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

 Blastx evalue: 1e-11
 Query name: gi|270288762|ref|NP_001161863.1| selenoprotein I [Equus caballus]
 Query range: 19-397  (total 397)

 Target: /data/www-rg/seblastian_results/437280787/tempfiles/temptarget.fasta
 Chromosome: gi|432096751|gb|KB110330.1|:subseq_5714462,140067_ Strand: -
 Positions:
 -Exon 1  69704        69775
 -Exon 2  69038        69146
 -Exon 3  67064        67138
 -Exon 4  62916        63178
 -Exon 5  61374        61482
 -Exon 6  57650        57698
 -Exon 7  54943        55123
 -Exon 8  53721        53903
 -Exon 9  50000        50095

 Redox box: no

Query   KYSAVDTNPLSLYIMHPFWNTVVK <---Intron---> VFPTWLAPNLITFSGFLLVVFNFLFMAYFDPDFYASA <---Intron---> PGHKHVP
        /||||||||||||/|||||||/|| <   557bp    > |||||||||||||||||||||||| /||||||||||| <   1899bp   > |||||||
Target  QYSAVDTNPLSLYVMHPFWNTIVK                VFPTWLAPNLITFSGFLLVVFNFLLLAYFDPDFYASA                PGHKHVP
        ctagggaacctctgaccttaaaga                gtcatcgcacaattgtccggtatcccgttgcgttgtg                cgcacgc
        aagctacactctattactgactta                ttccgtccattctcgttttttattttcatacatacc                ccgaaatc
        gcctatctactgtcgtatgctaag                atttggtatgatttctggtactcatgactttcttta                aatcattt
                                                                                                            

Query   DWVWIVVGILNFIAYTLD <---Intron---> GVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGSSGVSVFVLYLLLWVVLFSFILS
         |||||||||||/||||| <   3885bp   > ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Target  GWVWIVVGILNFVAYTLD                GVDGKQARRTNSSTPLGELFDHGLDSWSCVYFVVTVYSIFGRGPSGVSVFVLYLLLWVVLFSFILS
        gtgtagggacatggtacg                ggggacgcaaataactggctgcgcgatttgttggagttatgcgctggagtgctccctggttttact
        ggtgtttgttattcact                agtagaacggcacgcctgattaagtaggcgtatttctacttgggccgtgttttatttgttttctttc
        cgggtggccccctccta                ttgtagaccactcccgaggttctcactgattcttctgtcctaaatttctttttcggagttgttccgc
                                                                                                            

Query   HWEKYNTGILFLPWGYDISQV <---Intron---> TISFVYIVTAIVGVEAWYEPFLFNFLYRDLFTTMIIG <---Intron---> CALCVTLPMS
        ||||||||/|||||||||||| <   1433bp   > ||||||||||||||||||||||||||||||||||||| <   3675bp   > ||||||||||
Target  HWEKYNTGVLFLPWGYDISQV                TISFVYIVTAIVGVEAWYEPFLFNFLYRDLFTTMIIG                CALCVTLPMS
        ctgataaggctcctgtgaacg                aattgtagagagggggttgctctatttagctaaaaag                tgttgaccaa
        agaaaacgttttcggaatgat                ctcttattccttgtacgaactttattagattccttt                ggctgtctctg
        cgagtcaattcgggacctcgg                ttttccagtgtgatgcgtatcgttcatacactagtt                ttaatgttagt
                                                                                                            

Query   LLNFFR <---Intron---> SYKNNTLKHNSVYEVLVPFFSPCLLFVLSTAWILRSPSDILERHPRVFYFMVGTAFANST <---Intron---> CQ
        ||||// <   2526bp   > |||||/|||||/|| |||||||||||/|||||||/||||||| ||||||||||||||| | <   1039bp   > ||
Target  LLNFYK                SYKNNSLKHNSIYEALVPFFSPCLLFILSTAWILQSPSDILEMHPRVFYFMVGTAFANIT                CQ
        ttatta                ataaaatacatatggcgctttcttctattagtacctctgatgaccagtttaggagtgaaa                tc
        ttataa                gaaaagtaaactaacttcttccgtttttcccgttacccattatacgttatttgcctcatc                ga
        aactc                actatccgactgctatgcccttatgactgtacgtcgatcttaggttaacctgtaactctca                tg
                                                                                                            

Query   LIVCQMSSTRCPTLNWLLLPLFLVVMVINLGVASYIENILLFTLTTAFTLAHIHYGVRV <---Intron---> VKQLSSHFQIYPFSLRKPNSDULGM
        |||||||/||||||||||/||||||/|/|||||||||/|||/|/| ||||||||||||| <   3625bp   > |||||||||||||||||||||||||
Target  LIVCQMSNTRCPTLNWLLVPLFLVVVVVNLGVASYIESILLYTITAAFTLAHIHYGVRV                VKQLSSHFQIYPFSLRKPNSDULGM
        cagtcaaaaatcatattcgccttgggggatgggttagaacctaaaggtacgcactggcg                gaccaactcatctttaacatgtcga
        tttgatgacggcctagtttcttttttttatgtccatagtttactccctctcataagtgt                taatggatatactctgacacagtgt
        gtttagctcatatgtgggttccgtcggacaacctttgctcataaattctgcccttaaag                agagccttgtcgcaggaccataaag
                                                                                                        *   

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

 Distance CDS-SECIS: 1312 ; UGA-SECIS: 1342

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|432096751|gb|KB110330.1|:subseq_5714462,140067_ Strand = - Positions = 48687 - 48611
 Found by:  Infernal (score=25.53) Covels (score=23.36)
 Stem2 length = 10   Apical loop length = 18   Insertion in stem2 = 0, 1
 Free Energy = -5.77

         ..(((((((.......(((((((((((((((................))))).))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggc-caggcCuGAUGuuuuuucaugaccggc
         ...(({({((......{[[[((((((((((..................))).)))))))]]]}..--..-))})}))...
 target  GAAGUUUGUGCUUGAAUGAAGAGUGUAUCUUAAACCCUUUUUUUGGAUGGAUUGCACUUGGAUAA--AA-UAGGCACCAC
                         ****           ^^^                         ****