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

 Blastx evalue: 3e-20
 Query name: gi|929095373|ref|XP_014058532.1| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Salmo salar]
 Query range: 1-110  (total 110)

 Target: /data/www-rg/seblastian_results/960053919/tempfiles/temptarget.fasta
 Chromosome: KV884862.1:subseq_1337131,100000_ Strand: +
 Positions:
 -Exon 1  49506        49560
 -Exon 2  50010        50152
 -Exon 3  50378        50492
 -Exon 4  51071        51087

 Redox box: no

Query   MSFCSFFGGEVFKDHFKTG <---Intron---> LYVCAQCGHQLFSSRSKYEHSSPWPAFTETVLQDSVSKHEERPGAFK <---Intron---> VR
        ||||||||||||||||| | <   449bp    > /|||//|||||||| |||||||||||||||/|/|||||  ||| ||| <   225bp    > | 
Target  MSFCSFFGGEVFKDHFKPG                IYVCSKCGHQLFSSCSKYEHSSPWPAFTETILKDSVSKQPERPRAFK                VL
        attttttggggtagctacg                atgttatgcccttattatgcttctcgtagaacagagtaccgccagta                gc
        tctgcttggattaaatac                gtatgcaggaattcggcaaaacccgcctcacttaagtcaacagcgcta                tt
        gatcctttagctacttaa                cctttcgttcgccccccgcgcctcgatcagcctactgcaaggtcaatg                gg
                                                                                                            

Query   CGKCGNGLGHEFVGDGPKKGLSRFUIFSSSLKFVPKD <---Intron---> KVDGQ
        ||||||||||||| ||| || ||||||||||||/||| <   578bp    > |||||
Target  CGKCGNGLGHEFVNDGPAKGQSRFUIFSSSLKFIPKD                KVDGQ
        tgatgagcgcgtgaggcgagctcttataatcatacag                agggc
        ggaggagtgaattaagccagacgtgttggctattca                aataga
        tagtacagctgtgctaacaggtccaacccaggccta                tgttag
                                *                                 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 58 ; UGA-SECIS: 109

------- SECIS element -- id:1 -- grade:B ----
 Chromosome = KV884862.1:subseq_1337131,100000_ Strand = + Positions = 51146 - 51230
 Found by:  Infernal (score=16.88) Covels (score=10.82)
 Stem2 length = 7   Apical loop length = 21   Insertion in stem2 = 1, 0
 Free Energy = -15.53

         ..(((((((.........((((((((((.(((((.................)))))))))))))))...........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccug-gcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuu--u-uuucaugaccggc
         ..((((({((........([[(({((((.{((.....................))}))))}))]]).......-..))})))))..
 target  GACAGUGCGGUCAAUGAAUGAAGUGCCCUGGGACAAAGCCCAAAGUGGGAGCGCUGGGGCUCUGAGGAAUGGU-GUCCUCACUGGU
                           ****            ^^^                         ****                    
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 3e-20
 Query name: gi|929095373|ref|XP_014058532.1| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Salmo salar]
 Query range: 1-110  (total 110)

 Target: /data/www-rg/seblastian_results/960053919/tempfiles/temptarget.fasta
 Chromosome: KV884862.1:subseq_1337131,100000_ Strand: +
 Positions:
 -Exon 1  49506        49560
 -Exon 2  50010        50152
 -Exon 3  50378        50492
 -Exon 4  51071        51087

 Redox box: no

Query   MSFCSFFGGEVFKDHFKTG <---Intron---> LYVCAQCGHQLFSSRSKYEHSSPWPAFTETVLQDSVSKHEERPGAFK <---Intron---> VR
        ||||||||||||||||| | <   449bp    > /|||//|||||||| |||||||||||||||/|/|||||  ||| ||| <   225bp    > | 
Target  MSFCSFFGGEVFKDHFKPG                IYVCSKCGHQLFSSCSKYEHSSPWPAFTETILKDSVSKQPERPRAFK                VL
        attttttggggtagctacg                atgttatgcccttattatgcttctcgtagaacagagtaccgccagta                gc
        tctgcttggattaaatac                gtatgcaggaattcggcaaaacccgcctcacttaagtcaacagcgcta                tt
        gatcctttagctacttaa                cctttcgttcgccccccgcgcctcgatcagcctactgcaaggtcaatg                gg
                                                                                                            

Query   CGKCGNGLGHEFVGDGPKKGLSRFUIFSSSLKFVPKD <---Intron---> KVDGQ
        ||||||||||||| ||| || ||||||||||||/||| <   578bp    > |||||
Target  CGKCGNGLGHEFVNDGPAKGQSRFUIFSSSLKFIPKD                KVDGQ
        tgatgagcgcgtgaggcgagctcttataatcatacag                agggc
        ggaggagtgaattaagccagacgtgttggctattca                aataga
        tagtacagctgtgctaacaggtccaacccaggccta                tgttag
                                *                                 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 763 ; UGA-SECIS: 814

------- SECIS element -- id:2 -- grade:B ----
 Chromosome = KV884862.1:subseq_1337131,100000_ Strand = + Positions = 51851 - 51923
 Found by:  Infernal (score=11.8) Covels (score=7.27)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -14.93

         ..(((((((.......((((((((((.(((((...................))))).))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcC----cuuuuuggggcgggc-caggcCuGAUGuuuuuucaugaccggc
         ((((({(((---(...{[[{((((({[(((.------................)))]})))))}]]}..--...))))})))))
 target  UAUUUCCAC---CAGUUGAUGGUACCGUCUG------CCCUAAAAAUCUACAAAGAAUGUACCUGAUGC--CUCGGUGUAAAUA
                         ****                 ^^                        ****