||||||||||||||||||||||||||| <   2366bp   > ||||||||||||||||||||||||||||||||||| <   19
Target        DGASVQEVLTEISNQKTVPNIFVNKVHVGGCDRTFQ                AHQNGLLQKLLQDDSAHDYDLIIIGGGSGGLSCAK       
              gggagcggcagaaacaagcaatgaagcgggtgcatc                gccagtccacccggtgcgtgcaaagggtggcttga       
             aagcgtaattcatgaaactcatttaatatgggagcta                caaagttaattaaaccaaaattttgggcggtcgca       
             tcgcttgagcaactcgaggctttgtagcgtatcatcg                atgttagggccatcgtttcccccccgttcccttcg       
                                                                                                            

Query   tron---> EAANLGKKVMVLDFVVPSPQGTTWG <---Intron---> LGGTCVNVGCIPKKLMHQAALLGHALQDAKKYGWEYNQQV <---Intro
        0bp    > ||||||||||||||||||||||||| <   1560bp   > |||||||||||||||||||||||||||||/|||||||||| <   4956b
Target           EAANLGKKVMVLDFVVPSPQGTTWG                LGGTCVNVGCIPKKLMHQAALLGHALQDARKYGWEYNQQV          
                 gggatgaagagcgtggctccgaatg                cggatgaggtacaacaccggccgcgtcggaatgtgtaccg          
                 accatgaattttatttcccagccg                gtggcgtatggtcaattaaccttgactaacgaaggaaaaa           
                 atccgaggcggactgcagtgcgcg                ctccctgcacttaggggtgaccggttgatcgatcggtcgg           
                                                                                                            

Query   n---> KHNWEAMTEAIQSHIGSLNWGYRVTLREKGVTYVNSFGEFVDLHKIK <---Intron---> VQQLEKGLPGKLKVVAKSTEGPETVEGIYNT
        p   > ||||||||||||||||||||||||||||||||||||||||||||||| <   4090bp   > |||||||||||||||||||||||||||||||
Target        KHNWEAMTEAIQSHIGSLNWGYRVTLREKGVTYVNSFGEFVDLHKIK                VQQLEKGLPGKLKVVAKSTEGPETVEGIYNT
              acatggaaggacacagttatgtagaccgaggatgattggtggccaaa                gcctgagtcgatagggataggcgagggataa
             taaagactcactagatgctaggagtctgaagtcatactgattataata                taataagtcgatattcaccagcactagtaac
             ggccggcggatcgcctccgcgccgactggacgctccccggtgcgtaag                tagggataaaagacgtgccaagaaaagaccg
                                                                                                            

Query    <---Intron---> VLLAIGRDSCTRKIGLEKIGVKINEK <---Intron---> NGKIPVNDVEQTNVPHVYAIGDILDGKPELTPVAIQAGKLLA
         <   3497bp   > |||||||||||||||||||||||||| <   436bp    > ||||||||||||||||||||||||||||||||||||||||||
Target                  VLLAIGRDSCTRKIGLEKIGVKINEK                NGKIPVNDVEQTNVPHVYAIGDILDGKPELTPVAIQAGKLLA
                        gttgagcgttaaaagcgaaggaaaga                agaacgagggcaagccgtgaggacggacgcacggacggaccg
                        tttctggacgcgatgtaatgtataaa                agatctaataacatcatactgattagacatcctctacgattc
                        tgaatttcctagaaggggcgcactg                gtcaaaactgggccgttttttgcagccaagccctcagacggat
                                                                                                            

Query   RRLFGVSLEK <---Intron---> CDYINIPTTVFTPLEYGCCGLSEEKAIEMYKKENLE <---Intron---> VYHTLFWPLEWTVAGRDNNTCY
        |||||||||| <   2140bp   > |||||||||||||||||||||||||||||||||||| <   695bp    > ||||||||||||||||||||||
Target  RRLFGVSLEK                CDYINIPTTVFTPLEYGCCGLSEEKAIEMYKKENLE                VYHTLFWPLEWTVAGRDNNTCY
        cactggttga                tgtaaacaagtaccgtgttgctggagagataagacg                gtcatttccgtagggagaaatt
        ggttgtctaa                gaatatcccttcctaaggggtcaaactataaaaata                taacttgctagctcggaaacga
        aactgctaag                ttttctaaggcatgatcttaggagaccagtaagtga                gtccgtgtcggattcacccctt
                                                                                                            

Query   AKIICNKFDN <---Intron---> ERVVGFHLLGPNAGEITQGFAAAMKCGLTKQLLDDTIGIHPTCGE <---Intron---> VFTTLEITKSSGL
        |||||||||| <   1002bp   > ||||||||||||||||||||||||||||||||||||||||||||| <   500bp    > |||||||||||||
Target  AKIICNKFDN                ERVVGFHLLGPNAGEITQGFAAAMKCGLTKQLLDDTIGIHPTCGE                VFTTLEITKSSGL
        gaaataatga                gcgggtcccgcagggaacgtgggaatgcaacccggaagaccatgg                gtaatgaaattgc
        cattgaataa                agttgtattgcacgatcagtccctaggtcaattaactgtaccgga                ttcctatcaccgt
        agacccaccc                atggatctggatttacggatatagatgcgggagtcctaccccttg                acaagacagcagg
                                                                                                            

Query   DITQKGCUG
        |||||||||
Target  DITQKGCUG
        gaacagttg
        atcaagggg
        cttgaccac
               * 
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 167 ; UGA-SECIS: 170

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM004099.1:subseq_88703410,229586_ Strand = + Positions = 130317 - 130389
 Found by:  Infernal (score=28.45) Covels (score=22.18)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -21.82

         ..(((((((.......(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         .(((((({(---....{[[{{((((((((((.....--........))))))))))}}]]}.....-...)})))))).
 target  CAGGCUGCU---UCCUUGACACCUUGGCUCGGAACC--UGCAGAGGUGAGCCAAGGCCGAUUUCUG-CACGUCAGCCUC
                         ****            ^^                       ****             
