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

 Blastx evalue: 2e-05
 Query name: gi|387598071|ref|NP_001248375.1| thioredoxin reductase 1, cytoplasmic isoform 5 [Homo sapiens]
 Query range: 1-461  (total 461)

 Target: /data/www-rg/seblastian_results/155653343/tempfiles/temptarget.fasta
 Chromosome: KV389434.1:subseq_1333459,100236_ Strand: +
 Positions:
 -Exon 1  40552        40597
 -Exon 2  42925        43044
 -Exon 3  46795        46937
 -Exon 4  47425        47540
 -Exon 5  50005        50230
 -Exon 6  53294        53386
 -Exon 7  54572        54648
 -Exon 8  55315        55471
 -Exon 9  55998        56105
 -Exon 10 58264        58359
 -Exon 11 62298        62432
 -Exon 12 72590        72655

 Redox box: no

Query   MVLDFVTPTPLGTRWG <---Intron---> LGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETV <---Intron---> KHDWDRMIEAVQ
        |||||||||||||||| <   2327bp   > |||||||||||||||||||||||||||||||||||||||| <   3750bp   > ||||||||||||
Target  MVLDFVTPTPLGTRWG                LGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETV                KHDWDRMIEAVQ
        agcgtgacaccgaatg                cggatgaggtacaacaccggttgcgccgtcatgtagggag                acgtgaaagggc
        tttattcccctgcgg                gtggcgtatggtcaattaaccttgactaacgaaggataac                taaagagttacta
        gcgctctccttatag                tcaaatgtgtcataaggcattgaaacaactactagacgga                tgttgcagaatag
                                                                                                            

Query   NHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIK <---Intron---> ATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISS <---Intro
        ||||||||||||||||||||||||||||||||||| <   487bp    > ||||||||||||||||||||||||||||||||||||||| <   2464b
Target  NHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIK                ATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISS          
        acagttatgtcggccgaaggtgagtgctagccaaa                gaaaagagaattggatcagaggaccttgacggagttaaa          
        aatgctaggagtctgaaattaaacagattgcagta                ccaaagaaataccagtttccgagcgatgtcgaaaagtgg          
        tctctgcgccgatggggatctgtttgattttcgtg                aattacaagttaagatctcttaaatcgccttcaacccc           
                                                                                                            

Query   n---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIK <---Intron---> VEQ
        p   > ||||||||||||||/|||||||||||||||||||||||||||||||||||/|||||||||||||||||||||||| <   3063bp   > |||
Target        DDLFSLPYCPGKTLIVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQEMANKIGEHMEEHGIKFIRQFVPIK                VEQ
              ggctttcttcgaacagggttggtgtggtcggagtggagagataccagtgcgagaaaggcaggcgaataactgcaa                ggc
              aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataaagtattgattcta                taa
             ttttccatccgggccctaactttgattattttttatcttgtgctttaatcgagccattacgaatccgtaagcaata                caa
                                                                                                            

Query   IEAGTPGRLRVVAQSTNSEEIIEGEYNT <---Intron---> VMLAIGRDACTRKIGLETVGVKINEK <---Intron---> TGKIPVTDEEQTNV
        |||||||||||||||||||||||||||| <   1185bp   > |/|||||||||||||||||||||||| <   666bp    > ||||||||||||||
Target  IEAGTPGRLRVVAQSTNSEEIIEGEYNT                VLLAIGRDACTRKIGLETVGVKINEK                TGKIPVTDEEQTNV
        agggacgcccgggctaaaggaagggtaa                gttgagaggtaaaagtgagggaaaga                agaacgagggcaag
        tacgccggtgttcaccagaattagaaac                tttctggacgcgatgtactgtataaa                cgatctcaaaacat
        taagaacacaaatgtcttgactaagttg                gggaacattcaaatcaatagggata                gtaaatcataggccg
                                                                                                            

Query   PYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVK <---Intron---> CDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIE <---Intro
        ||||||||||| |||||||||||||||||||||||||| <   526bp    > |||||||||||||||||||||||||||||||||||| <   2158b
Target  PYIYAIGDILEGKVELTPVAIQAGRLLAQRLYAGSTVK                CDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIE          
        ctatgaggatggaggcacggacggatcgcactggtaga                tgtgagcaagtactgtggtgctggagggatgggaag          
        catactgattagatatcctctacggttcagtacgccta                gaaaatcccttcctaagcggtcaaactaatgaaata          
        tcctctctaggtgggtcatacgaaaggtggctatcttg                tctattgctatttgatattcttggatgggtgaattg          
                                                                                                            

Query   n---> VYHSYFWPLEWTIPSRDNNKCYAKIICNTKDN <---Intron---> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAE 
        p   > |||||||||||||||||||||||||||| ||| <   3938bp   > ||||||||||||||||||||||||||||||||||||||||||||| 
Target        VYHSYFWPLEWTIPSRDNNKCYAKIICNIKDN                ERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAE 
              gtcatttctgtaactagaaattgaaataaaga                gcgggtcgcgcaggggacgtgggcatgcaaaccgaaagaccgtgg 
              taagatgctagctccgaaaagacattgataaa                agttgtattgcacgatcagtccctaggtcaaatagctgtactgca 
              tcttctgagaggtaaatccattaaactttact                attgctcagtattaataaccatagatagcaaggccatacctctag 
                                                                                                            

Query   <---Intron---> VFTTLSVTKRSGASILQAGCUG
        <  10157bp   > ||||||||||||||||||||||
Target                 VFTTLSVTKRSGASILQAGCUG
                       gtaactgaactggaaccggttg
                       ttcctctcagcgcgttacgggg
                       acaactgcactgaccggtccat
                                           * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 219 ; UGA-SECIS: 222

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KV389434.1:subseq_1333459,100236_ Strand = + Positions = 72875 - 72961
 Found by:  Infernal (score=24.19) Covels (score=18.72)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 1, 0
 Free Energy = -11.19

         ..(((((((......................((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg---------------UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .(((((((((.....................([[[((((({.((((......---........))))})))))]]])----...))))))))).
 target  CAUUUGGCAGGGCAUUGUAAGGAUGCAUCCAUGAAGUCACCAGUCUCAAGCC---CAUGUGGUAGACAGUGAUGGAA----UAACUGUCAAAUC
                                        ****            ^^                        ****