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

 Blastx evalue: 8e-45
 Query name: gi|835944114|ref|XP_012776526.1| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Maylandia zebra] >gi|923815501|ref|XP_005734673.2| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Pundamilia nyererei] >gi|930739158|ref|XP_005925492.2| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Haplochromis burtoni]
 Query range: 1-104  (total 110)

 Target: /data/www-rg/seblastian_results/274088514/tempfiles/temptarget.fasta
 Chromosome: WARS01000035.1:subseq_1524413,200000_:subseq_0,120000_ Strand: +
 Positions:
 -Exon 1  99345        99399
 -Exon 2  100010       100152
 -Exon 3  100291       100404

 Redox box: no

Query   MSFCSFFGGEVFKDHFKSG <---Intron---> IYVCTKCDNQLFSSRSKYEHSSPWPAFTETIHENSVSKHEERPGAYK <---Intron---> VR
        |||||||||||/|/||| | <   610bp    > ||||/|||/||||||||||||||||||||||||/|||||/||||||| <   138bp    > ||
Target  MSFCSFFGGEVYKEHFKPG                IYVCSKCDHQLFSSRSKYEHSSPWPAFTETIHEDSVSKHQERPGAYK                VR
        atttattggggtagctacg                atgttatgcccttactatgcttctcgtagaacggagtaccgacggta                gc
        tctggttggataaaatac                gtatgcagaaattcggcaaaacccgcctcactaaagtcaaaagcgcaa                tg
        ggttttctagccaactaa                gttttcgttcgccctccgcgtatcggccagcctgctgaatgaatgatg                gg
                                                                                                            

Query   CGKCGNGLGHEFVNDGPSKGVSRFUIFSSSLKFIPK
        |||||||||||||||||/||/||||||||||||/||
Target  CGKCGNGLGHEFVNDGPAKGLSRFUIFSSSLKFVPK
        tgatgagcgcgtgaggcgagctcttataatcatgca
        ggaggagtgaattaagccagtcgtgttggctattca
        ttatatatctgtgtttacaggtctaacccaggccta
                                *           
 Sequence until next stop: 
GGTAACAGAAGTCAAATTATATCAGGACATTGGGAAACAGATACCGCCTGTGCCCTGTTACACTAG
 G  N  R  S  Q  I  I  S  G  H  W  E  T  D  T  A  C  A  L  L  H  * 

 Distance CDS-SECIS: 2719 ; UGA-SECIS: 2752

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = WARS01000035.1:subseq_1524413,200000_:subseq_0,120000_ Strand = + Positions = 103124 - 103197
 Found by:  Infernal (score=24.1) Covels (score=16.64)
 Stem2 length = 9   Apical loop length = 16   Insertion in stem2 = 1, 0
 Free Energy = -12.49

         ..(((((((.......((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .(({(([((.--....{[[(({((((.((((......-..........))))))))}))]]}..--....))]))})).
 target  UUGCGGACAG--UUGAUGAAGUGCUCCAGGACAAAGC-CUGAUGGAGCUCCUGGGCUCUGAUGC--AAGGUGGCCUCAC
                         ****            ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 8e-45
 Query name: gi|835944114|ref|XP_012776526.1| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Maylandia zebra] >gi|923815501|ref|XP_005734673.2| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Pundamilia nyererei] >gi|930739158|ref|XP_005925492.2| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Haplochromis burtoni]
 Query range: 1-104  (total 110)

 Target: /data/www-rg/seblastian_results/274088514/tempfiles/temptarget.fasta
 Chromosome: WARS01000035.1:subseq_1524413,200000_:subseq_0,120000_ Strand: +
 Positions:
 -Exon 1  99345        99399
 -Exon 2  100010       100152
 -Exon 3  100291       100404

 Redox box: no

Query   MSFCSFFGGEVFKDHFKSG <---Intron---> IYVCTKCDNQLFSSRSKYEHSSPWPAFTETIHENSVSKHEERPGAYK <---Intron---> VR
        |||||||||||/|/||| | <   610bp    > ||||/|||/||||||||||||||||||||||||/|||||/||||||| <   138bp    > ||
Target  MSFCSFFGGEVYKEHFKPG                IYVCSKCDHQLFSSRSKYEHSSPWPAFTETIHEDSVSKHQERPGAYK                VR
        atttattggggtagctacg                atgttatgcccttactatgcttctcgtagaacggagtaccgacggta                gc
        tctggttggataaaatac                gtatgcagaaattcggcaaaacccgcctcactaaagtcaaaagcgcaa                tg
        ggttttctagccaactaa                gttttcgttcgccctccgcgtatcggccagcctgctgaatgaatgatg                gg
                                                                                                            

Query   CGKCGNGLGHEFVNDGPSKGVSRFUIFSSSLKFIPK
        |||||||||||||||||/||/||||||||||||/||
Target  CGKCGNGLGHEFVNDGPAKGLSRFUIFSSSLKFVPK
        tgatgagcgcgtgaggcgagctcttataatcatgca
        ggaggagtgaattaagccagtcgtgttggctattca
        ttatatatctgtgtttacaggtctaacccaggccta
                                *           
 Sequence until next stop: 
GGTAACAGAAGTCAAATTATATCAGGACATTGGGAAACAGATACCGCCTGTGCCCTGTTACACTAG
 G  N  R  S  Q  I  I  S  G  H  W  E  T  D  T  A  C  A  L  L  H  * 

 Distance CDS-SECIS: 515 ; UGA-SECIS: 548

------- SECIS element -- id:2 -- grade:B ----
 Chromosome = WARS01000035.1:subseq_1524413,200000_:subseq_0,120000_ Strand = + Positions = 100920 - 100996
 Found by:  Infernal (score=22.53) Covels (score=13.67)
 Stem2 length = 9   Apical loop length = 22   Insertion in stem2 = 0, 0
 Free Energy = -24.35

         ..(((((((.......(((((((((((((((..................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC---cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ((({(((((.--....{[[((((((((((......................))))))))))]]}..--....)))))})))
 target  GUGCGGACAG--UGGGUGAAGAGUUCUGGGACAAAGCCCAGUCUGGGAGCACCAGGGCUCUGAUGA--AUGAUGUCCUCAC
                         ****            ^^                          ****