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

 Blastx evalue: 5e-30
 Query name: gi|1023023620|ref|XP_007499432.2| PREDICTED: methionine-R-sulfoxide reductase B1 [Monodelphis domestica]
 Query range: 1-106  (total 115)

 Target: /data/www-rg/seblastian_results/72128706/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000046.1:subseq_2366260,84740_ Strand: -
 Positions:
 -Exon 1  52398        52452
 -Exon 2  51753        51895
 -Exon 3  51505        51621

 Redox box: no

Query   MSFCS-FGGEVFQNHFEPG <---Intron---> VYVCAKCGYELFSSRSKYHHSSPWPAFTETIHADSVSKRPESGRSEALK <---Intron---> 
        ||||| |||| |//||/ | <   502bp    > /|||||| //|||| ||| ||||||||||||  |||||  |  |  | | <   131bp    > 
Target  MSFCSFFGGEAFKDHFKSG                IYVCAKCEHQLFSSHSKYEHSSPWPAFTETILEDSVSKHEE--RPGAYK                
        atttattggggtagctatg                atgtgatgcccttactatgcttctcgtagaacggagtacgg--acggta                
        tctggttggactaaatac                gtatgcagaaattcgacaaaacccgcctcacttaagtcaaaa--gcgcaa                
        ggtttccctgctacccaa                gttatcgtgcggcccccgcgcgccggccagcctgctgcatgg--acgatg                
                                                                                                            

Query   VSCGKCGNGLGHEFINDGPKKGQSRFUIFSSSLKFVPKG
        | ||||||||||||/|||| || ||||||||||||/|||
Target  VRCGKCGNGLGHEFVNDGPAKGLSRFUIFSSSLKFIPKG
        gctgatgagcgcgtgaggcgagctcttataatcatacag
        tgggaggagtgaattaagccagtcgtgttggctattcag
        ggtgatatgtctatgtcgacacgtccaacccaggcctat
                                  *            
 Sequence until next stop: 
ATGATTGCACGATTACACTGGGTCGCAGCTCCTTTTTCTGCCCTGTTACACTGGCACTGTTGTAATTTTGTCTCTTTTACATAG
 M  I  A  R  L  H  W  V  A  A  P  F  S  A  L  L  H  W  H  C  C  N  F  V  S  F  T  * 

 Distance CDS-SECIS: 2198 ; UGA-SECIS: 2234

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JXSJ01000046.1:subseq_2366260,84740_ Strand = - Positions = 49306 - 49225
 Found by:  Infernal (score=23.78) Covels (score=23.23)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 1, 0
 Free Energy = -20.22

         ..(((((((.........((((((((((.(((((...............)))))))))))))))...........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu--u-uuucaugaccggc
         ..((((({((........{[[(((((((.[(((......-..........)))])))))))]]}.......-..))})))))..
 target  GAUGGUGCAGACAGUGGAUGAAGCGCUCCAGGAUAAAUC-CUAAUGGAGCUCCGGGGCGCUGAUGGACGGU-GGCUUCACCAAU
                           ****            ^^^                       ****                    
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 5e-30
 Query name: gi|1023023620|ref|XP_007499432.2| PREDICTED: methionine-R-sulfoxide reductase B1 [Monodelphis domestica]
 Query range: 1-106  (total 115)

 Target: /data/www-rg/seblastian_results/72128706/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000046.1:subseq_2366260,84740_ Strand: -
 Positions:
 -Exon 1  52398        52452
 -Exon 2  51753        51895
 -Exon 3  51505        51621

 Redox box: no

Query   MSFCS-FGGEVFQNHFEPG <---Intron---> VYVCAKCGYELFSSRSKYHHSSPWPAFTETIHADSVSKRPESGRSEALK <---Intron---> 
        ||||| |||| |//||/ | <   502bp    > /|||||| //|||| ||| ||||||||||||  |||||  |  |  | | <   131bp    > 
Target  MSFCSFFGGEAFKDHFKSG                IYVCAKCEHQLFSSHSKYEHSSPWPAFTETILEDSVSKHEE--RPGAYK                
        atttattggggtagctatg                atgtgatgcccttactatgcttctcgtagaacggagtacgg--acggta                
        tctggttggactaaatac                gtatgcagaaattcgacaaaacccgcctcacttaagtcaaaa--gcgcaa                
        ggtttccctgctacccaa                gttatcgtgcggcccccgcgcgccggccagcctgctgcatgg--acgatg                
                                                                                                            

Query   VSCGKCGNGLGHEFINDGPKKGQSRFUIFSSSLKFVPKG
        | ||||||||||||/|||| || ||||||||||||/|||
Target  VRCGKCGNGLGHEFVNDGPAKGLSRFUIFSSSLKFIPKG
        gctgatgagcgcgtgaggcgagctcttataatcatacag
        tgggaggagtgaattaagccagtcgtgttggctattcag
        ggtgatatgtctatgtcgacacgtccaacccaggcctat
                                  *            
 Sequence until next stop: 
ATGATTGCACGATTACACTGGGTCGCAGCTCCTTTTTCTGCCCTGTTACACTGGCACTGTTGTAATTTTGTCTCTTTTACATAG
 M  I  A  R  L  H  W  V  A  A  P  F  S  A  L  L  H  W  H  C  C  N  F  V  S  F  T  * 

 Distance CDS-SECIS: 497 ; UGA-SECIS: 533

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = JXSJ01000046.1:subseq_2366260,84740_ Strand = - Positions = 51007 - 50929
 Found by:  Infernal (score=21.91) Covels (score=20.05)
 Stem2 length = 9   Apical loop length = 22   Insertion in stem2 = 0, 0
 Free Energy = -16.87

         ..(((((((.......(((((((((((((((..................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC---cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ((((({{((---....{[[((((((((((......................))))))))))]]}......-...))}})))))
 target  UGCGGGCAG---CGAAUGAAGAGUUCUGGAAUAAAGCCCAGUCUGGGAGCACCAGAGCUCUGAUGAAGAU-GGACUCGCUGUA
                         ****         ^^                             ****