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

 Blastx evalue: 2e-10
 Query name: gi|315360675|ref|NP_001186770.1| selenoprotein I [Oryctolagus cuniculus]
 Query range: 19-397  (total 397)

 Target: /var/www/seblastian_output/879729143/tempfiles/temptarget.fasta
 Chromosome: gi|511782579|gb|CM001955.1|subseq(81208461,125191) Strand: -
 Positions:
 -Exon 1  75120        75191
 -Exon 2  74578        74686
 -Exon 3  71930        72004
 -Exon 4  67224        67486
 -Exon 5  65279        65387
 -Exon 6  55815        55863
 -Exon 7  53999        54179
 -Exon 8  52612        52794
 -Exon 9  50000        50095

 Redox box: no

Query   KYSAVDTNPLSLYIMHPFWNTVVK <---Intron---> VFPTWLAPNLITFSGFLLVVFNFLLMAYFDPDFYASA <---Intron---> PGHKHVP
        /||||||||||||/|||||||/|| <   433bp    > ||||||||||||||||||||||||||||||||||||| <   2573bp   > |||||||
Target  QYSAVDTNPLSLYVMHPFWNTIVK                VFPTWLAPNLITFSGFLLVVFNFLLMAYFDPDFYASA                PGHKHVP
        ctagggaacctctgaccttaaaga                gtcatcgcacaattgtccggtatccagttgcgttgtg                cgcacgc
        aagctacactctattactgactta                ttccgtccattctcgttttttattttcatacatacc                ccgaaatc
        gcttgtctattgtcgtatgctaag                atttgggctgatttctggtacttaagactttcctca                aatcgtgt
                                                                                                            

Query   DWVWIVVGILNFIAYTLD <---Intron---> GVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGPTGVSVFVLYLLLWVVLFSFILS
        ||||||||||||/||||| <   4443bp   > ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Target  DWVWIVVGILNFVAYTLD                GVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSTGVSVFVLYLLLWVVLFSFILS
        gtgtagggacatggtacg                ggggacgcaaataactggctgcgcgatttgttggagttatgagtaggagtgctccctggttttact
        agtgtttgttattcacta                gtagaacggcacgcctgattaagtaggcgtatttctacttgggccgtgttttatttgttttctttc
        cgtgtagcccccacctat                tgcagatcacttctcaggttttcgttgattcttatttcctaaagttcttttttcgagatgttccgc
                                                                                                            

Query   HWEKYNTGILFLPWGYDISQVT <---Intron---> ISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTAMIIGC <---Intron---> ALCVTLPMS
        |||||||||||||||||||||| <   1836bp   > |||||||||||||||||||||||||||||||/||||| <   9415bp   > |||||||||
Target  HWEKYNTGILFLPWGYDISQVT                ISFVYIVTAVVGVEAWYEPFLFNFLYRDLFTSMIIGC                ALCVTLPMS
        ctgataagactcctgtgaacga                attgtagagggggggttgctctatttagctataaagt                gttgaccaa
        agaaaacgttttcggaatgatc                tcttattccttgtacgaactttattagattcctttg                gctgtctctg
        cgagtcagttcgagatctcgg                ttttccagtgtgatgcgtatcgttcatacactagttt                tggtgttagt
                                                                                                            

Query   LLNFFRSY <---Intron---> KNNTLKHNSVYEAMVPFFSPCLLFILSTAWILRSPSDILELHPRIFYFMVGTAFANITCQL <---Intron--->
        |||||||| <   1635bp   > |||||||||||||/|| ||||||||||| ||| |||||||||||/||||||||||| |||| <   1204bp   >
Target  LLNFFRSY                KNNTLKHNSVYEAVVPLFSPCLLFILSTVWILWSPSDILELHPRVFYFMVGTAFANSTCQL               
        tcattaat                aaaatacatgtggggctttcttctattagtacttctgatgcccagtttaggagtgaaatcc               
        ttattgg                aaaactaaactaacttcttccgtttttcctgttgcccattatacgttatttgcctcagcga                
        aactcac                tatccgactactatgtcattacggctgtaggctgatattagattaacctgtaactcccatg                
                                                                                                            

Query    IVCQMSSTRCPTLNWLLVPLFVVVMAVNLGVASYVESILLYALTAAFTLAHIHYGVRVVKQ <---Intron---> LSSHFQIYPFSLRKPNSDULGM
         |||||||||||||||||||||/||/ ||||||||/|||||| || |||||||||||||||| <   2516bp   > ||||||||||||||||||||||
Target   IVCQMSSTRCPTLNWLLVPLFLVVLVVNLGVASYIESILLYTLTTAFTLAHIHYGVRVVKQ                LSSHFQIYPFSLRKPNSDULGM
         agtcaaaactcatattcgccttggtggacgggttagaacctataagtacgcactggcggac                caactcatctttaacatgtcga
        tttgatggcggcctagtttcttttttttatgtccatagtttactccctctcataagtgttaa                tggatatactctgacacagtgt
        gttcagttcgtatgtgggttccgtcagacaaactctgctcgtaaagtttgcccttaaagagg                gccttgtcccaggaacataaag
                                                                                                        *   

Query   EEKNIAL
        ||||| |
Target  EEKNIGL
        ggaaagc
        aaaatgt
        aagttcg
               
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 1299 ; UGA-SECIS: 1329

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|511782579|gb|CM001955.1|subseq(81208461,125191) Strand = - Positions = 48700 - 48622
 Found by:  Infernal (score=27.74) Covels (score=21.25)
 Stem2 length = 10   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -6.11

         ..(((((((.......(((((((((((((((...................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC----cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...(({({((......{[[[((((((({(((...................)))})))))))]]]}..--..-))})}))...
 target  GAAGUUUGUGCUUGAAUGAAGAGUGUAUCUUAAACCUCCUUUUUUUGGACAGGCUGCACUUGGAUAA--CA-UAGGCACCAC
                         ****           ^^^                           ****