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

 Blastx evalue: 8e-39
 Query name: gi|929126265|ref|XP_013980823.1| PREDICTED: selenoprotein O-like [Salmo salar]
 Query range: 53-706  (total 706)

 Target: /data/www-rg/seblastian_results/441946270/tempfiles/temptarget.fasta
 Chromosome: CM007955.1:subseq_10992636,106607_ Strand: -
 Positions:
 -Exon 1  56084        56529
 -Exon 2  54926        55129
 -Exon 3  54307        54484
 -Exon 4  53899        54029
 -Exon 5  53336        53613
 -Exon 6  53030        53192
 -Exon 7  52191        52376
 -Exon 8  51661        51817
 -Exon 9  50000        50221

 Redox box: YES

Query   SRSPLERLEFDNVALKKLPLDTSEEPGPRRVTGACFSRVKPQPVVKPRFVAVSNDALALLGLNAMEVLNDPLGPEYLSGSKVMPGSEPAAHCYCGHQFGS
        / | |||| |/||||||||||/||||| | |/|||||||/|||/| | |||||  |||||||/  |/ /| |||||||||||/|||||||||||||||| 
Target  ASSSLERLPFNNVALKKLPLDSSEEPGSRTVSGACFSRVQPQPLVNPTFVAVSGPALALLGLDDKEIFHDLLGPEYLSGSKVLPGSEPAAHCYCGHQFGL
        gtttcgccctaaggcaacccgttggcgtcagaggtttcgcccccgacatgggtgcgcgccgcggagatcgtcgcgttagtagtcgtgcggctttgcctgc
        cccctagtctaatctaatctaccaacgcgctggcgtcgtacacttaccttctcgcctcttgtaaaattaattgcaatggcattcgcacccagaggaatgt
        acatcgcatcctcgaaatatcccaaagaaggcaacccccgaatttcctcgaacaaacggtgattgaatccgttaatgcttatagcgggtgttccttgtaa
                                                                                                            

Query   FAGQLGDGAACYLGELKAPADQCPELLRENPSGRWEIQVKGAGLTPYSR <---Intron---> QADGRKVLRSSIREFLCSEAVFALGVPTTRAGSLV
        ||||||||| |||||//|||||   / |/|| |||||||||||/||||| <   954bp    > //||||||||||||||||||/ |||/||||| |||
Target  FAGQLGDGAVCYLGEVEAPADQIGTMQRDNPCGRWEIQVKGAGVTPYSR                ESDGRKVLRSSIREFLCSEAMAALGIPTTRAASLV
        tggccgggggttcgggggcggcagaaccgactgctgacgaggggactta                gtggcagcctaacgtctaggaggcgacaacggtcg
        tcgatgagctgatgatacccaatgctagaacggggatatagcgtccacg                acaggattgcgtgattggactcctgtcccgccctt
        ttaggatgggtctcggaatgcactcggtccacgagaagggtatcatcc                agacaggcttcccggcgccgcgctgccccctcgtgt
                                                                                                            

Query   TSDSMVVRDVYYSGNPRKERCSVVLRIAPTFIR <---Intron---> FGSFEIFKATDENTGRQGPSYGHDAIRGQMMDYVIETFYPEIQQNHTDRVE
        |||  | ||   /|  | |||||||||||/||| <   441bp    > |||||||// || /|||||| |   || |//||||/||||/||/ | /| |
Target  TSDLYVNRDPLNNGRRRPERCSVVLRIAPSFIR                FGSFEIFQSRDEFSGRQGPSPGRHDIRAQLVDYVIDTFYPDIQRCHGNRKE
        atgctgaagccaagccccgattggccagcttaa                tgttgatctcggttgccgcacgccgacgccggtgagattcgacctcgacag
        ccatatagactaaggggcaggctttgtcccttg                tgctattacgaatcggagcgcggaatgcattaattactacataggagagaa
        agcctccacccctcgccgggtagcgccccccc                gcgctgctgtgtgtacagtctagccctgtgagcccccctctccaacccccag
                                                                                                            

Query   RNVAFFKE <---Intron---> VMLRTARLVAQWQCVGFCHGVLNTDNMSILGLTIDYGPYGFMDR <---Intron---> FDPDFICNASDNSGRY
        || ||||| <   277bp    > | /||||||||||||||||||||||||||||||/||||/||/|| <   285bp    > |||/|/|||||  |||
Target  RNTAFFKE                VTVRTARLVAQWQCVGFCHGVLNTDNMSILGLTVDYGPFGFIDR                FDPEFVCNASDRRGRY
        aaagttag                gagcagccggctctggttcggcaagaaaatgcaggtgctgtaga                tgcgtgtagtgcagct
        gaccttaa                tctgccgttcagagtgtgagttacaatgttgtctaagctgttag                tacattgaccagggga
        gcaatcag                gagggttggcggattcctttcccaccgcagattgtccctccac                accagtgcccgcgggcc
                                                                                                            

Query   SYQAQPAICRWNLARLAEALDPELPPGRAEAVLDEYLPLYNTFYLGNMRKKLGLLRREEPEDEMLITELLQTMHNTG <---Intron---> ADFTNTF
        ||||||//||||||||||||  ||   /| |/|||//||| | || |||/|||||||/||||/ |//|||| ||||| <   143bp    > |||||||
Target  SYQAQPSVCRWNLARLAEALGSELHASQAGAILDEFMPLYETLYLANMRRKLGLLRRKEPEDQELVSELLQLMHNTG                ADFTNTF
        ttcgcctgtctacgccgggcgtgccgtcgggacggtacctgactcgaaaaacgccacagcggcgcgtgccccacaag                ggtaaat
        caacacctgggatcgtcactgcataccacgcttaattctaactatcatggatgttggaacaaaattcattattaac                gcatcact
        acacggcgctgcgttgtgcgctgctacgagccttgcgcctgcccgccgggggcaggggaagcggtctggggcgcca                aacccccc
                                                                                                            

Query   RCLSQIPCPTAGDGEAEEGVIKMAKDLLLEQCASLEELKAANKPSMDPR <---Intron---> ELAMLLQLAQSNPSLFQMISDRRTVAMQLEKLGRL
        | || / ||  |/|/   |      ||||||| |||||| ||||/|/|| <   653bp    > ||||/| /||/||//| ///||  || ||||/|||
Target  RLLSGVSCPVVGEGKGATG--GPVVDLLLEQCVSLEELKVANKPTMEPR                ELAMVLSMAQTNPAMFGLVADRPEVAHQLEKMGRL
        ctcaggttcgggggaggag--gcgggcccgctgtcggcaggaacaagcc                gcgagctagcaacgatgcgggccgggcccgaagac
        gttggtcgcttgagagccg--gcttatttaagtctaatatcaacctacg                atctttctcacaccttgttcagcatcaataatggt
        cggtcgcctgggggggcag--cgggcccgggtccgggtggccgccggc                tggtgcctgcgccacgtcggacaaggctgggggcag
                                                                                                            

Query   KELLEADEVEVKAKHREDWATWITSYR <---Intron---> ERLAREVEGQSDVQALQEERVKVMDGTNPQYVLRNYIAQNAIEAAENGDFSE <---
        ||||  // |//|| ||||  ||/ || <   373bp    > /|| /| /|  /|  //|||//||| |||/ |||||||||||/||||||||| <   
Target  KELLNTNQDELRAKQREDWLRWISQYR                KRLVKECDGAREVCTIEEERIRVMDSTNPRVVLRNYIAQNAIQAAENGDFSE     
        agccaaacggcagacaggtcctaacta                actgagtgggaggtaagggaacgagaaaccggccatagcagacgggaggttg     
        aattacaaaatgcaagaagtggtgaag                agttaagagcgatgctaaagtgttagcacgtttgaatcaactaccaagatca     
        ggggcctgcgggaggagtgacgctgc                gggggggttaggggtcagaggctggccccacggcccctcgtaagttataccag     
                                                                                                            

Query   Intron---> VQRVLKVLEKPFSTQLGLD---QPSCLGRGGAEGQRNEEEEAQQGAEAASSRMRVPYDSKPPVWANEICVTUSS
        1439bp   > |/||||||| |/      /    |   |    /|   //|  /       //  ||||||||||| ||||||||
Target             VRRVLKVLENPYCAYPESELPGGPKTFGERYQKGMEKDKEGRKDEGRTDGNQNCVPYDSKPPVWAREICVTUSS
                   gcagcagcgacttgtcgtgccggcaatggatcagagagaggaagggaaggacatgctgaaccgtgcgatgattt
                   tggttattaacagcacacatcggcactgagaaagtaaaaaggaaaggcagaaagtcaagacctgcgatgtcgcc
                   ccataatagccctattgaaattgtaataggcgagggacagaggcgggatacattcatccgttggaagctccaaa
                                                                                          *  
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 182 ; UGA-SECIS: 188

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007955.1:subseq_10992636,106607_ Strand = - Positions = 49817 - 49749
 Found by:  Infernal (score=12.93) Covels (score=15.61)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -9.44

         ..(((((((.......(((((((((((((((..................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC---cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...(({[(((--(...([[[((({((((((------..............))))))})))]]])----..))))]}))...
 target  AAACUGAUGG--UGAAUGAAGACUCAGGUA------AUCAGUCAGUGACCUGUCUGUGUUGGAG----AGACCAGGAGCAC
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