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

 Blastx evalue: 9e-52
 Query name: gi|961811942|ref|XP_014879607.1| PREDICTED: selenoprotein P [Poecilia latipinna]
 Query range: 1-264  (total 301)

 Target: /data/www-rg/seblastian_results/307933375/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000024.1:subseq_2312841,100778_ Strand: +
 Positions:
 -Exon 1  49922        50124
 -Exon 2  50346        50558
 -Exon 3  50661        50778
 -Exon 4  50879        51142

 Redox box: YES

Query   MWVRLSLLLTLCLLHGGGAESEGGGPRCQPPSTWMIGEVEPMKGTAGQVTVVALLKASULFCLVQASR <---Intron---> IDGLRQKLETQGLNDV
        ||  ||||/||||||||||||/||||||| |  | | ||/|| |  |||||||| /|||||||||||| <   221bp    > /||||||||/|||  |
Target  MWACLSLLITLCLLHGGGAESDGGGPRCQLPPAWKIEEVDPMNGAMGQVTVVALFQASULFCLVQASR                MDGLRQKLESQGLKGV
        atgtcaccaactcccgggggaggggcctctccgtaaggggcaaggagcgagggctcgatttttgcgta                aggcccatgacgcagg
        tgcgtgtttctgttagggcagagggcggatcccgataatactagctgatcttcttacggttgttaccg                tagtgaatagagtagt
        gggcccgcctccgctgctagttgtgtctggaacggagggtagtgagcggaggctcgccagctgggtc                agtcgcggggtgtggtg
                                                                  *                                         

Query   VYMVINHQGEQAQRLHPMLAERLSDKISLYKQGEQQPDVWQALNGKKDDFIIYDR <---Intron---> CGRLTHHISLPYSVIGHGHIESAIKEAYC
        ||||/||||||/|||| |||/||// |/|||| |||||||| | |/|||| |||| <   102bp    > |||||||||||||/|||||/|||||| ||
Target  VYMVVNHQGEQSQRLHTMLAQRLTEPITLYKQEEQQPDVWQTLGGEKDDFFIYDR                CGRLTHHISLPYSIIGHGHVESAIKETYC
        gtaggaccggctcctcaacgcacagcaactacggcccggtcacgggaggttatga                tgccaccatccttaagcgcggagaagatt
        tatttaaagaacagtacttcagtcactctaaaaaaacatgactggaaaatttaag                gggtcaatctcacttgagatagctaacag
        gcgctccggagaacgccggagatcgcccccagggagttcgaacgagatctcttc                gtatctccaataccctatctggtccagccc
                                                                                                            

Query   NRMCGACSHE <---Intron---> TAETSEGCRATPNAQPEADGPAAVGDNTEHDHSRHHGHGHHGHG-HHGHGH-HGHGHHGHGHHG-QHGHHHHRH
         |/|| |/|| <   100bp    >   |  | |/   /|||/|  |        | |  ||||||  || /||| | ||| |  || || /||    / 
Target  KRICGECTHE                GTEIPEECKEKADAQPDAP-PVEEDTGNGHHHGHHHGHGHGHHGDNHGHDHNHGHHHGSHGGHGSEHGQSQSQQ
        acatggtacg                gagacggtagagggccggc-cggggagagcccgcccgcgcgccggacgcgcacgcccgacggcgagcgcacacc
        agtggagcaa                gcatcaagaaacacacacc-ctaaacgagaaagaaagagagaagaaagaaaaagaaaggaggaggaagagagaa
        acctcgcatg                ctgcaggcagaatagttca-tagactattcttatctctatcctgtttcttcctttctatttctctgtaatatga
                                                                                                            

Query   HGDHHGHQGDLEQSQ
           | ||| |/ | |
Target  GVSHQGHQQDVSQRQ
        ggaccgcccggtcac
        gtgaagaaaatcaga
        tttcgctgatataga
                       
 Sequence until next stop: 
GATCGTTTAGATTTAGGCCAGATGCAGCAAGTAGTGTACCAGATGCCACAGGAGGTCCATGAAGCCCCTGTGAACACCCCTTGA
 D  R  L  D  L  G  Q  M  Q  Q  V  V  Y  Q  M  P  Q  E  V  H  E  A  P  V  N  T  P  * 

 Distance CDS-SECIS: 782 ; UGA-SECIS: 1403

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JXSJ01000024.1:subseq_2312841,100778_ Strand = + Positions = 51925 - 52004
 Found by:  Infernal (score=25.54) Covels (score=24.71)
 Stem2 length = 8   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -17.46

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

 Blastx evalue: 9e-52
 Query name: gi|961811942|ref|XP_014879607.1| PREDICTED: selenoprotein P [Poecilia latipinna]
 Query range: 1-264  (total 301)

 Target: /data/www-rg/seblastian_results/307933375/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000024.1:subseq_2312841,100778_ Strand: +
 Positions:
 -Exon 1  49922        50124
 -Exon 2  50346        50558
 -Exon 3  50661        50778
 -Exon 4  50879        51142

 Redox box: YES

Query   MWVRLSLLLTLCLLHGGGAESEGGGPRCQPPSTWMIGEVEPMKGTAGQVTVVALLKASULFCLVQASR <---Intron---> IDGLRQKLETQGLNDV
        ||  ||||/||||||||||||/||||||| |  | | ||/|| |  |||||||| /|||||||||||| <   221bp    > /||||||||/|||  |
Target  MWACLSLLITLCLLHGGGAESDGGGPRCQLPPAWKIEEVDPMNGAMGQVTVVALFQASULFCLVQASR                MDGLRQKLESQGLKGV
        atgtcaccaactcccgggggaggggcctctccgtaaggggcaaggagcgagggctcgatttttgcgta                aggcccatgacgcagg
        tgcgtgtttctgttagggcagagggcggatcccgataatactagctgatcttcttacggttgttaccg                tagtgaatagagtagt
        gggcccgcctccgctgctagttgtgtctggaacggagggtagtgagcggaggctcgccagctgggtc                agtcgcggggtgtggtg
                                                                  *                                         

Query   VYMVINHQGEQAQRLHPMLAERLSDKISLYKQGEQQPDVWQALNGKKDDFIIYDR <---Intron---> CGRLTHHISLPYSVIGHGHIESAIKEAYC
        ||||/||||||/|||| |||/||// |/|||| |||||||| | |/|||| |||| <   102bp    > |||||||||||||/|||||/|||||| ||
Target  VYMVVNHQGEQSQRLHTMLAQRLTEPITLYKQEEQQPDVWQTLGGEKDDFFIYDR                CGRLTHHISLPYSIIGHGHVESAIKETYC
        gtaggaccggctcctcaacgcacagcaactacggcccggtcacgggaggttatga                tgccaccatccttaagcgcggagaagatt
        tatttaaagaacagtacttcagtcactctaaaaaaacatgactggaaaatttaag                gggtcaatctcacttgagatagctaacag
        gcgctccggagaacgccggagatcgcccccagggagttcgaacgagatctcttc                gtatctccaataccctatctggtccagccc
                                                                                                            

Query   NRMCGACSHE <---Intron---> TAETSEGCRATPNAQPEADGPAAVGDNTEHDHSRHHGHGHHGHG-HHGHGH-HGHGHHGHGHHG-QHGHHHHRH
         |/|| |/|| <   100bp    >   |  | |/   /|||/|  |        | |  ||||||  || /||| | ||| |  || || /||    / 
Target  KRICGECTHE                GTEIPEECKEKADAQPDAP-PVEEDTGNGHHHGHHHGHGHGHHGDNHGHDHNHGHHHGSHGGHGSEHGQSQSQQ
        acatggtacg                gagacggtagagggccggc-cggggagagcccgcccgcgcgccggacgcgcacgcccgacggcgagcgcacacc
        agtggagcaa                gcatcaagaaacacacacc-ctaaacgagaaagaaagagagaagaaagaaaaagaaaggaggaggaagagagaa
        acctcgcatg                ctgcaggcagaatagttca-tagactattcttatctctatcctgtttcttcctttctatttctctgtaatatga
                                                                                                            

Query   HGDHHGHQGDLEQSQ
           | ||| |/ | |
Target  GVSHQGHQQDVSQRQ
        ggaccgcccggtcac
        gtgaagaaaatcaga
        tttcgctgatataga
                       
 Sequence until next stop: 
GATCGTTTAGATTTAGGCCAGATGCAGCAAGTAGTGTACCAGATGCCACAGGAGGTCCATGAAGCCCCTGTGAACACCCCTTGA
 D  R  L  D  L  G  Q  M  Q  Q  V  V  Y  Q  M  P  Q  E  V  H  E  A  P  V  N  T  P  * 

 Distance CDS-SECIS: 1392 ; UGA-SECIS: 2013

------- SECIS element -- id:2 -- grade:B ----
 Chromosome = JXSJ01000024.1:subseq_2312841,100778_ Strand = + Positions = 52535 - 52604
 Found by:  Infernal (score=22.09) Covels (score=13.62)
 Stem2 length = 8   Apical loop length = 14   Insertion in stem2 = 1, 1
 Free Energy = -12.44

         ..(((((((.......((((((((((((.(((...............))))))))).))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggc-ccuAAAcCcuuuuuggggcgggccagg-cCuGAUGuuuuuucaugaccggc
         ..(((((((---....{[[{(({((({(.((......---........)))})))}.))}]]}..--.--.)))))))..
 target  ACUCUGUAC---UUAAUGAUGGCUUCUGCGGGAAGAU---AACAGUCACCCUGAAAACCUGAUGC--U--UGUACAGAAA
                         ****            ^^                         ****