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

 Blastx evalue: 5e-56
 Query name: gi|1035237468|ref|XP_008316560.2| PREDICTED: selenide, water dikinase 1-like [Cynoglossus semilaevis]
 Query range: 1-432  (total 432)

 Target: /data/www-rg/seblastian_results/272911872/tempfiles/temptarget.fasta
 Chromosome: JACSYO010000005.1:subseq_88650,100000_ Strand: -
 Positions:
 -Exon 1  56698        56968
 -Exon 2  55755        55858
 -Exon 3  55088        55195
 -Exon 4  54647        54801
 -Exon 5  53467        53557
 -Exon 6  53231        53330
 -Exon 7  50322        50534
 -Exon 8  49979        50226

 Redox box: no

Query   MSGSTSPPPLAEAGQTESCFPPGYKPFKPEEHGLERGFRLTAYSDLKGUGCKVPQEALLKLLAGLETDRVDGTGKAGDQAADFGQQLSAPRLG <---In
        ||||||||| |||  || ||||||||||||||||||||||||/||||||||||||||||||||||| || ||||||||||//|||||  |||| <   83
Target  MSGSTSPPPSAEAVATEGCFPPGYKPFKPEEHGLERGFRLTAFSDLKGUGCKVPQEALLKLLAGLEADRADGTGKAGDQASEFGQQL--PRLG       
        atgtatccctgggggaggttccgtactacggcgcgcgtccagttgcagtgtagccggccaccggcgggcgggagagggcgtgtgcct--cccg       
        tcgccccccccactccaggtccgaactacaaagtaggtgtcctcataggggatcaacttattcgtacagcagcgacgaaccatgaat--cgt        
        gacatcgtcgagtggcggctccacgtcacgaccggcgctcagtgcgaaaccgcgggtgcacggagggcgccgaggcccaaagccaag--tac        
                                                        *                                                   

Query   tron---> VGMDCCVIPLRHGGLSLVQTTDFFYPLVDDPYMM <---Intron---> GRIACANVLSDLYAMGITECDNMLMLLSVSQKMNEK <---
        9bp    > ||||||||||||||||||||||||||||/||||| <   559bp    > ||||||||||||||||||||||||||||||||||/| <   
Target           VGMDCCVIPLRHGGLSLVQTTDFFYPLVEDPYMM                GRIACANVLSDLYAMGITECDNMLMLLSVSQKMNDK     
                 ggagttgaccacggctcgcaagtttccgggctaa                gaagtgagcagctgagaagtgaacaccagacaaaga     
                gtgtaggttctgaggtcttaccattacttaacatt                ggtcgcattgatactgtcagaatttttgtgaataaa     
                tgggcctgtaggtagcagcgctcccctgggtccgg                cgagctcccttcccgccggtccgggagtccgggccg     
                                                                                                            

Query   Intron---> DRERVMPLIIQGFRDAAEEGGTSVTGGQTVINPWIIVGGVASVVCKPNDFIM <---Intron---> PDGAVPGDVLVLTKPLGTQVA
        286bp    > |||||||||||||||||||||||||||||||||||||||||||||/||/||| <   1089bp   > |||||||||||||||||||||
Target             DRERVMPLIIQGFRDAAEEGGTSVTGGQTVINPWIIVGGVASVVCQPNEFIM                PDGAVPGDVLVLTKPLGTQVA
                   gcgcgaccaacgtcgggggggatgaggcagaactaagggggtggtccagtaa                cggggcgggtgcaaccgacgg
                   agagttctttagtgaccaaggcctcggacttacgtttggtccttgacaattt                cagctcgattttcactgcatc
                   ctggggggttagtttacggggttgatcgcgcccgccgaaaaccgcggtgcc                ggtttaggccgtacatgggggt
                                                                                                            

Query   VNAHQWLDQ <---Intron---> SERWNKIKLVVTKEEVKEAYQEAMFSMATLNRTA <---Intron---> AGLMHKFQAHAATDVTGFGLLGHAN
        ||||||||| <   136bp    > /||||||||||||||||||||||||||||||||| <   2696bp   > |||||||||||||||||||||||||
Target  VNAHQWLDQ                TERWNKIKLVVTKEEVKEAYQEAMFSMATLNRTA                AGLMHKFQAHAATDVTGFGLLGHAN
        gagcctcgc                agataaaacggaagggaggtcggattagacacag                ggcacatcgcggaggagtgttgcga
        tacaagtaa                caggaatatttcaaataacaaacttctcctagc                ccgttaatacacccatcgtgttgaca
        gttcggctg                taggcgcgatcaggacagctgacgccgagccca                gactgcgcgtctaacgagtgggacac
                                                                                                            

Query   NLAAQQQNEVAFVIHNLPIIAKMAAISKACGNIFNLVQGTSAETSG <---Intron---> GLLVCLPREQAARFCAEMKNHSSGPGGPGPAGGAWIIG
        ||||||/|||||||||||||||||||||||||/|||/||||||||| <    95bp    > ||||||||||||/||/|||/ ||  || | ||||||||
Target  NLAAQQRNEVAFVIHNLPIIAKMAAISKACGNLFNLIQGTSAETSG                GLLVCLPREQAAKFCSEMKSQSSAAGGQGAAGGAWIIG
        acggcccagggtgacaccaagaaggaaagtgactacacgatggatg                gccgtccagcggatttgaaacatggggcggggggtaag
        atccaagaatctttaatcttcatcctgacggattattagcccacc                ggtttgtcgaaccatgcatagagcccggagccggcgttg
        cgaagaccggccgccccacacggtcccactacgccatgcgaggtt                cggggtacaggtcgtcagggcgcactatagggtaggacg
                                                                                                            

Query   IVEKGDRRARIIDKPRIIEVPPRGSQAANQDSISSSPAPSPNLS
        |||||||||||||||||||||||||||||||/ |/|||||||||
Target  IVEKGDRRARIIDKPRIIEVPPRGSQAANQDNNSASPAPSPNLS
        aggaggccgcaagaccaaggcccgacggacgaatgacgcacact
        ttaagaggcgttaacgttatccgggaccaaaaaccgcccgcatc
        cagacccctcttcgtctcgtaaaacgactgccccccctccctga
                                                    
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 707 ; UGA-SECIS: 1850

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JACSYO010000005.1:subseq_88650,100000_ Strand = - Positions = 49271 - 49185
 Found by:  Infernal (score=24.42) Covels (score=24.59)
 Stem2 length = 10   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -5.27

         ..(((((((.............(((((((((((((((..................))))))))))))))).........)))))))..
 model   uucggucaugcg------UuaAUGAcGgccuggcccuAAAcC---cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ....((({(.............{[[[(([(((((({(..................)}))))))]))]]]}.....-...)})))....
 target  UCCCUCCCACCCUUCCUUUUUAUGAAGCGCUGCCUUUAAACCCCAGCCAACGGGGGCAGGUGGAGUGGAUGUUUG-CCUUUGGAUUGG
                               ****           ^^^                          ****