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

 Blastx evalue: 6e-21
 Query name: gi|401461803|ref|NP_001257893.1| thioredoxin reductase 1, cytoplasmic [Taeniopygia guttata]
 Query range: 1-501  (total 501)

 Target: /data/www-rg/seblastian_results/995079485/tempfiles/temptarget.fasta
 Chromosome: SJPD01000048.1:subseq_5846400,113349_ Strand: -
 Positions:
 -Exon 1  70113        70202
 -Exon 2  64491        64563
 -Exon 3  63348        63467
 -Exon 4  62408        62553
 -Exon 5  61388        61503
 -Exon 6  59164        59389
 -Exon 7  56465        56557
 -Exon 8  55186        55262
 -Exon 9  54010        54166
 -Exon 10 52762        52869
 -Exon 11 51555        51650
 -Exon 12 49866        50000
 -Exon 13 45915        45980

 Redox box: no

Query   MEVNGLTPVPDSYDYDLIVIGGGSGGLAAAK <---Intron---> EAAKYEKKVMVLDFVTPTPQGSSWG <---Intron---> LGGTCVNVGCIP
        / |||    | ||||||||||||||||||/| <   5549bp   > ||||  |||/||||| ||| |/ || <   1023bp   > ||||||||||||
Target  LNVNGQAEEP-SYDYDLIVIGGGSGGLAASK                EAAKLGKKVLVLDFVVPTPLGTKWG                LGGTCVNVGCIP
        cagagcgggc-ttgtgcagagggtggcggta                gggacgaagcgcgtggcactgaatg                cggatgaggtac
        tatagacaac-caaaattttgggcggtccca                accatgaattttatttccctgcag                gtggcgtatggtc
        ttgtaaaggt-ttcctgtccaatacataccg                atcatcggtgtgtttctttgacag                tgaattatgcctg
                                                                                                            

Query   KKLMHQAALLGQALQDSRKFGWQF-TEE <---Intron---> VKHNWMTMAESVQNYIGSLNWGYRVALRDKKVTYENAYGEFVGPHTVK <---Int
        |||||||||||||/ |/  ||||      <   794bp    > ||| | || |//|||||||||||||/||/  |||||||||||||| /| <   904
Target  KKLMHQAALLGQAIGDAPNFGWQLDNAG                VKHRWDTMTEAIQNYIGSLNWGYRVSLRENSVTYENAYGEFVGPHRIK        
        aacaccggtcgcgagggcatgtccgagg                gacatgaaaggacatagtcatgtagtccgaagatgagtggtggccaaa        
        aattaaccttgactgaccatggataac                gtaaggactcactaaatgctaggagtctgaagtcaaacagattgcagta        
        agggcagtgtgaccatacctggggtca                tagcggtggaactatttttgcgacagtcagttcctgtttaattgacacg        
                                                                                                            

Query   ron---> ATNKKGVEKLYTAERFIIATGERPRYLGIPGDKEYCISS <---Intron---> DDLFSLPYCPGRTLVVGASYVALECAGFLAGLGLDVT
        bp    > ||| ||||| ||||||/||||||||||||||||||||/| <   1998bp   > |||||||||||/|||||||||||||||||||||||||
Target          ATNNKGVEKFYTAERFLIATGERPRYLGIPGDKEYCITS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVT
                gaaaagggattaggatcagaggacctcgacggagttaaa                ggctttcttcgaatggggttggcgtggtcggcgtgga
                ccaaagtaataccagtttccgagcgatgtcgaaaagtcg                aattctcagcgactttgccatctagcgttcgtgtatc
                aatcaaaggtcaaaatgtctaagcccgcctgcaatccc                cttcccggttaagaagtatcttatgtaataaattgttt
                                                                                                            

Query   VMVRSILLRGFDQDMANRIGEYMTEHGVKFIRQFVPIK <---Intron---> VERVEEGTPGVLKVTAKSTTGDQIIEGTYNT <---Intron--->
        |||||||||||||||||||||/| |||/ |/| ||| | <   2606bp   > /||/||| ||/|/|| / |   // /| /|| <   1202bp   >
Target  VMVRSILLRGFDQDMANRIGEHMEEHGIDFLRGFVPKK                IERIEEGNPGLLRVTGECTKTSEVYQGEFNT               
        gagctaccagtgcgagacaggcaggcgagtcagtgcaa                agaagggacgtcagaggtaaatggtcggtaa               
        tttgctttggtaaatcagtgaataaagtattggttcaa                tagtaagacgttgtcgagcaccataagatac               
        cggttttggcttgcggcaaaacgaatcccctattgtag                tagtaaatttaaacatatcactggtaaaccg               
                                                                                                            

Query    VLLAIGRDPCTRRIGLGKVGVNINEK <---Intron---> TGKIPVNDEEQTNVPYIYAIGDILQGKLELTPVAIQAGRLLVRRLYAGATTK <---
         ||/||||| |||/||| |||| ||/| <   1019bp   > ||||||||||||||||||||||/|/ ||||||||||||||| /||| |/  | <   
Target   VLVAIGRDACTRKIGLEKVGVEINKK                TGKIPVNDEEQTNVPYIYAIGDVLEDKLELTPVAIQAGRLLAQRLYGGSDKK     
         gtggagaggtaaaagtgaggggaaaa                agaacgagggcaagctatgagggtggacgcacggacggcctgcactggtgaa     
         tttctggacgcgatgtaatgtataaa                cgatctaaaaacatcatactgattaaatatcctctacggttcagtaggcaaa     
         agtcaagtccaaatcagataggcta                aaaactcttgaaacggcctccgtgggcggaccagccggcgcgaggtcgaacag     
                                                                                                            

Query   Intron---> CDYVNVPTTVFTPLEYGACGYSEETAVEKFGEENIE <---Intron---> VYHSHFWPLEWTVPSRDNNKCYAKIICNIQDN <---
        1140bp   > |||||||||||||/||| |||/|| |/||||/|||| <   1111bp   > |||//|/||||||  |/||||||||||/| |  <   
Target             CDYVNVPTTVFTPVEYGTCGYAEEKAIEKFGKENIE                VYHNYFFPLEWTVAPRENNKCYAKIICHIADQ     
                   tgtgagcaagtacggtgatgtgggagagatgagaag                gtcatttccgtaggccgaaattgaaatcaggc     
                   gaatatcccttcctaagcggacaaactaatgaaata                taaaattctagctccgaaaagacattgatcaa     
                   tccgctccaactatattcttcaaaaacgatcgattg                acctcctagagtcacagctactggcctttctg     
                                                                                                            

Query   Intron---> ERVIGFHVLGPNAGEITQGFAAAIKCGLTKEQLDSTVGIHPVCAE <---Intron---> VFTTLSVTKRSGESIAVSGCUG
        1554bp   > |||||||||||||||||||||||||||/||||||||/|||||||| <   3885bp   > ||||||/|||||| || |||||
Target             ERVIGFHVLGPNAGEITQGFAAAIKCGMTKEQLDSTIGIHPVCAE                VFTTLSITKRSGEEIAQSGCUG
                   gcgagtcgcgcagggaacgtgggaatgaaagccgaaagaccgtgg                gtaactaaactgggagctgttg
                   agttgtattgcacgatcagtccctaggtcaaatagctgtactgca                ttcctctcagcgaatcacgggg
                   gttctctcttattaactaataacaatagaaaggtcaaatcactag                accagtaagtaaagctacacat
                                                                                                    * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 260 ; UGA-SECIS: 263

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SJPD01000048.1:subseq_5846400,113349_ Strand = - Positions = 45654 - 45576
 Found by:  Infernal (score=30.86) Covels (score=25.61)
 Stem2 length = 9   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -15.11

         ..(((((((.......(((((((((((((((.................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .....(((((--....([[[((((({((((...................))))})))))]]])......-..))))).....
 target  UCAAGGUGCU--UCCAUGAAGUCACAGCCUCAAACCAGUGAUACCUGGUAGGCAGUGAUGGAAAAAUUG-UCGGCACAGCUU
                         ****           ^^^                         ****