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

 Blastx evalue: 6e-87
 Query name: gi|674749572|gb|AIL27817.1| selenoprotein P [Oreochromis niloticus]
 Query range: 1-405  (total 407)

 Target: /data/www-rg/seblastian_results/352763068/tempfiles/temptarget.fasta
 Chromosome: WARS01000015.1:subseq_7461800,200000_:subseq_0,120000_ Strand: -
 Positions:
 -Exon 1  100355       100557
 -Exon 2  100001       100213
 -Exon 3  99798        99915
 -Exon 4  99021        99680

 Redox box: YES

Query   MWAGLSLLLTLCLLHGGGAESEGGGPRCQLPSDWRIGDVEPMKGSVGRVTVVALLQASULFCLVQASR <---Intron---> LDGLQQKLERQGLKNV
        ||| ||||/||||||||||||/|||||||||  |/||/|/||||//|/|||||| ||||||||||||| <   141bp    > /| |/|/|| ||||/|
Target  MWACLSLLITLCLLHGGGAESDGGGPRCQLPPAWKIGEVDPMKGAMGQVTVVALFQASULFCLVQASR                MDNLRQELESQGLKDV
        atgtcaccaactcccgggggaggggcctccccgtaaggggcaaggagcgagggctcgatttttgcgta                agacccgcgacgcagg
        tgcgtgtttctgttagggcagagggcggatcccgatgatactagctgatcttcttacggttgttaccg                taatgaatagagtaat
        ggacccgcttccgctgctagttgtgtctgggacggagggtagggggtgggggctcgccagctgggtc                agccgcgaggtgtagtg
                                                                  *                                         

Query   VYMVVNHQGEQSRHLHPLLEAKLSKNIILYKQDGHQPDVWQTLAGEKDDFFIYDR <---Intron---> CGRLTHRISLPYSIIGEGHIEKAIKDTYC
        ||||/|| |||// || /|  /||/|| |||||  ||||||||/|||||| |||| <    85bp    > |||||| ||||||||| ||// |||||||
Target  VYMVINHHGEQAKRLHTMLAERLSENITLYKQDDQQPDVWQTLSGEKDDFLIYDR                CGRLTHHISLPYSIIGLGHVKGAIKDTYC
        gtagaaccggcgacccaacggactgaaactacggcccggtcacaggaggtcatga                tgccaccatccttaagcgcgaggaagatt
        tatttaaagaacagtacttcagtcaatctaaaaaaacatgactggaaaatttaag                gggtcaatctcacttgtgatagctaacag
        ccgcttctggaagcgccggagagagccaccagccagttcggaataaatctcttc                gtctcccctataccctaactggtgcatccc
                                                                                                            

Query   KRLCGDCTHE <---Intron---> SAEIPEECKDNAGVQPDVPAEQDDTRHDHHHGHGHGHHHGHGHHHGHGHGHHGDNQDVHPHGHGSDHNNGHHHR
        ||/||/|||| <   117bp    >   /||||||/ |  ||||         |  ||| |||||||||  |/ || |      | | /   |//|/|  
Target  KRICGECTHE                GTDIPEECKEKAVAQPDVDV-IPPVEGDTGHGHHHGHHHGHGHQGGN-HGFHPRG---HGHNNNHGHHHGNHDG
        acatggtacg                gagacggtagagggccgggg-accggggagcgcccgcccgcgccgga-cgtcccg---cgcaaacgcccgacgg
        agtggagcaa                gcatcaagaaactcacatat-tcctagacgagaaagaaagagaagga-agtacgg---agaaaaagaaagaaag
        acctcgcatg                ctccaggcagaatagtcata-tatagactattcttatctttccggtt-ttccctc---tctttctttctacttc
                                                                                                            

Query   NHDGADQTQHGVRPHGHFHEGDMPQTQHHFDLGQIPQEVHNHQVAQEAHAVIERPULSRKNRUKLKYNUQGLTGSDNEI--KSSUCUHURQLFGEAGSEQ
        /     |/| |||      /|   |/||| |/||/ | |    / |||/  / |||// | ||| |//||   |||||   |/|||||||/|||||||||
Target  HGSDHGQSQQGVRDQVPEQDGVASQSQHHVDVGQMQQAV----MPQEANGALVRPUVAEKARUKSKHSUQWTAGSDNEASPKASUCUHURRLFGEAGSEQ
        cgagcgcaccggagcgcgcggggtcacccggggcaccgg----accggaggcgactgggagatatacatctaggtgaggtcagatttctcactggggagc
        aggaagagaagtgaatcaaagtccagaaatatgataact----tcaacagcttgcgtcaacggacaaggagccgcaaacccacggggagggttgacggaa
        tctctaatgattacggtaattaatacattgtacgggaag----gaggctactggtaaaggtgagagccaggaactctacttgccacacacggtcaagtgg
                                                               *      *     *               * * *           

Query   SVGLUHCDEALPTSURUHGLIGDAVNDVRETUQURLPHAAUQEPQPAQUAUPPGV
         /|||||/|||| ||/|||| |/  |/|||||||||| | ||/||||||||| ||
Target  PLGLUHCNEALPASUQUHGLTGNVANNVRETUQURLPPADUQQPQPAQUAUPQGV
        ccgctctaggccgttctcgcagaggaagagatctctccggtcccccgctgtccgg
        ctgtgagaactcccgagagtcgatcaatgacgaggtcccagaacaccagcgcagt
        gctcacttgggcccagatagactactttgacagacgtttcaagtgacaacacatg
            *         * *              * *      *       * *    
 Sequence until next stop: 
AGCTGA
 S  * 

 Distance CDS-SECIS: 358 ; UGA-SECIS: 370

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = WARS01000015.1:subseq_7461800,200000_:subseq_0,120000_ Strand = - Positions = 98662 - 98583
 Found by:  Infernal (score=30.59) Covels (score=29.51)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -21.53

         ..(((((((.........(((((((((((((((...............)))))))))))))))..........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ..((((((((........([[(({((((((([(.....-.........)])))))))}))]])......-..))))))))..
 target  UGCUCUCUUCAACCUUUAUGAAACCAGACGCAGAAACU-AUGUCCUAGUGGCGUCUGUUUGAAGUCAGG-CAGGAGAGAGAG
                           ****           ^^^                       ****                   
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 6e-87
 Query name: gi|674749572|gb|AIL27817.1| selenoprotein P [Oreochromis niloticus]
 Query range: 1-405  (total 407)

 Target: /data/www-rg/seblastian_results/352763068/tempfiles/temptarget.fasta
 Chromosome: WARS01000015.1:subseq_7461800,200000_:subseq_0,120000_ Strand: -
 Positions:
 -Exon 1  100355       100557
 -Exon 2  100001       100213
 -Exon 3  99798        99915
 -Exon 4  99021        99680

 Redox box: YES

Query   MWAGLSLLLTLCLLHGGGAESEGGGPRCQLPSDWRIGDVEPMKGSVGRVTVVALLQASULFCLVQASR <---Intron---> LDGLQQKLERQGLKNV
        ||| ||||/||||||||||||/|||||||||  |/||/|/||||//|/|||||| ||||||||||||| <   141bp    > /| |/|/|| ||||/|
Target  MWACLSLLITLCLLHGGGAESDGGGPRCQLPPAWKIGEVDPMKGAMGQVTVVALFQASULFCLVQASR                MDNLRQELESQGLKDV
        atgtcaccaactcccgggggaggggcctccccgtaaggggcaaggagcgagggctcgatttttgcgta                agacccgcgacgcagg
        tgcgtgtttctgttagggcagagggcggatcccgatgatactagctgatcttcttacggttgttaccg                taatgaatagagtaat
        ggacccgcttccgctgctagttgtgtctgggacggagggtagggggtgggggctcgccagctgggtc                agccgcgaggtgtagtg
                                                                  *                                         

Query   VYMVVNHQGEQSRHLHPLLEAKLSKNIILYKQDGHQPDVWQTLAGEKDDFFIYDR <---Intron---> CGRLTHRISLPYSIIGEGHIEKAIKDTYC
        ||||/|| |||// || /|  /||/|| |||||  ||||||||/|||||| |||| <    85bp    > |||||| ||||||||| ||// |||||||
Target  VYMVINHHGEQAKRLHTMLAERLSENITLYKQDDQQPDVWQTLSGEKDDFLIYDR                CGRLTHHISLPYSIIGLGHVKGAIKDTYC
        gtagaaccggcgacccaacggactgaaactacggcccggtcacaggaggtcatga                tgccaccatccttaagcgcgaggaagatt
        tatttaaagaacagtacttcagtcaatctaaaaaaacatgactggaaaatttaag                gggtcaatctcacttgtgatagctaacag
        ccgcttctggaagcgccggagagagccaccagccagttcggaataaatctcttc                gtctcccctataccctaactggtgcatccc
                                                                                                            

Query   KRLCGDCTHE <---Intron---> SAEIPEECKDNAGVQPDVPAEQDDTRHDHHHGHGHGHHHGHGHHHGHGHGHHGDNQDVHPHGHGSDHNNGHHHR
        ||/||/|||| <   117bp    >   /||||||/ |  ||||         |  ||| |||||||||  |/ || |      | | /   |//|/|  
Target  KRICGECTHE                GTDIPEECKEKAVAQPDVDV-IPPVEGDTGHGHHHGHHHGHGHQGGN-HGFHPRG---HGHNNNHGHHHGNHDG
        acatggtacg                gagacggtagagggccgggg-accggggagcgcccgcccgcgccgga-cgtcccg---cgcaaacgcccgacgg
        agtggagcaa                gcatcaagaaactcacatat-tcctagacgagaaagaaagagaagga-agtacgg---agaaaaagaaagaaag
        acctcgcatg                ctccaggcagaatagtcata-tatagactattcttatctttccggtt-ttccctc---tctttctttctacttc
                                                                                                            

Query   NHDGADQTQHGVRPHGHFHEGDMPQTQHHFDLGQIPQEVHNHQVAQEAHAVIERPULSRKNRUKLKYNUQGLTGSDNEI--KSSUCUHURQLFGEAGSEQ
        /     |/| |||      /|   |/||| |/||/ | |    / |||/  / |||// | ||| |//||   |||||   |/|||||||/|||||||||
Target  HGSDHGQSQQGVRDQVPEQDGVASQSQHHVDVGQMQQAV----MPQEANGALVRPUVAEKARUKSKHSUQWTAGSDNEASPKASUCUHURRLFGEAGSEQ
        cgagcgcaccggagcgcgcggggtcacccggggcaccgg----accggaggcgactgggagatatacatctaggtgaggtcagatttctcactggggagc
        aggaagagaagtgaatcaaagtccagaaatatgataact----tcaacagcttgcgtcaacggacaaggagccgcaaacccacggggagggttgacggaa
        tctctaatgattacggtaattaatacattgtacgggaag----gaggctactggtaaaggtgagagccaggaactctacttgccacacacggtcaagtgg
                                                               *      *     *               * * *           

Query   SVGLUHCDEALPTSURUHGLIGDAVNDVRETUQURLPHAAUQEPQPAQUAUPPGV
         /|||||/|||| ||/|||| |/  |/|||||||||| | ||/||||||||| ||
Target  PLGLUHCNEALPASUQUHGLTGNVANNVRETUQURLPPADUQQPQPAQUAUPQGV
        ccgctctaggccgttctcgcagaggaagagatctctccggtcccccgctgtccgg
        ctgtgagaactcccgagagtcgatcaatgacgaggtcccagaacaccagcgcagt
        gctcacttgggcccagatagactactttgacagacgtttcaagtgacaacacatg
            *         * *              * *      *       * *    
 Sequence until next stop: 
AGCTGA
 S  * 

 Distance CDS-SECIS: 952 ; UGA-SECIS: 964

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = WARS01000015.1:subseq_7461800,200000_:subseq_0,120000_ Strand = - Positions = 98068 - 97997
 Found by:  Infernal (score=23.76) Covels (score=16.18)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -17.94

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..((((((((--....{[[{((((({(({((.....-.........))}))})))))}]]}..--..-))))))))..
 target  CACUCUGUAU--UUAAUGAUGGCUUCUGUGGGAAGA-UUACAAUCACCCUGAAAGUCUGAUGC--GC-GUACAGAGAA
                         ****            ^^                       ****