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

 Blastx evalue: 5e-05
 Query name: gi|373432689|ref|NP_001243286.1| thioredoxin reductase 1 [Monodelphis domestica]
 Query range: 94-499  (total 499)

 Target: /data/www-rg/seblastian_results/710336747/tempfiles/temptarget.fasta
 Chromosome: gi|432094352|gb|KB111329.1|:subseq_3850000,200000_ Strand: -
 Positions:
 -Exon 1  87859        88002
 -Exon 2  87335        87450
 -Exon 3  85749        85974
 -Exon 4  83294        83386
 -Exon 5  82584        82660
 -Exon 6  81112        81268
 -Exon 7  77519        77626
 -Exon 8  73929        74024
 -Exon 9  71632        71766
 -Exon 10 58024        58089

 Redox box: no

Query   VKHNWESMTEAVQNYIGSLNWGYRVALRENRVTYENAYGEFVGPHKIK <---Intron---> ATNNKGKEKFYTAERFLIATGERPRYPGIPGDKEYC
        | |/|  |||||||/|||||||||||||| /||||||||/|||||/|| <   408bp    >  |||||||| |/|||||||||||||| |||||||||
Target  VGHDWGKMTEAVQNHIGSLNWGYRVALREKKVTYENAYGQFVGPHRIK                TTNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYC
        ggcgtgaaagggcacagtcatgtcggccgaagatgagtgctggccaaa                aaaaagagaattggatcagaggaccttgacggagtt
        tgaaggatcactaaatgctaggagtctgaaatcaaacagattgcagta                ccaaagaaataccagtttccgagcgatgtcgaaaag
        tatcggagcacggtctctgcgcccgtggggacctgtatggtgtttgtg                agtcacaaattaagatcttctagatcgccttcaacc
                                                                                                            

Query   ISS <---Intron---> DDLFSLSYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEDHGIKFIKKFVPIK <---I
        ||| <   1360bp   > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||//||/||||/||||| <   2
Target  ISS                DDLFSLSYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMQEHGVKFIKQFVPIK      
        aaa                ggcttttttcgaacggggttggtgtggtcggagtggagagctaccagtgcgagaaaggcacgcggataactgcaa      
        tgg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataaagtattaattcta      
        cc                ttttccatccgcgcggcaactctaattgtttcttatcttgaactctaatcgcgccattacgaattcgtaaataaag      
                                                                                                            

Query   ntron---> IEQIKEGTPGTLRVVAQSTDGKETIEGEYNT <---Intron---> VLLAIGRDSCTRKIGLETVGVKINEK <---Intron---> T
        362bp   > /|||/ |||| |/|||/||/  | ||||||| <   633bp    > ||||||||/|||||||| |||||||| <   1315bp   >  
Target            VEQIEAGTPGRLKVVAKSTNSDEVIEGEYNT                VLLAIGRDACTRKIGLEAVGVKINEK                N
                  ggcagggacgccagggataaagggagggtaa                gtcgagaggtaaaagtgggggaaaga                a
                  taatacgccggtattcaccagaattagaaac                tttctggacgcgatgtactgtataaa                a
                  taataagaacacggatgccttcaccaagctg                aggaaaattcaaatcaacgtagata                gc
                                                                                                            

Query   GKIPVNDEEQTNVPYIYAIGDVLEDKLELTPVAIQAGRLLARRLYAGSTIK <---Intron---> CDYDNVPTTVFTPLEYGACGLSEERAVEKFGEE
        ||||| |||||||||||||||/|| | ||||||||||||||/|||||||/| <   3485bp   > |||/||||||||||||||||||||/||||||||
Target  GKIPVTDEEQTNVPYIYAIGDILEGKPELTPVAIQAGRLLAQRLYAGSTVK                CDYENVPTTVFTPLEYGACGLSEEKAVEKFGEE
        gaacgagggcaagctatgaggacggacgcacggacggatcgcactggtaga                tgtgagcaagtactgtggtgctggagggatggg
        gatctcaaaacatcatactgattagacatcctctacggttcagtacgccta                gaaaatcccttcctaagcggtcaaactaatgaa
        aaatcgtaggctgtcttctcttggggggcccaccggagagtggcctcctcg                tctattaatatttgatttttttaaatgaatgaa
                                                                                                            

Query   NIE <---Intron---> VYHSYFWPLEWTIPSRDNNKCYAKVICHVRDN <---Intron---> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKNQL
        ||| <   3494bp   > ||||||||||||/||||/||||||//|/ /|| <   2162bp   > |||||||/|||||||||||||||||||||| ||
Target  NIE                VYHSYFWPLEWTVPSRDSNKCYAKIVCNTKDN                ERVVGFHILGPNAGEVTQGFAAALKCGLTKQQL
        aag                gtcatttctgtagctagaaattgaagtaaaga                gcgggtcacgcaggggacgtgggcatgcaaccc
        ata                taagatgctagctccgagaagacattgacaaa                agttgtattgcacgatcagtccctaggtcaaat
        ttg                tcttctgagaggtaaatccactaaacttgact                attgcccagtaccaataactacgcgtagcgggg
                                                                                                            

Query   DSTIGIHPVCAE <---Intron---> VFTTLSVTKRSGGSILQAGCUG
        |||||||||||| <  13542bp   > ||||||||||||||||||||||
Target  DSTIGIHPVCAE                VFTTLSVTKRSGGSILQAGCUG
        gaaagaccgtgg                gtaactgaactggaaccggttg
        agctgtactgca                ttcctctcagcgggttacgggg
        ccctgcccccag                acgggggcgccggccggtccat
                                                        * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 224 ; UGA-SECIS: 227

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|432094352|gb|KB111329.1|:subseq_3850000,200000_ Strand = - Positions = 57799 - 57717
 Found by:  Infernal (score=24.81) Covels (score=18.86)
 Stem2 length = 11   Apical loop length = 12   Insertion in stem2 = 1, 0
 Free Energy = -18.37

         ..(((((((..............((((((((((.(((((...............)))))))))))))))..........)))))))..
 model   uucggucaugcg-------UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .({((({((((............([[[(((((.((((((.....---.......)))))))))))]]])......-)-)))})))}).
 target  CAGUGCAUCGUAGGGUGCGUCCAUGAAGUCACUGGCCUGAAGCC---CCCGCGGUGGGCCGUGAUGGAAUUACUG-G-CGAAGCAGUU
                                ****            ^^                        ****