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

 Blastx evalue: 2e-62
 Query name: gi|1002574596|ref|XP_015666346.1| PREDICTED: type I iodothyronine deiodinase [Protobothrops mucrosquamatus]
 Query range: 1-265  (total 265)

 Target: /data/www-rg/seblastian_results/943477500/tempfiles/temptarget.fasta
 Chromosome: ULFQ01000014.1:subseq_8260923,103159_ Strand: +
 Positions:
 -Exon 1  46104        46139
 -Exon 2  49883        50243
 -Exon 3  52194        52337
 -Exon 4  52981        53180
 -Exon 5  53682        53747

 Redox box: no

Query   MTEGFSSVGLLQ <---Intron---> NTAVSPSAKRFRMKRFMQRSWILLHVCLSTIIGKICMFFFPGTVKRYLLKQREKS----SNPKFMYENWGPT
        ||| |||||||| <   3743bp   > | | ||||| ||||||||| |||||||||||/||||||||||||| |||| ||||    /|| |/|||||||
Target  MTEEFSSVGLLQ                NVAASPSAKMFRMKRFMQRFWILLHVCLSTIVGKICMFFFPGTVKSYLLKHREKSGMGDNNPTFIYENWGPT
        aaggttaggccc                agggtctgaataaaatacattacccgtctaaggaatatttcgagaatccacagaagaggaacatatgatgca
        tcaatcgtgtta                atccccccattgtagttagtgtttatgtccttgatgttttcgctagattaagaaggtgaaaccttaaaggcc
        gaaacctggaag                taactttcggtaggatgggcgtcgtgcattcttaccgcccattggctcggcaagtcgacccaacctatgtat
                                                                                                            

Query   FFSFPYLLFVLKVKWKRLEDEAFQGCPAPNTPVADLSGKIHRILDFMQG <---Intron---> NRPLVLTFGSCTUPSFIFKFGEFNKLVEDFKSVAD
        |||| ||||||||||||||||||||  ||||||||| ||/| ||||||| <   1950bp   > ||||||||||||||||| /||||||||||||| ||
Target  FFSFSYLLFVLKVKWKRLEDEAFQGSSAPNTPVADLRGKMHCILDFMQG                NRPLVLTFGSCTUPSFIIRFGEFNKLVEDFKSAAD
        ttattttctgtagataacggggtcgttgcaacgggcagaactacgtacg                aactgcatgatatcttaaatggtaacgggtatggg
        ttgtcatttttatagagtaaactagccccacctcatggatagttatta                gagctttctgggcgcctttgtgataattaataccca
        ccccccactcgacagaggatactgctttttccaatcagagtctgtcga                tcgtgcaatattcatacataccgttattatcataac
                                                                                     *                      

Query   FLVIYIEEAHASD <---Intron---> GWAFKNNIVIKSHRTLQDRIAAAQMLLKQHPLCPVVLDTMENLSSNKYAALPERLYVLQKGKVVYK <---
        ||||||||||||| <   643bp    > |||||||||||||/|||||| |||||||| ||||||/|||||||/||||||||||||||||||||| <   
Target  FLVIYIEEAHASD                GWAFKNNIVIKSHQTLQDRIMAAQMLLKQLPLCPVVVDTMENLSTNKYAALPERLYVLQKGKVVYK     
        tcgatagggcgtg                gtgtaaaagaaaccaccgcaaggcaccacccttcggggaagacaaaatggccgactgccagaggta     
        ttttataacacc                aggctaaatttagaactaagttccatttaatctgctttactaatgcaaacctcagtattaagattaa     
        ttacctaattca                tagctgcttttatcactattagtaggcaagacataggacagacgctcatatgagagtgtagaatgtg     
                                                                                                            

Query   Intron---> GRPGPWKYCPQEVREFLEQFYM
        501bp    > |/|||| |||||||||||| ||
Target             GKPGPWNYCPQEVREFLEQLYM
                   gacgctattccggcgttgccta
                   gacgcgaagcaatgattaatat
                   taaatgttcgaaatatgaatcg
                                         
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 828 ; UGA-SECIS: 1197

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = ULFQ01000014.1:subseq_8260923,103159_ Strand = + Positions = 54576 - 54643
 Found by:  Infernal (score=21.31) Covels (score=24.65)
 Stem2 length = 10   Apical loop length = 10   Insertion in stem2 = 0, 0
 Free Energy = -12.6

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((.--....{[[{{((((((((((........-----..))))))))))}}]]}..--..-.)))))))..
 target  UUAAUAUUUG--UUUAUGAUAGUCAUAGUUUAAAACAUA-----GAGAACUAUGACCUGAUAU--GG-AAAAUAUUUA
                         ****           ^^^                       ****