_________________________________.______________________._________________________________________________________________________________

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

 Blastx evalue: 6e-22
 Query name: gi|915561497|ref|XP_005514610.2| PREDICTED: selenoprotein P [Columba livia]
 Query range: 1-389  (total 390)

 Target: /data/www-rg/seblastian_results/759386983/tempfiles/temptarget.fasta
 Chromosome: SJPD01000005.1:subseq_697511,101716_ Strand: -
 Positions:
 -Exon 1  53187        53389
 -Exon 2  51505        51714
 -Exon 3  49997        50111
 -Exon 4  48534        49004

 Redox box: YES

Query   MWAGLGLVLVLCLLPGGGTESQ----NCKEAPEWRIGEENPMLNSRGSVTVVALLQASUYLCLLQASR <---Intron---> LEDLRVRLKDEGLVNI
        || |||| | || |||||||||     |   ||| |||/||||/|||||||||||||||||||||||| <   1472bp   > |||||//|/ /||/ /
Target  MWVGLGLALALCFLPGGGTESQGSSTRCNVPPEWWIGEQNPMLDSRGSVTVVALLQASUYLCLLQASR                LEDLRLKLERDGLI-V
        atggcgcgcgcttccgggagacgtaactagccgttaggcacacgtagtgagggcccgattttctcgta                cggcccacgcggta-g
        tgtgtgtctctgttcgggcagagcgcggatccaggtgaaacttacggctcttcttacggatgttaccg                taatgtatagagtt-t
        ggtgggtcgtctccaaagagcgtatcatcgtaaggagggtgggccatggagatctatcacgtcggtt                agacgagggattggt-t
                                                                  *                                         

Query   SYVVVNHQGTHSQRKFHLLKESVSENITVYQQDEQQDDVWTTLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPYSFLSFQYVEEAIKIAYC
        |//|||||| ||| |/  |/| || || ||||| /| |||| ||| ||||||||| <   1393bp   > ||||||||||||||||| ||||||/| ||
Target  SFLVVNHQGQHSQLKYPQLREKVSTNIPVYQQDSKQPDVWTALNGRKDDFLIYDR                CGRLVYHLGLPYSFLSFPYVEEAIRITYC
        tttggaccgcctccatcccagagtaaacgtccgtaccggtagcagaaggtcatga                tgccgtccgtctttcatctggggacaatt
        cttttaaagaacataacatgaatccatctaaaacaacatgcctaggaaatttaag                gggttaatgtcacttgtcataactgtcag
        ctggctcaaatcgagtcaaaagtggcttacaataagttcgttataagtttgctc                gttctgtcttgtcttgttgtgaacttcact
                                                                                                            

Query   ENKCGNCSY <---Intron---> TEPDIDGICENITKTAEEELAEIAPEPAGQHSHHHNLHRHRHHHHHHHREGGRHSKNENHQASESHRHHSHSGRR
        |/||||||| <   992bp    >                                                              | /    | | |  
Target  ESKCGNCSY                ------------------------------------------------------------SAQDQLSPHGHHGHG
        gtatgattt                ------------------------------------------------------------tgcgcttccgccgcg
        acaggagca                ------------------------------------------------------------ccaaatccagaagag
        acgtacctc                ------------------------------------------------------------tagtggtttgtcgtg
                                                                                                            

Query   HRVFGRNRHDQTGSHEQVDTVPPGEGVEI-TQDKKLUKKGKTSCKNQLTUNWQTASDSTSSSUCCHCRHLLFEEVGNSVTUQCRGALPNSCRUHGQLLAE
        |   | /         /       | |/   | // |/|    |  ||/| ||  / | | ||| | ||||||// /  /| ||| ||/| || ||||||
Target  HHRHGHHPPQNNRGRNREGQAGSQEIVDAPPQGRRNURKENAVCNRQLSUTWQQLAGSASGSUCUHURHLLFEDLRSVASUHCRGELPSSURURGQLLAE
        ccacgcccccaacgcaaggcggacgagggcccgaaatcagaggtacctatatcccggtgtgatttctcctctggccaggttctcggcctttatcgcctgg
        aagagaaccaaagggagagacggaattacccagggaggaaactgagatggcgaatcgcccgggggaggatttaatggtccgagggatcccgggggattca
        tcgtgtctagctgatcagtgatcggtgttcaagggcagaattcccaggcacggggagttagcacacagcggtatacttccatctagcatcagatggggag
                                            *            *            * * *             *         * *       

Query   DITESUQURLLTAAUQSPAAGGSETSDTUQUQENARNUAUKT
        /|||| |||| ||||/| |   ||||/ |||     ||||||
Target  NITESCQURLPTAAURSQAGSESETSNAUQUARRTENUAUKT
        aaagttctcccaggtctcggagagatagtctgaaagatgtaa
        atcacgaggtccccggcacggagaccacgagcggcaagcgac
        tctgttgatgaattagaaagtgtacctcagaaggtacacaaa
             * *      *             * *      * *  
 Sequence until next stop: 
ATCTAA
 I  * 

 Distance CDS-SECIS: 385 ; UGA-SECIS: 391

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SJPD01000005.1:subseq_697511,101716_ Strand = - Positions = 48148 - 48077
 Found by:  Infernal (score=32.85) Covels (score=22.39)
 Stem2 length = 9   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -19.17

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(({(((((--....{[[((((((((((.......-...........))))))))))]]}..--..-)))))}))..
 target  UCUGUUUGCU--UUUGUGAAGACAGAAGCAGAAACU-AUAGCCUAGGGGCUUCUGUUUGAUAU--AU-AGCAACCAAG
                         ****           ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 6e-22
 Query name: gi|915561497|ref|XP_005514610.2| PREDICTED: selenoprotein P [Columba livia]
 Query range: 1-389  (total 390)

 Target: /data/www-rg/seblastian_results/759386983/tempfiles/temptarget.fasta
 Chromosome: SJPD01000005.1:subseq_697511,101716_ Strand: -