_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 2e-58
 Query name: gi|550822255|ref|NP_001272511.1| selenoprotein P, plasma, 1 precursor [Capra hircus] >gi|374305554|gb|AEZ06358.1| selenoprotein P1 [Capra hircus]
 Query range: 201-346  (total 346)

 Target: /data/www-rg/seblastian_results/598001962/tempfiles/temptarget.fasta
 Chromosome: SJYR01002566.1:subseq_259678,100000_ Strand: -
 Positions:
 -Exon 1  99563        100000

 Redox box: no

Query   SRRHHHHHRHKGHQRQGHSDNCDTPVGSENLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCTENLPSLCSUQGLLAE
        |  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  SGLHHHHHRHKGHQRQGHSDNCDTPVGSENLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCTENLPSLCSUQGLLAE
        tgccccccacagccacgctgatgacggagatcctcccaactcaataactctctcagtgtgtaatttctcccgtgaagtgaatctagacctttatcgctgg
        cgtaaaaagaagaagagacaagacctggaatatctcaaatggaggtaattgatcaacacctgggggaggatttaacgcctcgagcaatcctgggagttca
        atttccctgcgtcaagtcatcttaaaatataatttaaggcaagacatgacagtcataattgtcctcctatgataaagtaccagtaaccctatcagctgag
                                                *         *                              *           *      

Query   ENVIESUQURLPPAAUQAAGQQLNPTEASTKUSUKNKAKMUKUPSN
        |||||||||||||||||||||||||| |||||||||||||||||||
Target  ENVIESUQURLPPAAUQAAGQQLNPTGASTKUSUKNKAKMUKUPSN
        gagagttctctccggtcgggcccacaggaaatataaagaatatcta
        aattacgaggtccccgaccgaataccgcgcagggaaacatgagcca
        gcctatagatgtatcagaatggcccaacccaacaatgcagaaatat
              * *      *               * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 244 ; UGA-SECIS: 253

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = SJYR01002566.1:subseq_259678,100000_ Strand = - Positions = 99318 - 99247
 Found by:  Infernal (score=28.33) Covels (score=28.55)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -11.34

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...({((((.--....{[[{((((((((({(.....-.........)})))))))))}]]}..--..-.))))})...
 target  UCUACUUGCA--UUAAUGAGAACAGAAACGUAAACU-AUAACCUAGGGGUUUCUGUUGGAUAG--UU-GGCAACUUAG
                         ****           ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:1     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 2e-56
 Query name: gi|550822255|ref|NP_001272511.1| selenoprotein P, plasma, 1 precursor [Capra hircus] >gi|374305554|gb|AEZ06358.1| selenoprotein P1 [Capra hircus]
 Query range: 201-346  (total 346)

 Target: /data/www-rg/seblastian_results/598001962/tempfiles/temptarget.fasta
 Chromosome: SJYR01002566.1:subseq_259678,100000_ Strand: -
 Positions:
 -Exon 1  99563        100000

 Redox box: no

Query   SRRHHHHHRHKGHQRQGHSDNCDTPVGSENLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCTENLPSLCSUQGLLAE
        |  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  SGLHHHHHRHKGHQRQGHSDNCDTPVGSENLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCTENLPSLCSUQGLLAE
        tgccccccacagccacgctgatgacggagatcctcccaactcaataactctctcagtgtgtaatttctcccgtgaagtgaatctagacctttatcgctgg
        cgtaaaaagaagaagagacaagacctggaatatctcaaatggaggtaattgatcaacacctgggggaggatttaacgcctcgagcaatcctgggagttca
        atttccctgcgtcaagtcatcttaaaatataatttaaggcaagacatgacagtcataattgtcctcctatgataaagtaccagtaaccctatcagctgag
                                                *         *                              *           *      

Query   ENVIESUQURLPPAAUQAAGQQLNPTEASTKUSUKNKAKMUKUPSN
        |||||||||||||||||||||||||| |||||||||||||||||||
Target  ENVIESUQURLPPAAUQAAGQQLNPTGASTKUSUKNKAKMUKUPSN
        gagagttctctccggtcgggcccacaggaaatataaagaatatcta
        aattacgaggtccccgaccgaataccgcgcagggaaacatgagcca
        gcctatagatgtatcagaatggcccaacccaacaatgcagaaatat
              * *      *               * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 677 ; UGA-SECIS: 686

------- SECIS element -- id:1 -- grade:B ----
 Chromosome = SJYR01002566.1:subseq_259678,100000_ Strand = - Positions = 98885 - 98819
 Found by:  Infernal (score=29.06) Covels (score=13.38)
 Stem2 length = 9   Apical loop length = 10   Insertion in stem2 = 1, 0
 Free Energy = -9.3

         ..(((((((.......((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...((((((---....([[{(((({(.((((......--.-----...)))))}))))}]])..--....))))))...
 target  UUUCCAUAG---UCAAUGAUGGUUCAAUAGGCAAACC--A-----GGUCCUAUAAACCUGAAUU--AUUUUUAUGGUUA
                         ****            ^^^                       ****