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

 Blastx evalue: 8e-38
 Query name: gi|820987255|ref|XP_012362256.1| PREDICTED: type I iodothyronine deiodinase isoform X3 [Nomascus leucogenys]
 Query range: 1-187  (total 187)

 Target: /data/www-rg/seblastian_results/937555391/tempfiles/temptarget.fasta
 Chromosome: KN985624.1:subseq_7028008,116318_ Strand: +
 Positions:
 -Exon 1  50000        50150
 -Exon 2  60740        60883
 -Exon 3  62422        62621
 -Exon 4  66253        66318

 Redox box: no

Query   MGLPQAGLWLKRLWVLLEVAVHVVVGKVLLILFPDRVKRNILAMGEKTGMT <---Intron---> RNPLVLNFGSCTUPSFMFKFDQFKRLIEDFSSI
        |||||/|||/|/||||||||||||||||||||||||||||||||||||||| <  10589bp   >   |||||||||||||||||||||||||||||||
Target  MGLPQSGLWVKKLWVLLEVAVHVVVGKVLLILFPDRVKRNILAMGEKTGMT                NRPLVLNFGSCTUPSFMFKFDQFKRLIEDFSSI
        agccctgctgaactgctggggcggggagccactcgagacaacgaggaagaa                aaccgcatgatatcttatatgctaacaggtata
        tgtcacgtgtaatgtttatctatttgattttttcagtagattctgaacgt                cagctttatgggcgcctttataatagttaatgct
        gggcgaggggggcgatgggtctgcgtagtgagtacacggccgcgcggctg                ctgagggttattcatatgcaccacggttacttca
                                                                                       *                    

Query   ADFLVIYIEEAHASD <---Intron---> GWAFKNNMDIRNHQNLQDRLQAAHLLLARSPQCPVVVDTMQNQSSQLYAALPERLYVIQEGRILYK <-
        ||||/|||||||||| <   1538bp   > |||||||||||||/|||||||||||||||||||||||||||||||||||||||||||||||||||| < 
Target  ADFLIIYIEEAHASD                GWAFKNNMDIRNHRNLQDRLQAAHLLLARSPQCPVVVDTMQNQSSQLYAALPERLYVIQEGRILYK   
        ggtcaatagggcgtg                gtgtaaaagaaaccaccgcccggccccgaacctcggggaacacaacctggccgactgacggaacta   
        cattttataacacc                aggctaaatatgaagataagtaccatttcggcagctttactaaaggatacctcagtattaaggttaa   
        attcctctaaataa                tcgttgccgccatcgctgccggactaggcgccgctgagccggcgccgccaagtggccacggcgcccg   
                                                                                                            

Query   --Intron---> GKSGPWNYNPEEVRAVLEKLHS
          3631bp   > ||||||||||||||||||||/|
Target               GKSGPWNYNPEEVRAVLEKLYS
                     gatgctatacgggcggcgacta
                     gacgcgaaacaatgcttaatag
                     tatctgcctagattttgagcct
                                           
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 952 ; UGA-SECIS: 1321

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KN985624.1:subseq_7028008,116318_ Strand = + Positions = 67271 - 67341
 Found by:  Infernal (score=33.51) Covels (score=28.88)
 Stem2 length = 9   Apical loop length = 12   Insertion in stem2 = 0, 0
 Free Energy = -12.42

         ..(((((((.......(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ...((((((.--....{[[{(({(((((((.........-----...)))))))}))}]]}.....-...))))))...
 target  UACAUAUUUG--UUUAUGAUGGCCACAGCCUAAAGUACA-----UACGGCUGUGACUUGAUCCAAA-AGAAAAUGUUAU
                         ****           ^^^                       ****                  
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:4     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 4e-18
 Query name: gi|46850132|gb|AAT02488.1| type I iodothyronine deiodinase splice variant m [Homo sapiens] >gi|222080759|gb|ACM41656.1| iodothyronine deiodinase type 1 splice variant a [Homo sapiens]
 Query range: 1-85  (total 85)

 Target: /data/www-rg/seblastian_results/937555391/tempfiles/temptarget.fasta
 Chromosome: KN985624.1:subseq_7028008,116318_ Strand: +
 Positions:
 -Exon 1  50000        50144
 -Exon 2  50228        50337

 Redox box: no

Query   MGLPQPGLWLKRLWVLLEVAVHVVVGKVLLILFPDRVKRNILAMGEKTG <---Intron---> PLAATRGHDUARGSGPKLPGGPPLRTEVQHLGVYA
        ||||| |||/|/||||||||||||||||||||||||||||||||||||| <    83bp    > |||||||||||| |||||||||||||||||||/||
Target  MGLPQSGLWVKKLWVLLEVAVHVVVGKVLLILFPDRVKRNILAMGEKTG                PLAATRGHDUARRSGPKLPGGPPLRTEVQHLGLYA
        agccctgctgaactgctggggcggggagccactcgagacaacgaggaag                ctggaagcgtgaatgcaccggcccaaggcctgctg
        tgtcacgtgtaatgtttatctatttgattttttcagtagattctgaac                gctcccggaagcggcgcatcggcctgcataatgtac
        gggcgaggggggcgatgggtctgcgtagtgagtacacggccgcgcggc                tggagtaaccatggtccagcttgtcgaggatgatta
                                                                                  *                         

Query   R
        |
Target  R
        a
        g
        g
         
 Sequence until next stop: 
TCAGCAGGCTGCCGCACACTTGAGGGGTGCTTGAAATAG
 S  A  G  C  R  T  L  E  G  C  L  K  * 

 Distance CDS-SECIS: 41 ; UGA-SECIS: 119

------- SECIS element -- id:4 -- grade:B ----
 Chromosome = KN985624.1:subseq_7028008,116318_ Strand = + Positions = 50379 - 50469
 Found by:  Infernal (score=11.35)
 Stem2 length = 10   Apical loop length = 28   Insertion in stem2 = 1, 0
 Free Energy = -10.79

         ..(((((((.......((((((((((((.(((............................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggc-ccuAAAcC-------------cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ..(({(((((--(...{[[[(((({(((.(((............................))))))}))))]]]}......-.))))))}))..
 target  GUGGUAGAGG--GGGAUGAAGAGAUGGGUUGGAAAGCCCUGAAUUCUCCUACUACUCUUGCUGCUCCUUUUGGACCUUCUU-GUCCUCUUCCUG
                         ****            ^^^                                    ****