_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 8e-05
 Query name: gi|373432689|ref|NP_001243286.1| thioredoxin reductase 1, cytoplasmic [Monodelphis domestica]
 Query range: 94-499  (total 499)

 Target: /data/www-rg/seblastian_results/120925290/tempfiles/temptarget.fasta
 Chromosome: KZ836295.1:subseq_2355251,120914_ Strand: -
 Positions:
 -Exon 1  71277        71420
 -Exon 2  70799        70914
 -Exon 3  69248        69473
 -Exon 4  64604        64696
 -Exon 5  63973        64049
 -Exon 6  61210        61366
 -Exon 7  56172        56279
 -Exon 8  53678        53773
 -Exon 9  50003        50137
 -Exon 10 41667        41732

 Redox box: no

Query   VKHNWESMTEAVQNYIGSLNWGYRVALRENRVTYENAYGEFVGPHKIK <---Intron---> ATNNKGKEKFYTAERFLIATGERPRYPGIPGDKEYC
        |||/|  |||||||/|||||||||||||| /||||||/|/|||||/|| <   362bp    > ||||||||| |/|||||||||||||| |||||/|||
Target  VKHDWNKMTEAVQNHIGSLNWGYRVALREKKVTYENAFGQFVGPHRIK                ATNNKGKEKIYSAERFLIATGERPRYLGIPGDREYC
        gacgtaaaagggcacagtcatgtcggccgaagatgagtgctggccaaa                gaaaagagaattggatcagaggaccttgacggagtt
        taaagaatcactaaatgctaggagtctgaaatcaaactgattgcagta                ccaaagaaataccagtttccgagcgatgtcgagaag
        tatcgtagaacagcctttgcgccgatggggacctgtatggtgtttgtg                aatcacaaattaagatcttttggatcgccttcagcc
                                                                                                            

Query   ISS <---Intron---> DDLFSLSYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEDHGIKFIKKFVPIK <---I
        ||| <   1325bp   > |||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||/||/||||/|/||| <   4
Target  ISS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGVKFIKQFIPIK      
        aaa                ggctttcttcgaacggggttggcgtggtcggagtggagagctaccagtgcgagaaaggcaggcggataactacaa      
        tgg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataaagtattaattcta      
        cc                ttttccattcgtggggtaacttctattatttctcattttgaactctaatcgcgccattatgaattcgtaagtaaaa      
                                                                                                            

Query   ntron---> IEQIKEGTPGTLRVVAQSTDGKETIEGEYNT <---Intron---> VLLAIGRDSCTRKIGLETVGVKINEK <---Intron---> T
        551bp   > /|||/ |||| |||/|/||   | ||||||| <   554bp    > ||||||||/||||||||||||||||| <   2606bp   > |
Target            VEQIEAGTPGRLRVIAKSTSSDEIIEGEYNT                VLLAIGRDACTRKIGLETVGVKINEK                T
                  ggcagggacgccagagataaaggaagggtaa                gtcgagaggtaaaagtgagggaaaga                a
                  taatacgccggtgttcaccggaattagaaac                tttctggacgcgatgtactgtataaa                c
                  taataagaacacggatgcctttaccaagttg                aggaaaattcaaatcaacggagata                gt
                                                                                                            

Query   GKIPVNDEEQTNVPYIYAIGDVLEDKLELTPVAIQAGRLLARRLYAGSTIK <---Intron---> CDYDNVPTTVFTPLEYGACGLSEERAVEKFGEE
        ||||| |||||||||||||||/|| ||||||||||||||||/|||||| /| <   4930bp   > |||/||||||||||||||||||||/||| ||||
Target  GKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYAGSNVK                CDYENVPTTVFTPLEYGACGLSEEKAVETFGEE
        gaacgagggcaagctatgaggatggacgcacggacggatcgcactggtaga                tgtgagcaagtactgtggtgctggagggatggg
        gatctcaaaacatcatactgattagatatcctctacggttcagtacgcata                gaaaatcccttcctaagcggtcaaactactgaa
        aaatcatgagctgtcctctctaagggggtcaaacgaaaggtggtttcctgg                tctgttaatgtttgattcttttggatggatgaa
                                                                                                            

Query   NIE <---Intron---> VYHSYFWPLEWTIPSRDNNKCYAKVICHVRDN <---Intron---> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKNQL
        ||| <   2398bp   > |||||||||||||||||||||||||||///|| <   3540bp   > |||||||||||||||||||||||||||||| ||
Target  NIE                VYHSYFWPLEWTIPSRDNNKCYAKVICNIKDN                ERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQL
        aag                gtcatttctgtaactagaaattgagataaaga                gcgggtcgcgcaggggacgtgggcatgcaaacc
        ata                taagatgctagctccgaaaagacattgataaa                agttgtattgcacgatcagtccctaggtcaaat
        ttg                tcttctggggggtaaatccattaaacttcact                attgcccagtattaagaactatccgtagcaggg
                                                                                                            

Query   DSTIGIHPVCAE <---Intron---> VFTTLSVTKRSGGSILQAGCUG
        |||||||||||| <   8270bp   > ||||||||||||||||||||||
Target  DSTIGIHPVCAE                VFTTLSVTKRSGGSILQAGCUG
        gaaagaccgtgg                gtaactgaactggaaccggttg
        agctgtactgca                ttcctctcagcgggttacgggg
        ctctacccctag                acgtgagcgctgacccgcccat
                                                        * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 215 ; UGA-SECIS: 218

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = KZ836295.1:subseq_2355251,120914_ Strand = - Positions = 41451 - 41365
 Found by:  Infernal (score=27.93) Covels (score=26.56) SECISearch1.0 (pattern=default)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 1, 0
 Free Energy = -20.19

         ..(((((((......................((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg---------------UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((((....................([[[(((((((.(((......---........))))))))))]]])----..)))))))))..
 target  CAUUCGGCAGUGCAUCGGCGCGGUGCGUCCAUGAAGUCACUGGCCUCAAGCC---CAUGUGGUGGGCAGUGAUGGAA----CAGCUGUCGAGCA
                                        ****            ^^                        ****