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

 Blastx evalue: 2e-35
 Query name: gi|116283661|gb|AAH19786.1| Deiodinase, iodothyronine, type I [Mus musculus]
 Query range: 1-257  (total 257)

 Target: /data/www-rg/seblastian_results/961712967/tempfiles/temptarget.fasta
 Chromosome: CM004097.1:subseq_104186841,214810_ Strand: -
 Positions:
 -Exon 1  114474       114810
 -Exon 2  105405       105548
 -Exon 3  101821       102020
 -Exon 4  100000       100089

 Redox box: no

Query   MGLPQLWLWLKRLVIFLQVALEVAVGKVLMTLFPGRVKQSILAMGQKTGMARNPRFAPDNWVPTFFSIQYFWFVLKVRWQRLEDRAEFGGLAPNCTVVCL
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  MGLPQLWLWLKRLVIFLQVALEVAVGKVLMTLFPGRVKQSILAMGQKTGMARNPRFAPDNWVPTFFSIQYFWFVLKVRWQRLEDRAEFGGLAPNCTVVCL
        agcccctctcaccgatccggtgggggagcaactcgagacaacgagcaagagaacctgcgatgcattaacttttgcagctcacggaggtggcgcataggtc
        tgtcatgtgtagtttttatctatctgatttcttcggtaagttctgaacgtcgacgtccaagtccttgtaatgtttatggagtaagcatggtccagcttgt
        gggcgaggggggtgacgggcgggtacggagggcagacagccgcgcggcggcgccacctccgcccccccgccgtcggccggagacgtgtgggccctcgccc
                                                                                                            

Query   SGQKCNIWDFIQG <---Intron---> SRPLVLNFGSCTUPSFLLKFDQFKRLVDDFASTADFLIIYIEEAHATD <---Intron---> GWAFKNN
        ||||||||||||| <   8925bp   > |||||||||||||||||||||||||||||||||||||||||||||||| <   3384bp   > |||||||
Target  SGQKCNIWDFIQG                SRPLVLNFGSCTUPSFLLKFDQFKRLVDDFASTADFLIIYIEEAHATD                GWAFKNN
        tgcataatgtacg                aaccgtatgatatcttccatgctaacgggtgtaggtcaatagggcgag                gtgtaaa
        cgaagatgatta                gggctttatgggcgcctttataatagttaatccccattttataacacc                aggctaaa
        aaggcccgtcta                ccgcgggctctccatattcatcgcgacatcttcactccctctaatcca                tcgttgcc
                                                 *                                                          

Query   VDIRQHRSLQERVRAARLLLARSPRCPVVVDTMQNQSSQLYAALPERLYVIQEGRIRYK <---Intron---> GKAGPWNYNPEEVRAVLEKLCTPPR
        |||||||||||||/||||||||||/|||||||||||||||||||||||||||||||||| <   1731bp   > |||||||||||||| ||||||||||
Target  VDIRQHRSLQERVQAARLLLARSPQCPVVVDTMQNQSSQLYAALPERLYVIQEGRIRYK                GKAGPWNYNPEEVRVVLEKLCTPPR
        ggaccccaccgcgcggccccgaacctcggggaacacaacctggccgactgacggaacta                gaggctatacgggcggcgactacca
        tatgaaggtaagtaccgtttcggcagctttactaaaggatacctcagtattaaggtgaa                gacgcgaaacaatgtttaatgcccg
        gccggctccggcggaacgggtgccgctgggcaggcgctgctacgtggccgaggcgcccg                tatctgccttgacatcgagtctata
                                                                                                            

Query   HVPQL
        |||||
Target  HVPQL
        cgccc
        atcat
        cgtgc
             
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 762 ; UGA-SECIS: 1155

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM004097.1:subseq_104186841,214810_ Strand = - Positions = 99237 - 99169
 Found by:  Infernal (score=32.13) Covels (score=27.81)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -13.34

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         (({((((((.--....{[[{(((((((((..........-----....)))))))))}]]}..--....))))))}))
 target  UUUAUAUUUG--UGUAUGAUGGUCACAGUGUAAAGUUCC-----CACAGCUGUGACUUGAUUU--UUAAAAAUGUCGG
                         ****           ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:QUE_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 2e-35
 Query name: gi|116283661|gb|AAH19786.1| Deiodinase, iodothyronine, type I [Mus musculus]
 Query range: 1-257  (total 257)

 Target: /data/www-rg/seblastian_results/961712967/tempfiles/temptarget.fasta
 Chromosome: CM004097.1:subseq_104186841,214810_ Strand: -
 Positions:
 -Exon 1  114474       114810
 -Exon 2  105405       105548
 -Exon 3  101821       102020
 -Exon 4  100000       100089

 Redox box: no

Query   MGLPQLWLWLKRLVIFLQVALEVAVGKVLMTLFPGRVKQSILAMGQKTGMARNPRFAPDNWVPTFFSIQYFWFVLKVRWQRLEDRAEFGGLAPNCTVVCL
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  MGLPQLWLWLKRLVIFLQVALEVAVGKVLMTLFPGRVKQSILAMGQKTGMARNPRFAPDNWVPTFFSIQYFWFVLKVRWQRLEDRAEFGGLAPNCTVVCL
        agcccctctcaccgatccggtgggggagcaactcgagacaacgagcaagagaacctgcgatgcattaacttttgcagctcacggaggtggcgcataggtc
        tgtcatgtgtagtttttatctatctgatttcttcggtaagttctgaacgtcgacgtccaagtccttgtaatgtttatggagtaagcatggtccagcttgt
        gggcgaggggggtgacgggcgggtacggagggcagacagccgcgcggcggcgccacctccgcccccccgccgtcggccggagacgtgtgggccctcgccc
                                                                                                            

Query   SGQKCNIWDFIQG <---Intron---> SRPLVLNFGSCTUPSFLLKFDQFKRLVDDFASTADFLIIYIEEAHATD <---Intron---> GWAFKNN
        ||||||||||||| <   8925bp   > |||||||||||||||||||||||||||||||||||||||||||||||| <   3384bp   > |||||||
Target  SGQKCNIWDFIQG                SRPLVLNFGSCTUPSFLLKFDQFKRLVDDFASTADFLIIYIEEAHATD                GWAFKNN
        tgcataatgtacg                aaccgtatgatatcttccatgctaacgggtgtaggtcaatagggcgag                gtgtaaa
        cgaagatgatta                gggctttatgggcgcctttataatagttaatccccattttataacacc                aggctaaa
        aaggcccgtcta                ccgcgggctctccatattcatcgcgacatcttcactccctctaatcca                tcgttgcc
                                                 *                                                          

Query   VDIRQHRSLQERVRAARLLLARSPRCPVVVDTMQNQSSQLYAALPERLYVIQEGRIRYK <---Intron---> GKAGPWNYNPEEVRAVLEKLCTPPR
        |||||||||||||/||||||||||/|||||||||||||||||||||||||||||||||| <   1731bp   > |||||||||||||| ||||||||||
Target  VDIRQHRSLQERVQAARLLLARSPQCPVVVDTMQNQSSQLYAALPERLYVIQEGRIRYK                GKAGPWNYNPEEVRVVLEKLCTPPR
        ggaccccaccgcgcggccccgaacctcggggaacacaacctggccgactgacggaacta                gaggctatacgggcggcgactacca
        tatgaaggtaagtaccgtttcggcagctttactaaaggatacctcagtattaaggtgaa                gacgcgaaacaatgtttaatgcccg
        gccggctccggcggaacgggtgccgctgggcaggcgctgctacgtggccgaggcgcccg                tatctgccttgacatcgagtctata
                                                                                                            

Query   HVPQL
        |||||
Target  HVPQL
        cgccc
        atcat
        cgtgc
             
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 1450 ; UGA-SECIS: 1843

------- SECIS element -- id:2 -- grade:B ----
 Chromosome = CM004097.1:subseq_104186841,214810_ Strand = - Positions = 98549 - 98456
 Found by:  Infernal (score=19.84) Covels (score=8.95)
 Stem2 length = 9   Apical loop length = 20   Insertion in stem2 = 0, 0
 Free Energy = -23.2

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