_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 9e-45
 Query name: gi|1025446623|ref|XP_007557653.2| PREDICTED: selenoprotein P [Poecilia formosa]
 Query range: 1-394  (total 394)

 Target: /data/www-rg/seblastian_results/725788875/tempfiles/temptarget.fasta
 Chromosome: JACSYO010000335.1:subseq_407452,100000_ Strand: +
 Positions:
 -Exon 1  49919        50121
 -Exon 2  50511        50723
 -Exon 3  50824        50977
 -Exon 4  51057        51638

 Redox box: YES

Query   MWVRLSLLLTLCLLHGGGAESEGGGPRCQPPSTWMIGEVEPMKGTAGQVTVVALLKASULFCLVQASR <---Intron---> IDGLRQKLETQGLNDV
        ||  ||||/||||||||||||/||||||| |  | ||/||||||| |/|||||||/|||||||||||| <   389bp    > /||| ||||/||| ||
Target  MWACLSLLITLCLLHGGGAESDGGGPRCQLPPAWRIGDVEPMKGTMGRVTVVALLQASULFCLVQASR                MDGLHQKLESQGLKDV
        atgtcatcaactcccgggggaggggcctccccgtaaggggcaagaagcgagggctcgatttttgcgta                aggcccacgacgcagg
        tgcgtgtttctgttagggcagagggcggatcccggtgatactagctggtcttcttacggttgttaccg                tagtaaatagagtaat
        gggcccgcctccgccgctggttgtgtctggtgaggagcggagagggcgggggctagctagccgggtc                agccgcggggtgtggcg
                                                                  *                                         

Query   VYMVINHQGEQAQRLHPMLAERLSDKISLYKQGEQQPDVWQALNGKKDDFIIYDR <---Intron---> CGRLTHHISLPYSVIGHGHIESAIKEAYC
         |||/| |||||||||||||/|||  |/|||| ||||||| ||/| ||||//||| <   100bp    > |||||||||||||/|| ||/| ||| |||
Target  AYMVVNQQGEQAQRLHPMLAQRLSVNITLYKQEEQQPDVWLALSGDKDDFLVYDR                CGRLTHHISLPYSIIGQGHVEGAIKNAYC
        gtaggaccggcgcccccacgcactgaaactacggcccggtcgcaggaggtcgtga                tgccaccatccttaagcgcggggaaagtt
        catttaaagaacagtacttcagtctatctaaaaaaacatgtctggaaaatttaag                gggtcaatctcacttgagatagctaacag
        ccgctcggggaaacgccggagggggcccccagggagttcggagcatgcctcttc                gtctccccctcgccctcactcgcccatccc
                                                                                                            

Query   NRMCGACSHETAETSEGCRATPN <---Intron---> AQPEADGPAAVGDNTEHDHSRHHGHGHHGHGHHGHGHHGHGHHGHGHHGQHGHHHHRHHGD
        /| || |/||  /|/  |    / <    79bp    > /       ||  |              ||| |||| ||||||||  |  |   | | ||| 
Target  SRTCGDCTHE-VQTTHTCENILS                SAETPVECAARADAQPDAPPAVEEDAGHGH-HHGH-HHGHGHHGDNHGVQTNAHDH-HHGR
        acatggtacg-gcaacatgaact                aggacggtggagggccggccgggggggcgc-ccgc-ccgcgccggacggcaagcgc-ccgc
        ggcggagcaa-taccacgaattc                gcacctagccgcacacacccctaaacgaga-aaga-aagagaagaaagtacacaaa-aagg
        ccatgtcgcg-agcatccgtata                ctgaaggcagaacagtctcatagatcgctc-tcct-ccttcctgcctttactccct-cttt
                                                                                                            

Query   HHGHQGDLEQSQQGAGQDHGQHVFDSPQLQQAVDTEQLLQEAVAAPVRPUVAGKGRUKSKFTUQGTAGSENETVPKASUCUHURRVFGEAGSEQSLGLUH
        |||        |||      /     || |   |  |/   |/ || |||     /|||| /|| ||||/    |/|||||||||/||/ |||| |||||
Target  HHGDHD--GGGQQGVRHQGHEQDGRVPQRQHDFDMGQMQHAALVAPARPUAQEMAKUKSKHSUQWTAGSDGAASPQASUCUHURRLFGDVGSEQPLGLUH
        ccggcg--gggccggaccgcgcggagccaccgtgagcaccggcggcgactgcgagatatacatctaggtggggtccgatttctcactggggagcccgctc
        aagaaa--gggaagtgaagaaaaggtcagaaatatgataaccttcccgcgcaatcagacaaggagccgcagccccacggggagggttgatggaactgtga
        ccacct--ctcgataacgttgattgataggctctgcgggcgccgctggcaagggcgagagccaggaactcaacttgccacacacggcccggcgggctgac
                                                         *      *     *               * * *               * 

Query   CEEGLPASUQUQGLTSEAAADVRETUQURMPPAEUQQPQPDQ
        |/| ||||||| ||     | |||||||| |||/|||||| |
Target  CDEALPASUQUHGL----MAAVRETUQURSPPADUQQPQPAQ
        tgggccgttctcgc----agggagatctctccggtcccccgc
        gaactcccgagagt----tcctgacgaggccccagaacacca
        tcgggcccagacgg----gctcggcagacacctcaggtgaca
                * *              * *      *       
 Sequence until next stop: 
TGA
 * 

 Distance CDS-SECIS: 398 ; UGA-SECIS: 419

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = JACSYO010000335.1:subseq_407452,100000_ Strand = + Positions = 52037 - 52112
 Found by:  Infernal (score=20.06) Covels (score=23.95)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -17.13

         ..(((((((.......(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         (((({(((........([[([{((((((([(.....-.........)])))))))}])]]).....-.-..)))}))))
 target  CUCUCUCCAUCCUUUAUGAAGCCAGGCGCAGAAACU-AAGCUCUAGUGGCGUCUGUAUGAAGUCAG-G-CAGGAAAGAG
                         ****           ^^^                       ****                  
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:1     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 9e-45
 Query name: gi|1025446623|ref|XP_007557653.2| PREDICTED: selenoprotein P [Poecilia formosa]
 Query range: 1-394  (total 394)

 Target: /data/www-rg/seblastian_results/725788875/tempfiles/temptarget.fasta
 Chromosome: JACSYO010000335.1:subseq_407452,100000_ Strand: +
 Positions:
 -Exon 1  49919        50121
 -Exon 2  50511        50723
 -Exon 3  50824        50977
 -Exon 4  51057        51638

 Redox box: YES

Query   MWVRLSLLLTLCLLHGGGAESEGGGPRCQPPSTWMIGEVEPMKGTAGQVTVVALLKASULFCLVQASR <---Intron---> IDGLRQKLETQGLNDV
        ||  ||||/||||||||||||/||||||| |  | ||/||||||| |/|||||||/|||||||||||| <   389bp    > /||| ||||/||| ||
Target  MWACLSLLITLCLLHGGGAESDGGGPRCQLPPAWRIGDVEPMKGTMGRVTVVALLQASULFCLVQASR                MDGLHQKLESQGLKDV
        atgtcatcaactcccgggggaggggcctccccgtaaggggcaagaagcgagggctcgatttttgcgta                aggcccacgacgcagg
        tgcgtgtttctgttagggcagagggcggatcccggtgatactagctggtcttcttacggttgttaccg                tagtaaatagagtaat
        gggcccgcctccgccgctggttgtgtctggtgaggagcggagagggcgggggctagctagccgggtc                agccgcggggtgtggcg
                                                                  *                                         

Query   VYMVINHQGEQAQRLHPMLAERLSDKISLYKQGEQQPDVWQALNGKKDDFIIYDR <---Intron---> CGRLTHHISLPYSVIGHGHIESAIKEAYC
         |||/| |||||||||||||/|||  |/|||| ||||||| ||/| ||||//||| <   100bp    > |||||||||||||/|| ||/| ||| |||
Target  AYMVVNQQGEQAQRLHPMLAQRLSVNITLYKQEEQQPDVWLALSGDKDDFLVYDR                CGRLTHHISLPYSIIGQGHVEGAIKNAYC
        gtaggaccggcgcccccacgcactgaaactacggcccggtcgcaggaggtcgtga                tgccaccatccttaagcgcggggaaagtt
        catttaaagaacagtacttcagtctatctaaaaaaacatgtctggaaaatttaag                gggtcaatctcacttgagatagctaacag
        ccgctcggggaaacgccggagggggcccccagggagttcggagcatgcctcttc                gtctccccctcgccctcactcgcccatccc
                                                                                                            

Query   NRMCGACSHETAETSEGCRATPN <---Intron---> AQPEADGPAAVGDNTEHDHSRHHGHGHHGHGHHGHGHHGHGHHGHGHHGQHGHHHHRHHGD
        /| || |/||  /|/  |    / <    79bp    > /       ||  |              ||| |||| ||||||||  |  |   | | ||| 
Target  SRTCGDCTHE-VQTTHTCENILS                SAETPVECAARADAQPDAPPAVEEDAGHGH-HHGH-HHGHGHHGDNHGVQTNAHDH-HHGR
        acatggtacg-gcaacatgaact                aggacggtggagggccggccgggggggcgc-ccgc-ccgcgccggacggcaagcgc-ccgc
        ggcggagcaa-taccacgaattc                gcacctagccgcacacacccctaaacgaga-aaga-aagagaagaaagtacacaaa-aagg
        ccatgtcgcg-agcatccgtata                ctgaaggcagaacagtctcatagatcgctc-tcct-ccttcctgcctttactccct-cttt
                                                                                                            

Query   HHGHQGDLEQSQQGAGQDHGQHVFDSPQLQQAVDTEQLLQEAVAAPVRPUVAGKGRUKSKFTUQGTAGSENETVPKASUCUHURRVFGEAGSEQSLGLUH
        |||        |||      /     || |   |  |/   |/ || |||     /|||| /|| ||||/    |/|||||||||/||/ |||| |||||
Target  HHGDHD--GGGQQGVRHQGHEQDGRVPQRQHDFDMGQMQHAALVAPARPUAQEMAKUKSKHSUQWTAGSDGAASPQASUCUHURRLFGDVGSEQPLGLUH
        ccggcg--gggccggaccgcgcggagccaccgtgagcaccggcggcgactgcgagatatacatctaggtggggtccgatttctcactggggagcccgctc
        aagaaa--gggaagtgaagaaaaggtcagaaatatgataaccttcccgcgcaatcagacaaggagccgcagccccacggggagggttgatggaactgtga
        ccacct--ctcgataacgttgattgataggctctgcgggcgccgctggcaagggcgagagccaggaactcaacttgccacacacggcccggcgggctgac
                                                         *      *     *               * * *               * 

Query   CEEGLPASUQUQGLTSEAAADVRETUQURMPPAEUQQPQPDQ
        |/| ||||||| ||     | |||||||| |||/|||||| |
Target  CDEALPASUQUHGL----MAAVRETUQURSPPADUQQPQPAQ
        tgggccgttctcgc----agggagatctctccggtcccccgc
        gaactcccgagagt----tcctgacgaggccccagaacacca
        tcgggcccagacgg----gctcggcagacacctcaggtgaca
                * *              * *      *       
 Sequence until next stop: 
TGA
 * 

 Distance CDS-SECIS: 980 ; UGA-SECIS: 1001

------- SECIS element -- id:1 -- grade:B ----
 Chromosome = JACSYO010000335.1:subseq_407452,100000_ Strand = + Positions = 52619 - 52693
 Found by:  Infernal (score=23.21) Covels (score=14.33)
 Stem2 length = 10   Apical loop length = 15   Insertion in stem2 = 1, 1
 Free Energy = -13.86

         ..(((((((.......((((((((((((.(((...............))))))))).))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggc-ccuAAAcCcuuuuuggggcgggccagg-cCuGAUGuuuuuucaugaccggc
         ..({(({((((.....{[[{((((((((.((......--.........)))))))).))}]]}..--.)-)))}))})..
 target  UACACUCUGUACUCAAUGAUGGUUUCAGCGGGAAGAU--UAAACGUCACCCUGAAAACCUGAUGC--UU-GCACAGAGAA
                         ****            ^^                         ****