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

 Blastx evalue: 2e-27
 Query name: gi|929126265|ref|XP_013980823.1| PREDICTED: selenoprotein O-like [Salmo salar]
 Query range: 1-706  (total 706)

 Target: /data/www-rg/seblastian_results/680437607/tempfiles/temptarget.fasta
 Chromosome: CM007936.1:subseq_67641605,106935_ Strand: +
 Positions:
 -Exon 1  49955        50556
 -Exon 2  50717        50920
 -Exon 3  51025        51202
 -Exon 4  51679        51809
 -Exon 5  52007        52284
 -Exon 6  54225        54393
 -Exon 7  54653        54838
 -Exon 8  56415        56571
 -Exon 9  56714        56935

 Redox box: YES

Query   MRSLLSLNRPTGFSWMTSLKLRLARSNFLRSGIVVVVRYFSAVVMDDMGLAVSRSPLERLEFDNVALKKLPLDTSEEPGPRRVTGACFSRVKPQPVVKPR
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/|||
Target  MRSLLSLNRPTGFSWMTSLKLRLARSNFLRSGIVVVVRYFSAVVMDDMGLAVSRSPLERLEFDNVALKKLPLDTSEEPGPRRVTGACFSRVKPQPVLKPR
        aatccataacagtataattacccgctatcctgaggggatttgggaggagcggactccgccgtgaggcaacccgatggcgccagaggtttcgacccgcaca
        tgcttgtagccgtggtcctatgtcgcattgcgtttttgatcctttaatgtctggcctagtataatctaatctaccaacgcggtcgcgtcgtacacttacg
        ggtggtacatccttggttaattgagatttctttccgtaccctttgccgtggcttagcgccatctcacgatagtaaaattgaggaactctaaaagagcgca
                                                                                                            

Query   FVAVSNDALALLGLNAMEVLNDPLGPEYLSGSKVMPGSEPAAHCYCGHQFGSFAGQLGDGAACYLGELKAPADQCPELLRENPSGRWEIQVKGAGLTPYS
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Target  FVAVSNDALALLGLNAMEVLNDPLGPEYLSGSKVMPGSEPAAHCYCGHQFGSFAGQLGDGAACYLGELKAPADQCSELLRENPSGRWEIQVKGAGLTPYS
        tgggtaggtgtcgcagaggcagccgcgtcagtagacgtgcggctttgcctgttggctgggggttcggcagcggcttgcccgacagctgacgagggcactt
        ttctcaactcttgtactattaactgcaatggcattcgcacccagaggaatgctcgatgagccgatgatacccaagcattgaacggggatatagcgtccac
        tgccgtttatgtggccggtgccagtagcgcccaagagcgtagcccctcgcgaccagggcggcctgtaaataacgccgggagcctcgggtgcaataggccc
                                                                                                            

Query   R <---Intron---> QADGRKVLRSSIREFLCSEAVFALGVPTTRAGSLVTSDSMVVRDVYYSGNPRKERCSVVLRIAPTFIR <---Intron--->
        | <   160bp    > ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| <   104bp    >
Target  R                QADGRKVLRSSIREFLCSEAVFALGVPTTRAGSLVTSDSKVVRDVYYSGNPRKERCSVVLRIAPTFIR               
        a                cgggcagcctaaagtctagggtgcggcaaaggtcgatgaaggcggttagaccagattggccagcataa               
        g                acaggattgcgtgattggacttctgtcccgcgcttccagattgataaggacgaaggctttgtcccttg               
                        aagtgtgggacccggtgccaggttgcgccgggggggctccggagtgtctgcccaggctgccccacccc                
                                                                                                            

Query    FGSFEIFKATDENTGRQGPSYGHDAIRGQMMDYVIETFYPEIQQNHTDRVERNVAFFKE <---Intron---> VMLRTARLVAQWQCVGFCHGVLNT
         |||||||||||||||||||||||||||||||||||||||||||||||||||||||||/| <   476bp    > ||||||||||||||||||||||||
Target   FGSFEIFKATDENTGRQGPSYGHDAIRGQMMDYVIETFYPEIQQNHTDRVERNVAFFRE                VMLRTARLVAQWQCVGFCHGVLNT
         tgttgatagaggaagccgcatgcggaagcaagtgagattcgaccacagaggaaggttag                gatcagccggctctggttcggcaa
         tgctattaccaaacggagcgagaactggattaattactacataaaacagtagatcttga                tttgccgttcagagtgtgagttac
        gtgatgccggttgcaccgcccccttgcatgggttcagcccagcggcctcagggtgatcag                ggatatgggcgggtgtcctaccca
                                                                                                            

Query   DNMSILGLTIDYGPYGFMDR <---Intron---> FDPDFICNASDNSGRYSYQAQPAICRWNLARLAEALDPELPPGRAEAVLDEYLPLYNTFYLGNM
        |||||||||||||||||||| <   197bp    > |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Target  DNMSILGLTIDYGPYGFMDR                FDPDFICNASDNSGRYSYQAQPAICRWNLARLAEALDPELPPGRAEAVLDEYQPLYNTFYLGNM
        gaaaacgcaagtgctgtaga                tgcgtatagtgatgctttcgccgatctacgccgggcgcgcccgcggggcggtccctaattcgaa
        aatgttgtctaagcagttag                tacattgaccaacggacaacacctgggatcgtcactacatccggcacttaaaactaactatgat
        ccgctgacaactcctccgc                gtttcccctcaccacccctgcagtcccgcgtcgcacgcaggcacgagttgcgcgcccccccgtcg
                                                                                                            

Query   RKKLGLLRREEPEDEMLITELLQTMHNTG <---Intron---> ADFTNTFRCLSQIPCPTAGDGEAEEGVIKMAKDLLLEQCASLEELKAANKPSMDP
        ||||||||||||||||||||||||||||| <   1940bp   > ||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Target  RKKLGLLRREEPEDEMLITELLQTMHNTG                ADFTNTFRCLSQIPCPTEGDGEAEEGVIKMAKDLLLEQCASLEELKAANKPSMDP
        aaacgccaaggcgggacaagcccaacaag                ggtaaatctcacactcaggggggggggaaagagcccgctgtcggcaggaacaagc
        gaatgttggaacaaatttcattactaac                gcatcactggtgatcgccagagacaagttatcaatttaagcctaataccaacgtac
        ggggcggggaaggcggcctggggcgtca                aaccccacctgcgcccctgatgaagaaccagcacccgggtctgggcgtccgccgca
                                                                                                            

Query   R <---Intron---> ELAMLLQLAQSNPSLFQMISDRRTVAMQLEKLGRLKELLEADEVEVKAKHREDWATWITSYR <---Intron---> ERLAR
        | <   259bp    > |||||/|||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1576bp   > |||||
Target  R                ELAMLMQLAQSNPSLFQMISDRRTVAMQLEKLGRLKELLEADEVEVKAKHREDWATWITSYR                ERLAR
        c                gtgacactgcaactctcaatgcaaggaccgacgacagccgggggggagacaggtgataatta                gccga
        g                atctttatcagaccttattcaggctctataatggtaattacaatatacaagaagccgtccag                agtcg
                        tggcgggggcgccgcgcggaacggggcggggggcgggggtgttgagcgcgcggcgccgccat                ggtgtg
                                                                                                            

Query   EVEGQSDVQALQEERVKVMDGTNPQYVLRNYIAQNAIEAAENGDFSE <---Intron---> VQRVLKVLEKPFSTQLGLDQPSCLGRGGAEGQRN---
        ||||||||||||||||||||||||/|||||||||||||||||||||| <   142bp    > ||||||||||||||||||/||| | / |||||||   
Target  EVEGQSDVQALQEERVKVMDGTNPRYVLRNYIAQNAIEAAENGDFSE                VQRVLKVLEKPFSTQLGLEQPSWLAQRGAEGQRNEEE
        ggggcaggcgccggagagaggaacctgcaatagcagaggggaggtag                gccgtagcgacttaccgcgccatcgcaggggcaaggg
        atagagatactaaagtattagcacgattgaatcaactaccaagatga                tagttattaactccatgtaacggtcaggcagagaaaa
        gcgcgttcgaggggaggggtcccaatccgcctcgtaagacgcacctg                cgggggtgagtctcggtggggcgtcgggaggggtggg
                                                                                                            

Query   EEEEAQQGAEAASSRMRVPYDSKPPVWANEICVTUSS
        |||||||||||||||||||||||||||||||||||||
Target  EEEEAQQGAEAASSRMRVPYDSKPPVWANEICVTUSS
        gggggccgggggttcacgctgaaccgtgagatgattt
        aaaacaagcaccccgtgtcaagacctgcaatgtcgcc
        ggggagggaaaaacagttctccgcgtgctacttcatg
                                          *  
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 342 ; UGA-SECIS: 348

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007936.1:subseq_67641605,106935_ Strand = + Positions = 57278 - 57353
 Found by:  Infernal (score=19.11) Covels (score=22.47)
 Stem2 length = 9   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -14.07

         ..(((((((........(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...([(((((((.....([[{((({((((((..................))))))})))}]])----.)))))))])...
 target  GACUGUCUGGUUAUGAAUGACGGCCCAGACGUCCAGUCCCACAGUGACCCGUCUGAGUCUGAG----AGACUAGGAGUAU
                          ****           ^^                         ****