Seblastian output

Selenoprotein id: 1 Category: known selenoprotein

Protein prediction
Predicted by: exonerate Blastx evalue: 6e-34
Query protein: gi|929298464|ref|XP_014026610.1| PREDICTED: selenoprotein P [Salmo salar] >gi|929298466|ref|XP_014026611.1| PREDICTED: selenoprotein P [Salmo salar]
Positions on query: 1-390 Query length: 401

Target name: JARO01000244.1:subseq_119608,55720_
Positions on target: 51900-52102,51153-51365,50923-51040,50030-50653 Strand: -
Has a Redox Box!

  Query   MWAGLSLLLALCLLPGGGTESEGEGTRCKPPPGWSIGEVEPMKEVMGQVTVVALLQASULFCLVQASL <
          |||||  |||||||| | |||| ||/|||| | |//| |||||  /| |||| ||/||| /||||||  <
  Target  MWAGLGPLLALCLLPWGATESEDEGSRCKPAPPWTVGGVEPMKAALGTVTVVGLLKASUYYCLVQASR
          atggcgcccgctccctggagaggggactacgcctagggggcaaggtgagagggccagatttttgcgta
          tgcgtgcttctgttcggccagaaaggggaccccgctggtactacctgctcttgttacggaagttaccg
          ggagcctcgtccgcagagggtgcggcccggcacgttaggggggccgggctggcttaacatctgggac
                                                                    *

  Query   ---Intron---> LDGLRLKLEGQGLENVTYMVVNHQGEQAQRLHTLLRQKLSENITLYKQQPKQDDVW
             534bp    > /| || ||| || /|/|||||| |   |/  |  ||||/||||||| | |||||/|
  Target                MDDLRQKLEQQGFDNITYMVVNSQELVARLFHHHLRQKMSENITLYVQDPKQDDIW
                        aggcccacgccgtgaaataggaacgcggcctccccacaatgaaattgcgcacggat
                        taatgaataaagtaatcatttagaattcgttaaatgaatcaatctataacaaaatg
                       agttgcggggagcccccccgcaccgagaagcctcccggagtacccgcggcgggtctg


  Query   QTLAGEKDDFLVYDR <---Intron---> CGRLTYHISLPYSILGTPYVENAIKKTYCTRICGDCSYE
          | |/|/||||||||| <   112bp    > || ||| ||/|/| |  |||||||/||||  || /|  |
  Target  QILSGDKDDFLVYDR                CGLLTYQISMPFSKLSMPYVENAIRKTYCKNICANCLLE
          cactggaggtcgtga                tgccatcatacttactactggagaaaattaaatgatttg
          attcgaaaatttaag                ggttcaatctctcatctcataactgacagaatgcagtta
          atgaatgttcggtcg                tctctcaccggcaaccgatgatccaaaccgcctactaag


  Query   S <---Intron---> QEIPAECNRTVEAKPEGEEKPVTGRETTHGGHGHHHHGHGHNDNRHGHNGNR-
            <   269bp    >       ||//||/  | / / /   |  |     ||| | |    |||| /
  Target  H                PGTTEICNKSVESTTEEKTEEIVVSEVDHSRLPSHHHVHSH---AHGHNRDHF
          c                cgaagataatggtaaggaaggaggtgggcaacctcccgcac---gcgcacgct
                          acgccatgaactacccaaacaatttcataaggtccaaataga---cagaagaat
                          cagaggaccgagaagtggaaggtgtaagcccgttgtttgctt---tttctcttt


  Query   HGHDHHGERGMGRGHGRDHGAERQQQHQHDTEGLQHGQAQGQLHVGQEHMGQQAVQLGQMPQEGQRGHIM
          ||| ||   |  / |   | /  |  |/|     ||         |  //  | /  ||        |
  Target  HGHSHHHSHGHNQHHHVQHESLEQHNHRH-----QHDHTDNIAQEGAINLPPQLILHGQQEVLDHPIHPR
          cgcacccacgcaccccgccgacgccacac-----ccgcagaagcgggaacccccaccgccggcgccaccc
          agagaaagagaaaaaataaagtaaaaaga-----aaaacaatcaagctatccatttagaaattaactacg
          ttctctctttttattttatacggacccgc-----atctaccatgaaaatcaaggcgttagggactttcaa


  Query   QNPUVKGMSRUKAEHSUQWKEGSDLSPSSKASUCUHURRLFGDGESNEPIGLUHCDEALPASUQUQGLMG
          //||    |||| //||| //    | /| /|||||||/|||    | |  ||||/| ||/|||| ||||
  Target  RDPUKTEQSRUKVQYSUQ-RQAETPSLNSLSSUCUHURQLFGSEGGNGPAALUHCEEELPSSUQUHGLMG
          agctaagctatagctatc-ccggacatatctatttctccctgagggagcggctctgggcctttctcgtag
          gacgacaacggataagga-gacaccgtactcggggaggattggaggagccctgagaaatcccgagagttg
          gtcaagggcgaatgccag-ggagcccgcggccacacatagtccagctgattcactgagactcagatcagc
             *      *     *               * * *               *         * *

  Query   ----LRETUQURSSPADUQQPQP
              /|||||||/  | ||| ||
  Target  GTHAVRETUQURTPLAAUQQHQP
          gacggagatctcaccggtccccc
          gcactgacgaggcctccgaaaac
          cctatgacagacgcttcaggcgc
                  * *      *

SECIS prediction

Predicted by: Infernal (score 26.69)
Covels score: 28.6
Free Energy of structure: -18.8
Target name: JARO01000244.1:subseq_119608,55720_
Positions on target: 49477-49546 Strand: -
Distance between candidate CDS and SECIS: 483
Distance between Sec-UGA and SECIS: 498
SECIS grade: A

SEQ GGUGUUGCCUAAAUGAAGUCAGGUGCAGAAACUAUGCUCUAGUGGUGCCUGUUGGAUGCCGGGCAACUCU
SS (({(((((((...{[[[({((((((([(..............)])))))))})]]]}...)))))))}))

Selenoprotein id: 2 Category: known selenoprotein

SECIS prediction

Predicted by: Infernal (score 13.66)
Covels score: 8.72
Free Energy of structure: -11.9
Target name: JARO01000244.1:subseq_119608,55720_
Positions on target: 48776-48842 Strand: -
Distance between candidate CDS and SECIS: 1187
Distance between Sec-UGA and SECIS: 1202
SECIS grade: B

SEQ UACGUGUACUUAAUGAAGGUGUUGGGGAAAAUAAUAACCCCACGUAACCUGAAAAUCUGUAUAUAAA
SS ...((((((....([[((((({(((((..........)))))}.)).)))]]).....))))))...

Output page