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

 Blastx evalue: 1e-44
 Query name: gi|930230925|ref|XP_005417340.2| PREDICTED: redox-regulatory protein FAM213A [Geospiza fortis]
 Query range: 1-224  (total 224)

 Target: /data/www-rg/seblastian_results/369294491/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: -
 Positions:
 -Exon 1  53583        53760
 -Exon 2  53124        53215
 -Exon 3  51137        51277
 -Exon 4  50228        50392
 -Exon 5  50000        50095

 Redox box: YES

Query   MSFLPDLGAFTMGMWSVGLGAIGAAVTGIVLANTDLFLSKPEKATLEFLEEIELKTLGSE <---Intron---> QRTFKAGELWKDNGAVIMAVRRPG
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   367bp    > |||||||||||/||||||||||||
Target  MSFLPDLGAFTMGMWSVGLGAIGAAVTGIVLANTDLFLSKPEKATLEFLEEIELKTLGSE                QRTFKAGELWKENGAVIMAVRRPG
        attccgcggtaagattggcggaggggagagcgaagttttacgagatgttggagcaatgtg                caatagggctagagggaaggcacg
        tcttcatgctctgtgctgtgctgcctcgtttcacatttcacaacctattaatatactgc                aagctacgatgaaagctttctggcg
        gccgtcggcccgcggttcgacttatgagccttctcatgcgaagtaggtaggagagtgaa                aagacaatangggttagcgtaaata
                                                                                                            

Query   UFLCRE <---Intron---> EASELSSLKPQLSKLGVPLYAVVKEKIGTEVEDFQHYFKGEIFLDEK <---Intron---> KGFYGPRRRKMMLSG
        |||||| <   1846bp   > ||||||||||||||||||||||||||||||||||||||||||||||| <   744bp    > |||||||||||||||
Target  UFLCRE                EASELSSLKPQLSKLGVPLYAVVKEKIGTEVEDFQHYFKGEIFLDEK                KGFYGPRRRKMMLSG
        ttttag                ggtgcttcaccctacggcctgggagaagaggggtccttaggatcgga                agttgccacaaattg
        gttgga                accatcctacatcatgtctacttaaatgcataataaatagatttaaa                agtagcgggatttcg
        atgcag                gttgcctgacggcggtctctttgaggagtaggttgtccaaactgtag                actttacaaagggtc
        *                                                                                                   

Query   FFRLGVWQNFFRAWRNGYSGNLEGEGFTLGGVYVIGAGRQ <---Intron---> GVLLEHREKEFGDKVSLPSVLEAAEKIKPQAS
        ||||||||||||||| |||||||||||||||||||||||| <   132bp    > ||||||||||||||||||||||||||||||||
Target  FFRLGVWQNFFRAWRRGYSGNLEGEGFTLGGVYVIGAGRQ                GVLLEHREKEFGDKVSLPSVLEAAEKIKPQAS
        ttctggtcattcgtaagtagacggggtacgggtgagggac                ggtcgccgagtggagacctgcggggaaaccgt
        ttgtgtgaattgcggggaggatagagtctggtattgcgga                gtttaagaaatgaatgtccttaccaatacacc
        cccgatgatccttgagattatgaaaaccgatatgtgaaag                ttaggttgaatacacctatctattggaaaata
                                                                                                
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 211 ; UGA-SECIS: 628

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = - Positions = 49788 - 49722
 Found by:  Infernal (score=27.92) Covels (score=19.71)
 Stem2 length = 9   Apical loop length = 8   Insertion in stem2 = 0, 0
 Free Energy = -25.4

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..((((((((......{[[{(((((({(((.......---------.)))}))))))}]]}..--...))))))))..
 target  UAUCUGGCUGUAUUAAUGAAAGGCUGAGUCUAAAAUC---------UGACCUAGCCUAGAUGU--UUCCAGUCAGAGA
                         ****           ^^^                       ****